Fluid flows shaping organism morphology

A dynamic self-organized morphology is the hallmark of network-shaped organisms like slime moulds and fungi. Organisms continuously reorganize their flexible, undifferentiated body plans to forage for food. Among these organisms the slime mould Physarum polycephalum has emerged as a model to investigate how an organism can self-organize their extensive networks and act as a coordinated whole. Cytoplasmic fluid flows flowing through the tubular networks have been identified as the key driver of morphological dynamics. Inquiring how fluid flows can shape living matter from small to large scales opens up many new avenues for research. This article is part of the theme issue 'Self-organization in cell biology'.

Periodic traction in migrating large amoeba of Physarum polycephalum

The slime mould Physarum polycephalum is a giant multinucleated cell exhibiting well-known Ca(2+)-dependent actomyosin contractions of its vein network driving the so-called cytoplasmic shuttle streaming. Its actomyosin network forms both a filamentous cortical layer and large fibrils. In order to understand the role of each structure in the locomotory activity, we performed birefringence observations and traction force microscopy on excised fragments of Physarum. After several hours, these microplasmodia adopt three main morphologies: flat motile amoeba, chain types with round contractile heads connected by tubes and motile hybrid types. Each type exhibits oscillations with a period of about 1.5 min of cell area, traction forces and fibril activity (retardance) when fibrils are present. The amoeboid types show only peripheral forces while the chain types present a never-reported force pattern with contractile rings far from the cell boundary under the spherical heads. Forces are mostly transmitted where the actomyosin cortical layer anchors to the substratum, but fibrils maintain highly invaginated structures and contribute to forces by increasing the length of the anchorage line. Microplasmodia are motile only when there is an asymmetry in the shape and/or the force distribution.

[Spectral analysis of self-oscillating motility in isolated plasmodial strand of Physarum polycephalum]

In this study the experimental dependencies of the velocity of shuttle endoplasmic motion in the isolated plasmodial strand of Physarum polycephalum obtained by laser Doppler microscopy are presented. The spectral analysis of the time dependencies of the endoplasm allows obtaining two distinct harmonic components. Influence of KCN and SHAM--inhibitors of cellular respiration--leads to a complete cessation of endoplasmic motion in the strand. After removal of the inhibitors the respiratory system becomes normal, gradually restoring the activity of both harmonic oscillation sources. Based on the spectral analysis the simulated time-dependent velocity of the endoplasmic motion is rather good consistent with experimental data.

Material approximation of data smoothing and spline curves inspired by slime mould

The giant single-celled slime mould Physarum polycephalum is known to approximate a number of network problems via growth and adaptation of its protoplasmic transport network and can serve as an inspiration towards unconventional, material-based computation. In Physarum, predictable morphological adaptation is prevented by its adhesion to the underlying substrate. We investigate what possible computations could be achieved if these limitations were removed and the organism was free to completely adapt its morphology in response to changing stimuli. Using a particle model of Physarum displaying emergent morphological adaptation behaviour, we demonstrate how a minimal approach to collective material computation may be used to transform and summarise properties of spatially represented datasets. We find that the virtual material relaxes more strongly to high-frequency changes in data, which can be used for the smoothing (or filtering) of data by approximating moving average and low-pass filters in 1D datasets. The relaxation and minimisation properties of the model enable the spatial computation of B-spline curves (approximating splines) in 2D datasets. Both clamped and unclamped spline curves of open and closed shapes can be represented, and the degree of spline curvature corresponds to the relaxation time of the material. The material computation of spline curves also includes novel quasi-mechanical properties, including unwinding of the shape between control points and a preferential adhesion to longer, straighter paths. Interpolating splines could not directly be approximated due to the formation and evolution of Steiner points at narrow vertices, but were approximated after rectilinear pre-processing of the source data. This pre-processing was further simplified by transforming the original data to contain the material inside the polyline. These exemplary results expand the repertoire of spatially represented unconventional computing devices by demonstrating a simple, collective and distributed approach to data and curve smoothing.

Assessment of cell cycle phase-specific effects of zerumbone on mitotically synchronous surface cultures of Physarum polycephalum

Zerumbone, a natural cyclic sesquiterpene, has been the focus of recent research as it has been found to exhibit selective toxicity towards cancer cells compared to normal cells. Studies on the cell cycle phase-specific effects of this interesting compound, however, remain sparse. Hence, concentration and time-dependent effects of zerumbone were evaluated employing a suitable model system, the naturally synchronous surface cultures of Physarum polycephalum. Zerumbone treatment in S, early, and late G2 phases resulted in G2 arrest. Early G2 phase exhibited the highest sensitivity (P < 0.001) to the compound. Protein profiles showed a complete inhibition of cyclin B1 expression following zerumbone treatment. Furthermore, FACS and comet analysis revealed that zerumbone inhibited DNA synthesis (P < 0.001) without being genotoxic at the concentrations tested. Differential display of mRNA showed distinct zerumbone-induced variations in transcript profiles, an analysis of which suggested a likely link between cellular networks involving stress-related gene expression and G2 arrest in P. polycephalum.

An active poroelastic model for mechanochemical patterns in protoplasmic droplets of Physarum polycephalum

Motivated by recent experimental studies, we derive and analyze a two-dimensional model for the contraction patterns observed in protoplasmic droplets of Physarum polycephalum. The model couples a description of an active poroelastic two-phase medium with equations describing the spatiotemporal dynamics of the intracellular free calcium concentration. The poroelastic medium is assumed to consist of an active viscoelastic solid representing the cytoskeleton and a viscous fluid describing the cytosol. The equations for the poroelastic medium are obtained from continuum force balance and include the relevant mechanical fields and an incompressibility condition for the two-phase medium. The reaction-diffusion equations for the calcium dynamics in the protoplasm of Physarum are extended by advective transport due to the flow of the cytosol generated by mechanical stress. Moreover, we assume that the active tension in the solid cytoskeleton is regulated by the calcium concentration in the fluid phase at the same location, which introduces a mechanochemical coupling. A linear stability analysis of the homogeneous state without deformation and cytosolic flows exhibits an oscillatory Turing instability for a large enough mechanochemical coupling strength. Numerical simulations of the model equations reproduce a large variety of wave patterns, including traveling and standing waves, turbulent patterns, rotating spirals and antiphase oscillations in line with experimental observations of contraction patterns in the protoplasmic droplets.

Physarum polycephalum percolation as a paradigm for topological phase transitions in transportation networks

We study the formation of transportation networks of the true slime mold Physarum polycephalum after fragmentation by shear. Small fragments, called microplasmodia, fuse to form macroplasmodia in a percolation transition. At this topological phase transition, one single giant component forms, connecting most of the previously isolated microplasmodia. Employing the configuration model of graph theory for small link degree, we have found analytically an exact solution for the phase transition. It is generally applicable to percolation as seen, e.g., in vascular networks.

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.

Doppler OCT imaging of cytoplasm shuttle flow in Physarum polycephalum

The Doppler optical coherence tomography technique was applied to image the oscillatory dynamics of protoplasm in the strands of the plasmodium of slime mould Physarum polycephalum. Radial contractions of the gel-like walls of the strands and the velocity distributions in the sol-like endoplasm streaming along the plasmodial strands are imaged. The motility inhibitor effect of carbon dioxide on the cytoplasm shuttle flow and strand-wall contraction is shown. The optical attenuation coefficient of cytoplasm is estimated.

Automatic reconstruction of molecular and genetic networks from discrete time series data

We apply a mathematical algorithm which processes discrete time series data to generate a complete list of Petri net structures containing the minimal number of nodes required to reproduce the data set. The completeness of the list as guaranteed by a mathematical proof allows to define a minimal set of experiments required to discriminate between alternative network structures. This in principle allows to prove all possible minimal network structures by disproving all alternative candidate structures. The dynamic behaviour of the networks in terms of a switching rule for the transitions of the Petri net is part of the result. In addition to network reconstruction, the algorithm can be used to determine how many yet undetected components at least must be involved in a certain process. The algorithm also reveals all alternative structural modifications of a network that are required to generate a predefined behaviour.

Physarum machines: encapsulating reaction-diffusion to compute spanning tree

The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction-diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction-diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction-diffusion system is enclosed in a membrane with few 'growth points', sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction-diffusion computation by enriching it with ideas of slime mold computation.

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.

Progress in plasmodial differentiation improves regularity of oscillating contractions in Physarum polycephalum

Based on the knowledge about subcellular morphogenetic processes in the acellular slime mold Physarum polycephalum, we hypothesized that during differentiation of undifferentiated endoplasm to the highly differentiated complex structure of the contractile apparatus of this organism, the regularity of oscillating contractions must improve. We measured the endogenous contraction automaticity starting from the de novo generation within minutes after sampling small portions of undifferentiated endoplasm. The standard deviation of the normalized period duration of these samples was compared to the respective values of radial contractions of differentiated protoplasmic plasmodial strands. The mean normalized standard deviation in endoplasmic drops was 28.3+/-12.2%. Respective values in protoplasmic strands were 10.0+/-3.7%. The difference between the experimental groups was highly significant (p<<0.0001). We interpret the verification of our hypothesis as an indication that the very regular oscillating contractions in fully differentiated stages of Physarum require the complex structure of the sophisticated contractile apparatus, represented by the circular plasmalemma invagination system of protoplasmic strands, while the regularity is lower in stages, where the differentiation is still in progress. We believe that this is due to deficits in coordination capabilities, which need a directional and spatially oriented protoplasmic streaming as a precondition.

[Cell biology researches aboard the robotic space vehicles: preparation and performance]

The article reviews the unique aspects of preparation and performance of cell biology experiments flown on robotic space vehicles Bion and Foton, and gives an overview of key findings in researches made under the author's leadership over the past decades. Described are the criteria of selecting test objects, and the conditions required for preparation and implementation of space and control (synchronous) experiments. The present-day status and issues of researches into cell responsivity to space microgravity and other factors are discussed. Also, potentialities of equipment designed to conduct experiments with cell cultures in vitro and populations of single-celled organisms are presented, as well as some ideas for new devices and systems. Unveiled are some circumstances inherent to the development and performance of space experiments, setting up laboratory facilities at the launch and landing site, and methods of safe transportation and storage of biosamples. In conclusion, the author puts forward his view on biospecies, equipment and areas of research aboard future space vehicles.

Early zygote-specific nuclease in mitochondria of the true slime mold Physarum polycephalum

The active, selective digestion of mtDNA from one parent is a possible molecular mechanism for the uniparental inheritance of mtDNA. In Physarum polycephalum, mtDNA is packed by DNA-binding protein Glom, which packs mtDNA into rod-shaped mt-nucleoids. After the mating, mtDNA from one parent is selectively digested, and the Glom began to disperse. Dispersed Glom was retained for at least 6 h after mtDNA digestion, but disappeared completely by about 12 h after mixing two strains. We identified two novel nucleases using DNA zymography with native-PAGE and SDS-PAGE. One is a Ca2+-dependent, high-molecular-weight nuclease complex (about 670 kDa), and the other is a Mn2+-dependent, high-molecular-weight nuclease complex (440-670 kDa); the activity of the latter was detected as a Mn2+-dependent, 13-kDa DNase band on SDS-PAGE. All mitochondria isolated from myxamoebae had mt-nucleoids, whereas half of the mitochondria isolated from the zygotes at 12 h after mixing had lost the mt-nucleoids. The activity of the Mn2+-dependent nuclease in the isolated mitochondria was detected at least 8 h after mixing of two strains. The timing and localization of the Mn2+-dependent DNase activity matched the selective digestion of mtDNA.

Obtaining multiple separate food sources: behavioural intelligence in the Physarum plasmodium

To evaluate performance in a complex survival task, we studied the morphology of the Physarum plasmodium transportation network when presented with multiple separate food sources. The plasmodium comprises a network of tubular elements through which chemical nutrient, intracellular signals and the viscous body are transported and circulated. When three separate food sources were presented, located at the vertices of a triangle, the tubular network connected them via a short pathway, which was often analogous to the mathematically shortest route known as Steiner's minimum tree (SMT). The other common network shape had high fault tolerance against accidental disconnection of the tubes and was known as cycle (CYC). Pattern selection appeared to be a bistable system involving SMT and CYC. When more than three food sources were presented, the network pattern tended to be a patchwork of SMT and CYC. We therefore concluded that the plasmodium tube network is a well designed and intelligent system.

A PSTAIRE CDK-like protein localizes in nuclei and cytoplasm of Physarum polycephalum and functions in the mitosis

CDKs play key roles in controlling cell cycle progression in all eukaryotes. In plants, multiple CDKs are present, among which the best characterized CDKs are PSTAIRE CDKs. In this study, we carried out Western blot, immunoelectron microscopy and antibody treatment with an anti-PSTAIRE monoclonal antibody to explore the subcellular localization and functions of PSTAIRE CDKs in Physarum polycephalum. The results of western blot and immunoelectron microscopy showed that in P. polycephalum, a PSTAIRE CDK-like protein was 34 kD in molecular weight and located in both nuclei and cytoplasm. In nuclei, the protein was mainly associated with chromosomes and nucleoli. The expression of the PSTAIRE CDK-like protein in both the plasmodia and nuclei showed little fluctuation through the whole cell cycle. When treated with an anti-PSTAIRE monoclonal antibody at early S phase, the cells were arrested in S phase, and the mitotic onset of P. polycephalum was blocked for about 1 h when treated at early G2 phase. Our data indicated that the PSTAIRE CDK- like protein has a direct bearing on the mitosis.

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.

Beyond input-output computings: error-driven emergence with parallel non-distributed slime mold computer

The emergence derived from errors is the key importance for both novel computing and novel usage of the computer. In this paper, we propose an implementable experimental plan for the biological computing so as to elicit the emergent property of complex systems. An individual plasmodium of the true slime mold Physarum polycephalum acts in the slime mold computer. Modifying the Elementary Cellular Automaton as it entails the global synchronization problem upon the parallel computing provides the NP-complete problem solved by the slime mold computer. The possibility to solve the problem by giving neither all possible results nor explicit prescription of solution-seeking is discussed. In slime mold computing, the distributivity in the local computing logic can change dynamically, and its parallel non-distributed computing cannot be reduced into the spatial addition of multiple serial computings. The computing system based on exhaustive absence of the super-system may produce, something more than filling the vacancy.

Localization of fluorescence-labeled poly(malic acid) to the nuclei of the plasmodium of Physarum polycephalum

The nuclei in the plasmodium of Physarum polycephalum, as of other myxomycetes, contain high amounts of polymalate, which has been proposed to function as a scaffold for the carriage and storage of several DNA-binding proteins [Angerer, B. and Holler, E. (1995) Biochemistry 34, 14741-14751]. By delivering fluorescence-labeled polymalate into a growing plasmodium by injection, we observed microscopic staining of nuclei in agreement with the proposed function. The fluorescence intensity was highest during the reconstruction phase of the nuclei. To examine whether the delivery was under the control of polymalatase or related proteins [Karl, M. & Holler, E. (1998) Eur. J. Biochem.251, 405-412], the cellular distribution of these proteins was also examined by staining with antibodies against polymalatase. Double-stained plasmodia revealed a fluorescent halo around each fluorescent nucleus during the reconsititution. Fluorescent nuclei were not observed when the hydroxyl terminus of polymalate, known to be essential for the binding of polymalatase, was blocked by labeling with fluorescein-5-isothiocyanate. By immune precipitation, it was shown that polymalate and polymalatase or related proteins were in the precipitate. It is concluded that polymalate is delivered to the surface of nuclei in the complex with polymalatase or related proteins. The complex dissociates, and polymalate translocates into the nucleus, while polymalatase or related proteins remain at the surface.

Molecular identification of PpHDAC1, the first histone deacetylase fron the slime mold Physarum polycephalum

The dynamic state of post-translational acetylation of eukaryotic histones is maintained by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs and HDACs have been shown to be components of various regulatory protein complexes in the cell. Their enzymatic activities, intracellular localization and substrate specificities are regulated in a complex, cell cycle related manner. In the myxomycete Physarum polycephalum multiple HATs and HDACs can be distinguished in biochemical terms and they exhibit dynamic activity patterns depending on the cell cycle stage. Here we report on the cloning of the first P. polycephalum HDAC (PpHDAC1) related to the S. cerevisiae Rpd3 protein. The expression pattern of PpHDAC1 mRNA was analysed at different time points of the cell cycle and found to be largely constant. Treatment of macroplasmodia with the HDAC inhibitor trichostatin A at several cell cycle stages resulted in a significant delay in entry into mitosis of treated versus untreated plasmodia. No effect of TSA treatment could be observed on PpHDAC1 expression itself.

The DNA-polymerase inhibiting activity of poly(beta-l-malic acid) in nuclear extract during the cell cycle of Physarum polycephalum

The naturally synchronous plasmodia of myxomycetes synthesize poly(beta-l-malic acid), which carries out cell-specific functions. In Physarum polycephalum, poly(beta-l-malate) [the salt form of poly(beta-l-malic acid)] is highly concentrated in the nuclei, repressing DNA synthetic activity of DNA polymerases by the formation of reversible complexes. To test whether this inhibitory activity is cell-cycle-dependent, purified DNA polymerase alpha of P. polycephalum was added to the nuclear extract and the activity was measured by the incorporation of [3H]thymidine 5'-monophosphate into acid precipitable nick-activated salmon testis DNA. Maximum DNA synthesis by the reporter was measured in S-phase, equivalent to a minimum of inhibitory activity. To test for the activity of endogenous DNA polymerases, DNA synthesis was followed by the highly sensitive photoaffinity labeling technique. Labeling was observed in S-phase in agreement with the minimum of the inhibitory activity. The activity was constant throughout the cell cycle when the inhibition was neutralized by the addition of spermidine hydrochloride. Also, the concentration of poly(beta-l-malate) did not vary with the phase of the cell cycle [Schmidt, A., Windisch, C. & Holler, E. (1996) Nuclear accumulation and homeostasis of the unusual polymer poly(beta-l-malate) in plasmodia of Physarum polycephalum. Eur. J. Cell Biol. 70, 373-380]. To explain the variation in the cell cycle, a periodic competition for poly(beta-l-malate) between DNA polymerases and most likely certain histones was assumed. These effectors are synthesized in S-phase. By competition they displace DNA polymerase from the complex of poly(beta-l-malate). The free polymerases, which are no longer inhibited, engage in DNA synthesis. It is speculated that poly(beta-l-malate) is active in maintaining mitotic synchrony of plasmodia by playing the mediator between the periodic synthesis of certain proteins and the catalytic competence of DNA polymerases.

Assembly into chromatin and subtype-specific transcriptional effects of exogenous linker histones directly introduced into a living Physarum cell

The apparent diversity of linker histone subtypes may be related to their specific roles in defining functional states of chromatin in vivo. We have developed a novel method to study constitutive peptides throughout the cell cycle and have demonstrated that an exogenous linker histone could be introduced into a living cell of the slime mold Physarum polycephalum. Here, we have used this method to assess the functional differences between three somatic linker histone subtypes in vivo, and to demonstrate the general applicability of this method. Exogenous linker histone proteins H1 degrees, H5 and H1 were directly absorbed into living cell segments of the naturally synchronous Physarum macroplasmodia at precise cell cycle stages. Fluorescence microscopy, native nucleoprotein gels and immunoblotting of nuclei and chromatin with subtype-specific antibodies revealed that exogenous linker histones were efficiently transported into nuclei and were integrated into chromatin. The immunoreactivity of a preparation of anti-H1 degrees antibodies that are blocked from binding to specific H1 degrees epitopes in native chromatin indicates that the exogenous linker histones were similarly associated into Physarum chromatin. Interestingly, linker histones were found to be less stably associated with Physarum chromatin during S-phase than during G(2)-phase. Furthermore, we show that exogenous linker histones incorporated in early G(2)-phase inhibited transcription and that the level of inhibition correlates with the apparent role of the linker histone subtype in regulating transcription in cells where it normally occurs.

[Effects of cytochalasin B upon mitosis of Physarum polycephalum]

Cytochalasin B, known as a functional inhibitor of actin, was microinjected into naturally synchronous plasmodia of Physarum polycephalum, and the mitotic behaviours of both CB-treated specimens and the control were examined with light and electron microscopy. Mitosis in the CB-treated specimens began about 20 to 60 minutes later than that of the control. It was delayed 35 minutes in the specimens treated with CB in the S phase of the cell cycle, and the delayed time was 20 minutes and 45 minutes, respectively. In the specimens treated with CB in early and middle G2 phase, the longest delay was 60 minutes found in the specimens treated in late G2 phase, indicating that mitosis was affected in Physarum polycephalum when the function of actin was inhibited by CB treatment. The CB-treated specimens and the control showed similarities in the process of mitosis and dynamic changes of nuclear structures, suggesting that the main effect of CB treatment upon mitosis may be to delay the triggering of the mitosis.

Expression of ras-family genes in the cell cycle and during differentiation of the lower eukaryote Physarum polycephalum

Messenger RNA levels of three ras-family genes (Ppras1, Ppras2, and Pprap1) were measured in different life forms and throughout the cell cycle of the slime mold Physarum polycephalum. All three genes are expressed at constant rates in the uninucleate amoebae and flagellates, regardless of the culture conditions (solid or liquid medium, particulate or dissolved nutrients). In the multinucleate stages (micro- and macroplasmodia) Ppras1 and Pprap1 mRNAs are somewhat less abundant, while Ppras2 is not expressed at all. The early stages of the amoeba-plasmodium transition proceed without any drop in Ppras2 expression. During the synchronous cell cycle in macroplasmodia Ppras1 and Pprap1 are expressed at a constant level.

Phytochrome-induced expression of lig1, a homologue of the fission yeast cell-cycle checkpoint gene hus1, is associated with the developmental switch in Physarum polycephalum plasmodia

Lig1 was found in a differential-display screen for early genes expressed during phytochrome-controlled sporulation of Physarum polycephalum plasmodia. A stretch of 218 amino acids of the predicted sequence of Lig1 shares 32% sequence identity to that of the Schizosaccharomyces pombe cell-cycle and DNA-damage checkpoint gene hus1. In addition Lig1 is homologous to proteins of unknown function in Homo sapiens (35% identity) and Mus musculus (31% identity). Induction of lig1 expression was found to be controlled downstream from the point of integration of the phytochrome-activated pathway and the pathway sensing the metabolic state, but upstream of the developmental switch. The lig1 expression level in individual plasmodia correlated positively with the probability to sporulate. Sensory control of the lig1 expression level and its association with the developmental switch suggests a possible mechanism for the coordination of differentiation and the control of cell-cycle progression during the sporulation of P. polycephalum.

Early activated replication origins within the cell cycle-regulated histone H4 genes in Physarum

It was previously shown that the two members of the cell cycle-regulated histone H4 gene family, H4-1 and H4-2, are replicated at the onset of S phase in the naturally synchronous plasmodium of Physarum polycephalum, suggesting that they are flanked by replication origins. It was further shown that a DNA fragment upstream of the H4-1 gene is able to confer autonomous replication of a plasmid in the budding yeast. In this paper, we re-investigated replication of the unlinked Physarum histone H4 genes by mapping the replication origin of these two loci using alkaline agarose gel and neutral/neutral 2-dimensional agarose gel electrophoreses. We showed that the two replicons containing the H4 genes are simultaneously activated at the onset of S phase and we mapped an efficient, bidirectional replication origin in the vicinity of each gene. Our data demonstrated that the Physarum sequence that functions as an ARS in yeast is not the site of replication initiation at the H4-1 locus. We also observed a stalling of the rightward moving replication fork downstream of the H4-1 gene, in a region where transient topoisomerase II sites were previously mapped. Our results further extend the concept of replication/transcription coupling in Physarum to cell cycle-regulated genes.

G1-phase arrest is not a prerequisite for encystment in Physarum

Amoebae of the Myxomycete Physarum polycephalum form resistant, walled cysts when the food bacteria in a culture have been consumed. No G1 phase has been detected in the vegetative amoebal cell cycle, most of which comprises the G2 phase. Mature cysts are also in G2, but it has been reported that a G1 phase of roughly 24 h, followed by an S phase, is obligatory prior to encystment. We used flow cytometry to determine the distribution of DNA contents in amoebal cultures at intervals during vegetative growth and encystment. In all cultures, the cells were predominantly in G2 phase, and the percentage of cells with G1 DNA content remained very low. We conclude that an extended G1 phase of 24 h did not occur in our cultures and cannot be a prerequisite for encystment.

Histone acetyltransferases during the cell cycle and differentiation of Physarum polycephalum

The dynamic state of histone acetylation is maintained by histone acetyltransferases (HATs) and deacetylases. Cellular fractionation of plasmodia of Physarum polycephalum and partial purification of subcellular fractions by chromatography revealed the existence of a cytoplasmic B-type and four nuclear A-type HATs. The cytoplasmic B-enzyme was highly specific for histone H4, causing di-acetylation of H4 in vitro. The nuclear enzymes (HAT-A1 to HAT-A4) accepted all core histones as substrates, but differed by the preference for certain histone species. Enzymes were analyzed during the naturally synchronous cell cycle of macroplasmodia. Each of the enzymes had its individual cell cycle activity pattern, indicating diverse functions in nuclear metabolism. When growing plasmodia were induced to undergo differentiation into dormant sclerotia, an additional enzyme (HAT-AS) appeared at a late stage of sclerotization which correlated with differentiation-specific histone synthesis and acetylation in the absence of DNA replication. When dormant sclerotia were induced to reenter the cell cycle, a further enzyme form (HAT-AG) appeared during a short time period prior to the first post-germination mitosis. This enzyme had a strong preference for H2B, correlating with the overproportional in vivo acetate incorporation in H2B. Both differentiation-associated HATs were undetectable in growing plasmodia. The results demonstrate that different functions of core histone acetylation are based on multiple enzyme forms that are independently regulated during the cell cycle. Transitions from one developmental stage into another are accompanied by specific enzyme forms. With respect to recent data in the literature it may be assumed that these HAT-forms are subunits of a HAT-complex whose composition changes during the cell cycle and differentiation.

Secretion of slime, the extracellular matrix of the plasmodium, as visualized with a fluorescent probe and its correlation with locomotion on the substratum

Slime, the extracellular matrix of Physarum plasmodium, is secreted by the exocytosis of a vesicles that contain a slime precursor. Using an antibody raised against biochemically purified slime, we detected the intracellular localization of the slime vesicle. Slime vesicles are abundant in the advancing front of the plasmodium, as confirmed by electron microscopic observation in two different cross-sectional angles. Screening various reagents, we found that rhodamine-phosphatidylethanolamine (Rh-PE) binds specifically to slime in both its intravesicular and extracellular forms, as confirmed by immunoelectron microscopy using an antibody against fluorochrome rhodamine. The plasmodia vitally stained with Rh-PE exhibited dynamic fluorescent patterns during the course of locomotion. The fluorescence was conspicuous at the periphery of the leading pseudopods and oscillated according to the shuttle streaming that accompanied the relaxation and contraction of the periphery; it was intense in the relaxation phase when pseudopods extended, and became weak in the contraction phase when pseudopods contracted. The results collectively mean that the slime vesicles carried by the cytoplasmic streaming accumulated prior to secretion at the advancing margin of the plasmodium.

Cell cycle-dependent activation of telomerase in naturally synchronized culture of a true slime mold, Physarum polycephalum

Telomeres of Physarum plasmodia did not shorten with numerous repeats of nuclear division, and an apparent activity of telomerase was detected in this organism. In naturally synchronized culture of Physarum plasmodia, an evident activation of telomerase was observed at the late S-phase, just prior to the completion of in vivo DNA replication, and the low telomerase activity was detected throughout the cell cycle. In the nuclei isolated from different phases of synchronized plasmodia, a higher activity of telomerase was also observed at late S-phase. These results clearly show the existence of a cell cycle-dependent regulatory mechanism of telomerase activity in growing, naturally synchronized cells.

Localization of the newly initiated and processed ribosomal primary transcripts during the mitotic cycle in Physarum polycephalum

We analyzed the fate of the rRNA released as a result of the prophasic disintegration of the nucleolus, during the "closed" mitosis of the naturally synchronous plasmodium of Physarum polycephalum. Using a probe complementary to the mature 19S and 26S rRNA, we previously showed that the nucleolus-derived rRNAs are stable in mitosis, mainly associated with numerous fibrillar nucleolar remnants (Pierron and Puvion-Dutilleul, 1993, Exp. Cell Res. 208, 509-517). However, a significant fraction of these mitotic rRNA precursors were also found in more diffuse nuclear, granular zones. In this paper, we trace pre-rRNA molecules in the early stages of their maturation by using probes derived from the 5' external transcribed spacer (5'-ETS), upstream and downstream of the processing site located 1.7 kb from the transcription initiation site. In agreement with a previous S1-mapping study (Blum et al., 1986, Nucleic Acids Res., 10, 4121-4133), we observed that the rRNA transcripts complementary to the 5'-ETS portion downstream of the processing site are stable in mitosis, and we demonstrate that they are specifically associated with the border of the fibrillar nucleolar remnants. On the other hand, the pre-rRNA chains containing the upstream portion of the 5'-ETS become undetectable in mitosis, marking the cessation of rDNA transcription. Since the reappearance of these nascent pre-rRNA molecules signals the resumption of the transcriptional activity, we determined that a burst of rRNA synthesis is taking place within the prenucleolar bodies, immediately after the separation of the daughter nuclei. Taken together, our results illustrate the persistence of the nucleolar components of Physarum, within nucleolar remnants that, although transcriptionally inactive during mitosis, function as independent entities very early in interphase.

Characterization of npf mutants identifying developmental genes in Physarum

In Physarum polycephalum, uninucleate haploid amoebae develop into macroscopic multinucleate plasmodia. Wild-type, sexual development is triggered when two amoebae carrying different alleles of matA fuse to form a zygote which develops into a diploid plasmodium. Mutations in the matA genetic region give rise to apogamic strains in which a single haploid amoeba can develop into a haploid plasmodium. An essential stage in both sexual and apogamic plasmodium formation is an extended cell cycle in uninucleate cells, which ends with the formation of a binucleate cell by mitosis without cytokinesis. Using a 'brute force' screening method, we have isolated mutants blocked in apogamic plasmodium development. Genetic analysis showed that the mutations we have identified were unlinked to matA, unlike mutations previously identified following an enrichment step. Most of the loci revealed by our screen were represented by only one allele, indicating that further screening should lead to the identification of additional genes required for plasmodium development. Phenotypic analysis showed that different mutants were blocked at different stages of plasmodium formation. Some of the mutations blocking apogamic development at an early stage, close to the start of the long cell cycle, failed to block sexual development in zygotes homozygous for the mutation. Since the two modes of plasmodium formation differ only in the initiation of development, these mutations presumably interfere with the initiation process. In the remaining mutants, in which both sexual and apogamic development were blocked, development first became abnormal towards the end of the long cell cycle. This suggested that the wild-type gene products were required by this time and was consistent with previous evidence that many changes in cellular organization and gene expression occur during the long cell cycle. Each of these mutants showed a different terminal phenotype and some aspects of plasmodium development occurred normally although others were blocked, suggesting that development involves multiple pathways rather than a dependent sequence of events. Phenotypic analysis of double mutants supported this conclusion and also revealed epistatic interactions, presumably due to blocks in the same pathway. In several of the mutants, terminally differentiated cells died by an apoptosis-like mechanism; since this was never observed in vegetative cells, it was presumably triggered by the failure of development. Phenotypic analyses of additional mutants will extend our understanding of the pathways involved in plasmodium development.

A non-cycling mitotic cyclin in the naturally synchronous cell cycle of Physarum polycephalum

A universal model of the control of the cell cycle in eukaryotic organisms has emerged from the discovery that MPF (maturation or mitosis promoting factor) is a heterodimer consisting of a catalytic subunit (p34cdc2) and a regulatory subunit (mitotic cyclin) encoded by a pair of conserved genes. A prominent feature of the periodic activation of the protein kinase p34cdc2 is the gradual accumulation of cyclin in interphase and its abrupt degradation in mitosis, which is believed to be required for inactivation of MPF and exit from mitosis. Utilizing the precise natural synchrony of mitosis of the plasmodium of the myxomycete Physarum, the high affinity of the p34cdc2/cyclin B complex to p13suc1 Sepharose beads, and immunological reagents including three different anticyclin B antibodies and the anti-PSTAIR antibody, a transient histone H1 kinase activation but not fluctuation in the abundance of cyclin B have been detected during mitosis. It is argued that cyclin degradation may be required for cytokinesis and/or postmitotic controls of cell proliferation in G1 phase and cell-to-cell signaling in development but not for the inactivation of histone H1 kinase in mitosis.

Time-resolved detection of three intracellular signals controlling photomorphogenesis in Physarum polycephalum

Incompetent plasmodia of Physarum polycephalum exposed to a light pulse sporulated after reaching the competent stage. Fusion of irradiated plasmodia with dark-incubated plasmodia and analysis of sporulation indicated the presence of a morphogenetic signal. It is concluded that a logic AND gate integrates the photoreceptor signal and the competence signal and controls the formation of the morphogenetic signal.

Microtubules are required in amoeba chemotaxis for preferential stabilization of appropriate pseudopods

Amoebae of Physarum polycephalum exhibit chemotactic responses to glucose and to cAMP. The chemotaxing amoebae exhibit alternating locomotive movements: relatively linear locomotion and movements that change the direction of the locomotion. Such locomotive activity is tightly coupled with the changes in the number and the positions of the pseudopods; cells have one pseudopod at the leading edge during their linear locomotion, while they have multiple pseudopods when they are changing the direction of locomotion. Treatment of cells with microtubule-disrupting reagents inhibited the chemotaxis of the cells. To characterize the role of the microtubule system in chemotaxis, we quantitatively analyzed the relationship between the positions of multiple pseudopods of the amoebae and the relative stability of the pseudopods during reorientation. No significant differences were observed in the pseudopod dynamics between the untreated and the treated amoebae. In both cases, one pseudopod at the leading edge continued to expand during linear locomotion. It then split into two to three pseudopods in the reorientation phase, and the positions of the multiple pseudopods were random. Among multiple pseudopods, however, the pseudopods closer to the microneedle tip were selectively stabilized more often than those distant from the tip in the presence of the microtubule system. By contrast, such preferential stabilization of the appropriate pseudopods was completely abolished by microtubule inhibitors. The microtubule-dependent selection of appropriately located pseudopods enables amoebae to turn correctly at the reorientation step.

Changes in phospholipids during the cell cycle of myxomycete Physarum polycephalum

The rate of 32Pi incorporation into the main membrane phospholipid fractions, i.e. phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI), as well as their contents in the cells during synchronous growth of the myxomycete, Physarum polycephalum, have been studied. It has been found that both the phospholipid levels and the rates of 32Pi incorporation increase during the S phase till the early G2 phase, remain nearly constant during the G2 phase and fall to the initial level at the end of the G2 phase and in mitosis. It has been revealed that the rate of 32Pi incorporation into PC is very low compared to PE and PI, in spite of the fact that the PC level is the highest. The possible reasons of this phenomenon are discussed.

A developmental mutation (npfL1) resulting in cell death in Physarum polycephalum

In Physarum, microscopic uninucleate amoebae develop into macroscopic multinucleate plasmodia. In the mutant strain, RA614, plasmodium development is blocked. RA614 carries a recessive mutation (npfL1) in a gene that functions in sexual as well as apogamic development. In npfL+ apogamic development, binucleate cells arise from uninucleate cells by mitosis without cytokinesis at the end of an extended cell cycle. In npfL1 cultures, apogamic development became abnormal at the end of the extended cell cycle. The cells developed a characteristic rounded, vacuolated appearance, nuclear fusion and vigorous cytoplasmic motion occurred, and the cells eventually died. Nuclei were not visible by phase-contrast microscopy in most of the abnormally developing cells, but fluorescence microscopy after DAPI staining revealed intensely staining, condensed nuclei without nucleoli. Studies of tubulin organization during npfL1 development indicated a high frequency of abnormal mitotic spindles and, in some interphase cells, abnormally thick microtubules. Some of these features were observed at low frequency in the parental npfL+ strain and may represent a pathway of cell death, resembling apoptosis, that may be triggered in more than one way. Nuclear fusion occurred during interphase and mitosis in npfL1 cells, and multipolar spindles were also observed. None of these features were observed in npfL+ cells, suggesting that a specific effect of the npfL1 mutation may be an incomplete alteration of nuclear structure from the amoebal to the plasmodial state.

Localization by high resolution in situ hybridization of the ribosomal minichromosomes during the nucleolar cycle of Physarum polycephalum

We have used biotinylated rDNA probes to localize by in situ hybridization the extrachromosomal genes for ribosomal RNA in the slime mold Physarum polycephalum. We established conditions that allow for highly specific hybridization at the ultrastructural level and determined that the 60-kb palindromic rDNA molecules are confined to the nucleolus in interphase. Our study definitively locates these extrachromosomal genes in mitosis in the form of thin DNA fibers contained within nucleolar remnants. We further show that these rDNA minichromosomes do not condense and that they segregate as entities independent of the condensed chromosomal DNA. In telophase, these minichromosomes migrate from the poles toward the equatorial region of the nucleus in a direction opposite that of the chromosomes. Our results illustrate the discontinuous nature of the nucleolar organizing region in Physarum.

Cellular and molecular analysis of plasmodium development in Physarum

The development of an amoeba into a plasmodium involves extensive changes in cellular organisation and gene expression. The genetic basis of a number of recessive mutations that block plasmodium development has been elucidated. The stage at which development becomes abnormal has been determined for all the mutants, as has the terminal phenotype. In order to investigate the changes in gene expression that accompany plasmodium development, a cDNA library has been made using RNA isolated from cell populations in which development was occurring.

Cell cycle-dependent assembly and disassembly of cytoplasmic microtubules in the plasmodium of the myxomycete Physarum polycephalum

The giant syncytium of Physarum plasmodia possesses a complex cytoplasmic microtubule network except during the occurrence of the intranuclear mitosis. In early prophase stages, intranuclear spindles assemble concomitantly as the cytoplasmic microtubule network disassembles. No cytoplasmic microtubules are present in metaphase. They begin to reassemble in telophase. The complex cytoplasmic microtubule network reappears in early reconstruction stages. The assembly of cytoplasmic microtubules occurs on cytoplasmic foci, both in telophase stage and during rewarming after cold microtubule disassembly. These foci, independent of the nuclei, correspond to the foci observed in the cytoplasm during interphase, both by immunofluorescence and electron microscopy. As cytoplasmic and intranuclear microtubule-organizing centers are spatially distinct, plasmodial syncytia offer the possibility to study the effects of cell regulatory pathways on two types of microtubule-organizing centers that differ in their nucleating activity during the cell cycle.

Mechanisms of cell shape change: the cytomechanics of cellular response to chemical environment and mechanical loading

Processes such as cell locomotion and morphogenesis depend on both the generation of force by cytoskeletal elements and the response of the cell to the resulting mechanical loads. Many widely accepted theoretical models of processes involving cell shape change are based on untested hypotheses about the interaction of these two components of cell shape change. I have quantified the mechanical responses of cytoplasm to various chemical environments and mechanical loading regimes to understand better the mechanisms of cell shape change and to address the validity of these models. Measurements of cell mechanical properties were made with strands of cytoplasm submerged in media containing detergent to permeabilize the plasma membrane, thus allowing control over intracellular milieu. Experiments were performed with equipment that generated sinusoidally varying length changes of isolated strands of cytoplasm from Physarum polycephalum. Results indicate that stiffness, elasticity, and viscosity of cytoplasm all increase with increasing concentration of Ca2+, Mg2+, and ATP, and decrease with increasing magnitude and rate of deformation. These results specifically challenge assumptions underlying mathematical models of morphogenetic events such as epithelial folding and cell division, and further suggest that gelation may depend on both actin cross-linking and actin polymerization.

Differential effect of cordycepin on S and G2 phases of cell cycle in plasmodia of Physarum polycephalum Schw

Effect of pulse treatments of cordycepin, an analog of adenosine, on S and G2 phases of the cell cycle of the mitotically synchronous plasmodia of Physarum polycephalum has been studied. Various concentrations of the drug (50-200 micrograms ml-1) were found to be effective in delaying mitosis by several hours in both the phases. However, there was a significant increase in mitotic delay in those treated during G2. It is suggested that this extra delay during G2 could be due to the transcriptive level inhibition of specific RNA types, such as that of tubulins, whose gene activity is cell cycle regulated and turned on during G2 in Physarum, or alternatively because of a deficiency for ATP and the consequent inhibition of events such as mitotic spindle assembly and phosphorylation of histones.

Classification of gravity effects on "free" cells

When cell physiologists detect gravity related reactions of their objects it is often difficult to decide where the receptors for the observed effects are located. Answering this question is necessary for any further analysis of a detected gravity effect on cells. In previous papers we have discussed direct and indirect gravity effects in relation to the smallest functional units where the primary receptor, which interacts with gravity, is positioned inside and outside of such a unit, respectively. So, in a first approximation we can conclude that in a multicellular aquatic organism, which changes its metabolism in weightlessness, the primary receptors of gravity are located inside the cells of that organism. A special approach is necessary when free living cells, the density of which may be higher than the one of the (liquid) medium, or even cells living on a free surface are observed. In these two cases also indirect effects have to be taken into account, which will be demonstrated with the aid of the slime mold Physarum polycephalum. Additionally the environment of the organisms can be changed directly and indirectly by gravity.

Confirmation of gravisensitivity in the slime mold Physarum polycephalum under near weightlessness

We have investigated Physarum polycephalum, a unicellular organism with no special gravity receptors, on its ability to react to gravity. The first experiments were 0 g-simulation experiments on the fast-rotating clinostat conducted with plasmodial strands of this acellular slime mold. In these earth-bound experiments the observed parameters were periodicity of the contractions and dilatations of the strand's ectoplasm as well as the periodicity and velocity of the striking cytoplasmic (endoplasmic) shuttle streaming. During 0 g-simulation these parameters showed significant changes indicating the existence of a gravisensitivity of the slime mold. The Space-Shuttle experiment (ESA-Biorack in D 1-Mission) should demonstrate the validity of the 0 g-simulation on the fast-rotating clinostat. The experiment was designed in a way enabling the registration of the same parameters as on the clinostat (using the light microscope in combination with a photo diode and a cinecamera). Only one of the two planned measurement sessions was fully successful and provided us with data confirming the results gained on the fast-rotating clinostat: The slime mold showed under real near weightlessness in the D 1-Space Shuttle Mission a transient frequency increase in tis contraction rhythmicity and a (steady) increase in the streaming velocity of its endoplasm.

Influence of zero gravity simulation on time course of mitosis in microplasmodia of Physarum polycephalum

Detrimental effects of weigntlessness are no longer expected to hinder successful mitosis. Experiments in space and on the fast clinostat give no hints of this. Nevertheless we are thinking of a g sensitivity during the process of chromosome condensation and distribution. The time course of nuclear division in microplasmodia of the slime mold Physarum polycephalum was investigated under 0 g simulation on the fast rotating clinostat in comparison to 1 g controls. The result of this experiment is: A significant shortening of mitosis under 0 g simulation compared to 1 g controls.