Abstracts

University of the Arts London

As an artist and an educator I work with the emergent and adaptive properties of slime mould, developing a range of studies, methods and practices employing the organism as artistic medium, educational model and social metaphor. The intention of the work is to draw connections between networked systems in biological, technological and social contexts; to develop interdisciplinary methods of collective enquiry; and to create the conditions for interspecies encounters between human and nonhuman intelligence. Here, I will give an overview of practices employed in the creation of artworks, experiences and collective experiments. Discussion will focus on projects currently in development, which aim to reveal slime mould learning behaviours and decision-making mechanisms within live artworks.

www.heatherbarnett.co.uk

PTB Berlin

Many processes in living cells are controlled by biochemical substances regulating active stresses. We argue that deformation patterns and waves in microplasmodia of Physarum polycephalum are an intriguing example of this. In order to model these structures, we employ a description of an active poroelastic material, where we incorporate the active stress into a two-phase model of the cytoplasm which accounts for the spatiotemporal dynamics of the cytoskeleton and the cytosol. The cytoskeleton is described as a solid matrix that together with the cytosol as an interstitial fluid constitutes a poroelastic material. We find different forms of mechanochemical waves including traveling, standing, and rotating waves even in this model [1]. A complete description of Physarum microplasmodia requires, however, a coupling of an active poroelastic medium to a reaction-diffusion dynamics, that can describe temporal oscillations as well as the regulation of the free calcium concentration in the cytosol [2,3]. Recent findings on the influence of the passive material properties on the dynamics of such patterns in active solids and fluids are presented. The model for Physarum microplasmodia [2] is revisited and critically assessed in light of a plethora of recent experimental papers providing new insights into the material properties of Physarum cytoplasm as well as the pattern dynamics in stationary and moving microplasmodia.

References:

[1] M. Radszuweit, S. Alonso, H. Engel, and M. Bär, Phys. Rev. Lett. 2013.
[2] M. Radszuweit, H. Engel, and M. Bär, PLoS One 2014.
[3] S. Alonso, U. Strachauer, M. Radszuweit, M. Bär, and M. Hauser, Physica D 2016.
[4] S. Alonso, M. Radszuweit, H. Engel, and M. Bär, J. Phys. D: Appl. Phys. 2017.

Jacobs University

Proteases are catalysts of the most important post-translational protein modification, namely they mediate protein processing through hydrolytic cleavage of peptide bonds. In almost all instances, this process is irreversible and therefore essential for regulation of unidirectional protein fate decisions of cells. Proteolytic enzymes cleave their endogenous peptide and protein substrates resulting in their activation or inactivation, and in maturation or degradation. Proteases become instrumental in trafficking by unmasking targeting sequences or by removing them once a protein arrived in the specific compartment to which it is destined. Therefore, proteases are involved in determining cellular differentiation or proliferation, and at the same time, are critical regulators of cell survival, or act as initiators and executioners of cell death programs. Hence, proteolytic enzymes engage in cellular decision-making and signaling pathways as much as they are vitally important and critical factors in maintaining protein homeostasis (proteostasis) of any cell, tissue, or organism.

So far, we analyzed the spatio-temporal regulation of proteolysis and protease interactions with their substrates and regulatory co-factors or endogenous inhibitors in mammalian cells. The aim is to reach a better understanding of epithelial cell biology, in particular, under physiological and pathological conditions. Further goals of our work comprise deciphering cellular decision-making and signaling by investigating canonical and non-canonical trafficking, regulated secretion and non-regulated release of endo-lysosomal proteases, thereby identifying their natural substrate targets within and outside of eukaryotic cells. Thus, our specific research focus is on monitoring and visualizing protease activities in organs like the brain, gastro-intestinal tract, skin, and thyroid gland. However, recently we extended our projects and included studies on the abundance and importance of peptidases upon ageing which requires using sophisticated tools of systems biology.

According to the compendium of proteolytic enzymes, their substrates and inhibitors, i.e. the Merops database, Physarum polycephalum features expression of cysteine, serine, and metallopeptidases (www.ebi.ac.uk/merops/index.shtml). While substantial investigations on their structure, biochemical features, and biological functions exist, more work is required in approaching in vivo-imaging of their transport pathways and functional activities. We suggest using activity based probes and fluorescent protein-tagged proteases to visualize their trafficking and enzymatic actions on the spot and in real time, while Physarum is taking decisions in its movements through e.g. complex mazes.

References:

• Oettmeier, C., K. Brix, and H.-G. Döbereiner (2017). Topical Review: Physarum polycephalum – a new take on a classic model system. J. Phys. D: Appl. Phys. 50, no. 41. doi.org/10.1088/1361-6463/aa8699
• Couture, F., A.M. Jansen, P. Taghert, and K. Brix (2017). Molecular basis of protein fates in the secretory and endocytic pathways, and beyond. Eur. J. Cell Biol. 96, 369–371. Doi:10.1016/j.ejcb.2017.06.006
• Brix, K., J. McInnes, A. Al-Hashimi, M. Rehders, T. Tamhane, M.H. Haugen (2015). Proteolysis mediated by cysteine cathepsins and legumain - recent advances and cell biological challenges. Protoplasma 252, 755-774. Doi: 10.1007/s00709-014-0730-0.
• Arampatzidou, M., M. Rehders, S. Dauth, D.M.T. Yu, S. Tedelind, and K. Brix (2011). Imaging of protease functions – current guide to spotting cysteine cathepsins in classical and novel scenes of action in mammalian epithelial cells and tissues. It. J. Anat. Embryol. 116, 1-19.
• Proteases: Structure and Function, edited by Klaudia Brix and Walter Stöcker, Springer-Verlag Wien 2013. 564 p. Doi:10.1007/978-3-7091-0885-7
• Brix, K., A. Dunkhorst, K. Mayer, and S. Jordans (2008). Cysteine cathepsins: Cellular roadmap to different functions. Biochimie 90, 194-207. Doi:10.1016/j.biochi.2007.07.024
• Brix, K., and S. Jordans (2005). News & Views: Watching proteases in action. Nat. Chem. Biol. 1, 186-187.
• Stockem, W., and K. Brix (1994). Analysis of microfilament organization and contractile activities in Physarum. Int. Rev. Cytol. 149, 145-215.

Bauhaus-Universität Weimar

Decision making within the artistic working process is highly different to decisions in scientific experiments. An artist refers to him/herself, to his/her own body and own experience. An artist is within the artistic working process the highest instance and ultimate reference. Therefore, agency in art is linked to autonomy and openly developing, emergent processes.

In my presentation I will show some examples from my work to demonstrate how aesthetic values in art are guided through the freedom provided by the experimental setting.

Universität Bremen

The efficient construction and navigation of transportation networks remains a challenging task, and the analysis of real-world systems is often hindered by the lack of time-resolved data. This furthers the need for model systems such as the unicellular slime mold Physarum polycephalum, which self-organizes into a planar network of tubes optimized for transport efficiency and fault tolerance.

Remarkably, artificial and self-organized networks share important structural and functional traits, raising the question whether similar principles guide their assembly. We describe and model the time evolution of topology in P. polycephalum based on the statistics of events that modify network structure.

¹Department of Plant Sciences, University of Oxford, UK
²Department of Zoology, University of Oxford, UK

Physarum forages for food as an interconnected network and has to balance expenditure of energy in exploration to find new resources, exploitation to harvest ones already encountered, and transportation through the network between these sources and sinks. We previously developed a comprehensive network analysis program to characterise network structure and dynamics during evacuation from enclosed arenas. We have now extended this approach to handle network evolution in growing systems. In addition, we have started to analyse how biomass is allocated during foraging when the organism can choose between different strategies. Following the approach adopted in animal foraging studies, we set out to determine which currency is the best descriptor of the slime mould’s foraging behaviour. Slime mould plasmodia were presented with a choice between two foraging lanes, one fixed and the other variable, either in delay to, or quality of, food items, both with the same gross-rate of energy gain, but with different predicted returns if the organism were maximising another currency, such as the average per patch rate or a hyperbolic discounted rate. Generally, slime mould plasmodia showed an equal preference for either foraging option, consistent with maximising the gross-long term rate. However, gross-rate maximisation did not account all of the behaviour displayed by the slime mould, particularly switches in growth direction. It is also not clear over what length scale and time scale decisions are actually made, and the extent that animal foraging models are an appropriate framework to understand slime mold behaviour.

Universität Köln

An accurate genome sequence is the basis for subsequent molecular analyses. Our first attempt to analyse a draft sequence of the Physarum polycephalum genome resulted in insights about gene content and capabilities [1]. It however also revealed that the genome organization with overwhelming numbers of simple repeats and even long G stretches hindered the assembly and resulted in a highly fragmented draft genome. It was not possible to use this draft genome for accurate gene predictions. Rather, transcript data were needed to evaluate the full gene content of P. polycephalum [2]. Thus, I decided to reevaluate the assembly, add new data and try to complete the genome sequence using various techniques (mate pair sequencing, Rescaffolding, Bionano, etc.). Here I present the outcome of this endeavor and give an overview on new analysis data with this updated genome sequence.

1. Schaap, P. et al. 2016. The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Genome Biology and Evolution 8: 109-125.
2. Glöckner, G., Marwan, W. 2017. Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks. Scientific Reports 7: 12304.

Universität Graz

The plasmodia of the coenocytic Myxogastria contain a large number of synchronized nuclei, which are shuttled throughout the plasmodial system of tubes by peristaltic forces. Nuclei as well as other cellular components can be visualized using fluorescent staining. In my presentation, I present preliminary information about arrangement and density of nuclei from different parts of plasmodia of Physarum polycephalum and will compare these with other slime molds. I will discuss whether variation in internal cellular organisation might influence information processing and the growth behaviour of slime molds.

Otto-von-Guericke Universität Magdeburg

The motility of amoeboid cells of the plasmodial slime mould Physarum polycephalum was studied experimentally. Analysis of their trajectories and of their mean square displacements reveal two characteristic types of behaviour that depend on the time interval τ between any pair of points along the trajectory. Whereas free migration of cells is observed for time intervals τ > 300 s, at short time intervals (of up to τ ≈ 100 s) the motility is due to changes in the cell shape induced by the peristaltic pumping of protoplasm though the cell. Freely migrating cells display persistent random motion with very long persistence times of up to ≈ 1.5 h. Superdiffusive motion typically lasts for ≈ 5 h, while at longer times the dynamics becomes diffusive. Whereas symmetric velocity distributions are found for short time intervals τ, the typical velocity distributions from freely migrating cells show an asymmetric component, which reflects the long-lasting persistent motions. We observed that high propagation velocities are correlated with both, episodes of straight motion and an elongated cell shape. Furthermore, the patterns of cell thickness oscillations (that provide for the intracellular peristaltic pumping of protoplasm) also changed as a function of the propagation velocity of the cell.

Tanja Huxoll, Universität Bremen

Physarum polycephalum is an optimal model organism to study binary decision making. It finds the shortest path through a maze (1), it finds the highest food quality source out of three options (2) and it was also observed that Physarum shows a speed-accuracy trade-off (3).

In our experiments we let Physarum decide between two different environments, which differ in chemical attractor concentrations (Glucose). The behaviour is then observed for one day. We are interested in the occupied area of each environment and with which probability. Another parameter we are interested in is the time point of the decision.

The goal of this work is to develop a model, which describes the decision making. Here, we present our first approach of a model to describe the occupation probability for concentration ranges. It is a statistical physics approach. We also present our experimental set-up and the latest results.

References:

1. Nakagaki, T., H. Yamada, and Á. Tóth, Maze-solving by an amoeboid organism. Nature, 2000, 407(6803): p. 470-470.
2. Latty, T. and M. Beekman, Food quality and the risk of light exposure affect patch-choice decisions in the slime mold Physarum polycephalum. Ecology, 91(1), 2010, pp. 22-27
3. Latty, T. and M. Beekman, Speed-accuracy trade-offs during foraging decisions in the acellular slime mould Physarum polycephalum. Proceedings of the Royal Society of London, Series B: Biological Sciences, 2011. 278(1705): p. 539-545.

Jean-Daniel Julien, MPI for Dynamics and Selforganization Göttingen

Cytoplasmic streaming, the active transport of the fluid contained in a cell, is observed in very diverse organisms. It is involved in fundamental physiological functions, such as growth, migration, or long-range distribution of molecules. One example of cytoplasmic streaming is the periodic shuttle flow found in the plasmodium of slime moulds. These single-celled organisms form networks of tubes. Periodic streaming of the cytoplasm takes place inside these tubes, driven by the mechanical contraction of the acto-myosin network wrapping them. Previous models for the organization of these mechanical waves rely on the diffusion of tension-activating molecules in the peripheral layer of the tube. However, plasmodia are able to grow to almost arbitrary sizes, and the remarkable coherence of cytoplasmic flows, even for large individuals, seems incompatible with simple diffusion.

I will present a mechanochemical model of a contracting tube, coupled to a contraction-regulating molecule advected in the cytoplasm. The model generates patterns of contraction waves and oscillatory flows. Surprisingly, simulated patterns can extend beyond the intrinsic length scale of the model instability. Although long-range patterns appear randomly at first, they can be robustly generated in a growing system or with different boundary conditions.

Dirk Kulawiak, Technische Universität Berlin

Motivated by recent experiments, we model the flow-driven amoeboid motility that is exhibited by protoplasmic droplets of Physarum. Here, a feedback loop between a chemical regulator, active mechanical deformations, and induced flows give rise to spatio-temporal contraction patterns that result in directed motion. Our model describes the droplet's cytoskeleton as an active viscoelastic solid phase that is permeated by a passive viscous fluid representing the cytosol. The active tension in the solid phase depends on the concentration of a regulating agent that is advected by the fluid phase. Previously, it was shown that under rigid boundary conditions that impose a fixed shape, this model reproduces a large variety of mechano-chemical patterns such as antiphase oscillations and rotating spirals. This in line with experimental observations of contraction patterns in these droplets. Here, we present an approach that includes free boundary conditions, nonlinear friction between droplet and substrate and a nonlinear reaction kinetic for the regulator to model the movement of these droplets. We find deformations of the droplet boundary as well as oscillatory changes in the droplets position with a net motion in each cycle.

Jonghyun Lee, Universität Bremen

All organisms constantly make decisions during foraging to maximize gain and minimize the risk. This is reflected in the unicellular organism Physarum polycephalum, which normally grows as an optimized network.

We utilize Physarum microplasmodia, quasi-spherical fragments on the micrometer range, and observe foraging patterns under different environmental conditions.

Generally, Physarum grows as an extended network, of which the transition from micro- to macroplasmodia occurs via percolation [1]. However, under starvation conditions, this transition does not occur. Instead, several bodies on the millimeter scale form and migrate radially away from the site of inoculation. We term these motile mesoplasmodia satellites.

A satellite growth is induced only when microplasmodia are starved, suggesting that it is a type of emergency response. Satellite growth mode has defined phases of motility and rest, and their behaviour is spatio-temporally correlated. Satellites also have a stable and defined morphology, as well as a constant direction of movement.

We describe the satellite growth in various aspects. First, we present a description of this growth mode with simplified geometrical shapes. We describe scaling relationships of the number of satellites produced and their size based on initial conditions. The model predicts the size to increase and the number to decrease as the initial biomass increases, which fits well with the data.

Then, we conjecture a diffusion-based model which implements detection of a signal molecule above a threshold concentration. Then we calculate how far the satellites must travel until the concentration signal falls below the threshold. These calculated distances are in good agreement with the distances where satellites stop.

1.  Fessel, A. et al. (2012), Physical Review Letters 109, 078103

Jakob Löber, MPI Dresden

Motivated by the slime mold Physarum polycephalum, we present a mechanism for crawling cell motility based on an isotropic and incompressible continuum-mechanical model with free boundaries and no actin polymerization. In biological systems, mechanical deformations are driven by chemical reactions. Linear irreversible thermodynamics determines an isotropic active stress as the exclusive coupling between chemical reactions and mechanics allowed by symmetry in such a model. However, an isotropic active stress can excite only longitudinal deformations. While simple incompressible fluids do not support longitudinal deformations, a two-fluid model, also called two-phase or poroelastic model, exhibits an additional longitudinal deformation mode. This deformation mode is analogous to second sound in superfluid helium and can be excited by an isotropic active stress. We identify a nonlinear substrate friction as a necessary condition for the rectification of these deformations into persistent unidirectional motion.

Wolfgang Marwan, Otto-von-Guericke Universität Magdeburg

The developmental switch to sporulation in the unicellular eukaryote Physarum polycephalum is a phytochrome-mediated far-red light-induced cell fate decision. It synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we quantitatively analysed differential gene expression to obtain a time series dataset for each cell. Computational analyses of the gene expression data reveal individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression allows to reconstruct Petri nets that model and predict the behavior of single cells. Structural analyses of these Petri nets reveals the global behaviour of the regulatory network, the differential regulation of individual genes, and it gives access to the quasipotential landscape that determines the developmental decision.

References:

1. Werthmann, B., Marwan, W. 2017. Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape. J. Phys. D: Appl. Phys. 50: 464003 (18pp)
2. Glöckner, G., Marwan, W. 2017. Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks. Scientific Reports 7: 12304.
3. Schaap, P. et al. 2016. The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Genome Biology and Evolution 8: 109-125.
4. Rätzel, V., Marwan, W. 2015. Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation. Develop. Growth Differ. 57: 408-420.

Chrstina Oettmeier, Universität Bremen

Physarum polycephalum exhibits various types of locomotion (e.g., exploratory, taxis, and avoidance behaviors) on different length- and size scales (1,2), and can switch its behavior depending on the environment (3). Regarding the absence of a central nervous system or even neuronal structures, this is an amazing feat.

The slime mold can detect input signals from the environment, e.g. stimuli from food sources and light, and integrates this information within the cytoplasm. This ultimately leads to a quantifiable output, i.e. organized and integrated cell behavior, which, in higher animals, would be achieved by a nervous system.

To understand how behavioral diversity can be achieved, we focus on the cytoplasm as the Fluid Information Processing System of the amoeboid cell. As a model, we use so-called mesoplasmodia (4), i.e. small autonomous units which move continuously in search of food.

As an example, the locomotion of mesoplasmodia is driven by strong oscillations in the back of the cell, which act as a pacemaker. These contractions lead to a net flow of endoplasm towards the front, and persistent forward movement is the result. However, higher oscillation frequencies in the back are filtered out along the way, and at the front, only lower frequencies persist. Using the electronic-hydraulic analogy, this makes the mesoplasmodium a low-pass filter.

We view and model the cytoplasm of P. polycephalum as a fluidic circuit consisting of resistors and capacitors, which can produce different output patterns depending on the configuration of its components (e.g. vein diameter, branching). Resistance, mainly defined by vein diameter, and capacitance, due to elastic effects, can both easily be controlled by the organism without the need for complex biochemical pathways. We suppose that a simple and decentralized mode of control is required for different locomotion types which allow the slime mold to switch between them spontaneously: A fluidic network, consisting of a few simple components, can achieve to control the transport of fluid according to complex patterns in space and time.

References

1. Oettmeier, C., Brix, K., and Döbereiner, H.-G. (2017). Topical Review: Physarum polycephalum – a new take on a classic model system. J. Phys. D: Appl. Phys. 50, no. 41. doi.org/10.1088/1361-6463/aa8699
2. Bernitt, E., Oettmeier, C., and Döbereiner, H.-G. (2010). Micoplasmodium dynamics of Physarum polycephalum. IFMBE Proceedings, 1, Volume 31, 6th World Congress of Biomechanics (WCB 2010):1333, pp. doi.org/10.1007/978-3-642-14515-5_288
3. Fessel, A., Oettmeier, C., Bernitt, E., Gauthier, N.C., and Döbereiner, H.-G., (2012) Physarum polycephalum percolation as a paradigm for topological phase transitions in transportation networks. PRL 109:078103. doi.org/10.1103/PhysRevLett.109.078103
4. Oettmeier, C., Lee, J., and Döbereiner, H.-G. (2018). Form follows function: ultrastructure of different morphotypes of Physarum polycephalum. J. Phys. D: Appl. Phys. 51, no. 13. doi.org/10.1088/1361-6463/aab147

Daniel Schenz, Hokkaido University

Exploring free space (scouting) efficiently is a non-trivial task for organisms of limited perception, such as the amoeboid Physarum polycephalum. The organism needs its veins to move its body mass around and will use the same veins to connect to food sources, but the location of food sources is unknown at the time of the veins’ construction. In addition, constructed veins can be disassembled if unused, but within the area already spanned, new veins are not – at least for some considerable time – systematically built anew. All this poses the question how these veins are constructed to allow for efficient migration.

In this study we characterise Physarum’s vein construction during exploration, and introduce first a simple, phenomenological algorithm based on the fact that the organism’s vein network development and growth front dynamics are interdependent. [1]

After verification of the algorithm’s applicability, we then briefly discuss a mathematical model rooted in Physarum’s physiology. Current reinforcement dynamics for the development of the vein network [2], reaction-diffusion dynamics for the development of the growth front [3], and actomyosin contraction waves propagating through the organism [4] are combined into a mathematical model. This model can be evaluated numerically and yields results with striking similarity to the behaviour of the real organism. Variations of the parameters of the model confirm the importance of the link between the growth front dynamics and the vein network development for the emergence of the characteristic vein trajectory.

The success of the algorithm and the model suggest that local optimisation provides Physarum with a powerful approach to minimise the total length of its vein system during exploratory migration and suggests a biological context for the current reinforcement rule in Physarum, that is, achieving efficiency of its exploratory migration.

References:

1. D. Schenz, Y. Shima, S. Kuroda, T. Nakagaki, and K-I. Ueda, J. Phys. D: Appl. Phys. 50 434001 (2017)
2. A. Tero, R. Kobayashi, and T. Nakagaki, Jour. Theor. Biol. 244, 553–564 (2007)
3. K-I. Ueda, S. Takagi, Y. Nishiura, and T. Nakagaki, Phys Rev. E 83 021916-9 (2011)
4. D. A. Smith and R. Saldana, Biophys. J. 61 368-80 (1992)