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Tanya Latty - One of the best experts on this subject based on the ideXlab platform.
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brainless but multi headed decision making by the acellular slime mould Physarum polycephalum
Journal of Molecular Biology, 2015Co-Authors: Tanya LattyAbstract:Because of its peculiar biology and the ease with which it can be cultured, the acellular slime mould Physarum polycephalum has long been a model organism in a range of disciplines. Due to its macroscopic, syncytial nature, it is no surprise that it has been a favourite amongst cell biologists. Its inclusion in the experimental tool kit of behavioural ecologists is much more recent. These recent studies have certainly paid off. They have shown that, for an organism that lacks a brain or central nervous system, P. polycephalum shows rather complex behaviour. For example, it is capable of finding the shortest path through a maze, it can construct networks as efficient as those designed by humans, it can solve computationally difficult puzzles, it makes multi-objective foraging decisions, it balances its nutrient intake and it even behaves irrationally. Are the slime mould's achievements simply “cute”, worthy of mentioning in passing but nothing to take too seriously? Or do they hint at the fundamental processes underlying all decision making? We will address this question after reviewing the decision-making abilities of the slime mould.
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speed accuracy trade offs during foraging decisions in the acellular slime mould Physarum polycephalum
Proceedings of The Royal Society B: Biological Sciences, 2011Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:Speed–accuracy trade-offs (SATs) are thought to be a fundamental feature of biological information processing, yet most evidence of SATs comes from animals. Here, we examine SATs in the foraging decisions of an acellular, amoeboid organism: the slime mould Physarum polycephalum . Slime moulds were given a simple discrimination task: selecting the highest-quality food item from a set of three options. We investigated the effect of two stressors, light exposure and hunger, on the speed and accuracy of decision-making. We also examined the effect of task difficulty. When given a difficult discrimination task, stressed individuals tend to make faster decisions than non-stressed individuals. This effect was reversed in plasmodia given easy discrimination tasks, where stressed individuals made slower decisions than non-stressed individuals. We found evidence of SATs, such that individuals who made fast decisions were more likely to make costly errors by selecting the worst possible food option. Our results suggest that SATs occur in a wider range of taxa than previously considered.
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food quality affects search strategy in the acellular slime mould Physarum polycephalum
Behavioral Ecology, 2009Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:When searching for resources, organisms can increase the efficiency of search and exploitation behavior by using information about the quality of a current resource patch in their decision making. The search strategy used by an organism can in turn affect its performance in different landscapes. Here we examine the effect of resource quality on 2 foraging decisions: how much time to allocate to explore the environment for new resources and what search strategy to use during exploration. We used the slime mould Physarum polycephalum as our model system. Physarum polycephalum is an amoeboid organism that forages as a flowing mass of pseudopods. We quantified the search pattern of plasmodia after engulfment of food of 6 different qualities. Food quality had a significant, positive effect on how long plasmodia waited before resuming search behavior and on how long it took to abandon food disks. Food quality had a positive effect on fractal dimension, indicating that the amount of localized search performed by plasmodia increased with food quality. Our results suggest that increasing food quality results in a shift from extensive to intensive search. Next, we examined foraging performance in landscapes with different patch structures. Plasmodia in correlated landscapes (half the patches contained only high-quality food, half contained only low-quality food) gained more weight than plasmodia foraging in noncorrelated landscapes (patches contained both high- and low-quality food disks). Our results show that food quality affects exploitation and search behavior and that both behaviors influence foraging performance in different landscapes. Copyright 2009, Oxford University Press.
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food quality affects search strategy in the acellular slime mould Physarum polycephalum
Behavioral Ecology, 2009Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:When searching for resources, organisms can increase the efficiency of search and exploitation behavior by using information about the quality of a current resource patch in their decision making. The search strategy used by an organism can in turn affect its performance in different landscapes. Here we examine the effect of resource quality on 2 foraging decisions: how much time to allocate to explore the environment for new resources and what search strategy to use during exploration. We used the slime mould Physarum polycephalum as our model system. Physarum polycephalum is an amoeboid organism that forages as a flowing mass of pseudopods. We quantified the search pattern of plasmodia after engulfment of food of 6 different qualities. Food quality had a significant, positive effect on how long plasmodia waited before resuming search behavior and on how long it took to abandon food disks. Food quality had a positive effect on fractal dimension, indicating that the amount of localized search performed by plasmodia increased with food quality. Our results suggest that increasing food quality results in a shift from extensive to intensive search. Next, we examined foraging performance in landscapes with different patch structures. Plasmodia in correlated landscapes (half the patches contained only high-quality food, half contained only low-quality food) gained more weight than plasmodia foraging in noncorrelated landscapes (patches contained both high- and low-quality food disks). Our results show that food quality affects exploitation and search behavior and that both behaviors influence foraging performance in different landscapes. Key words: amoeboid, area-restricted search, exploitation, exploration, foraging, myxomycophyta. [Behav Ecol]
Andrew Adamatzky - One of the best experts on this subject based on the ideXlab platform.
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Routing of Physarum polycephalum “signals ” using simple chemicals
2016Co-Authors: Benjamin Paul, Ben Lacy Costello, De Lacy Costello, Andrew AdamatzkyAbstract:In previous work the chemotaxis towards simple organic chemicals was assessed. We utilise the knowledge gained from these chemotactic assays to route Physarum polycephalum signals at a series of junctions. By applying chemical inputs at a simple T-junction we were able to reproducibly control the path taken by the plasmodium of P. polycephalum. Where the chemoattractant farnesene was used at one input a routed signal could be reproducibly generated i.e. P. polycephalum moves towards the source of chemoattractant. Where the chemoattractant was applied at both inputs the signal was reproducibly split i.e. at the junction the plasmodium splits and moves towards both sources of chemoattractant. If a chemorepellent was used then the signal was reproducibly suppressed i.e. P. polycephalum did not reach either output and was confined to the input channel. This was regardless of whether a chemoattractant was used in combination with the chemorepellent showing a hierarchy of inhibition over attraction. If no chemical input was used in the simple circuit then a random signal was generated, whereby P. polycephalum would move towards one output at the junction, but the direction was randomly selected. We extended this study to a more complex series of T-junctions to explore further th
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bio inspired game theory the case of Physarum polycephalum
BICT '14 Proceedings of the 8th International Conference on Bioinspired Information and Communications Technologies, 2014Co-Authors: Andrew Schumann, Krzysztof Pancerz, Andrew Adamatzky, Martin GrubeAbstract:In this paper, first, we show that the true slime mould (plasmodial stage of Physarum polycephalum) is a natural transition system which can be considered a biological model for concurrent games, i.e. it can simulate the game semantics in the form of concurrent games. Second, we extend the notion of concurrent games to context-based games and show that this new form of games is a game semantics that is more suitable for the implementation multi-agent games in the slime mould behavior. The notion of context-based games as strong extension of concurrent games is introduced for the first time. Games on the medium of one-cell organism are defined for the first time, too. In context-based games, we appeal to the following game-theoretic assumptions: (i) each game can be assumed infinite, because its rules can change; (ii) players can change their strategies and the set of actions is infinite for each player; (iii) resistance points for players are reduced to the payoffs if all actions are well-founded; (iv) for any game there is performative efficiency, when hybrid actions of players belong to the interval of expected modifications. Logic circuits on the medium of slime mould can be designed in the form of context-based games.
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sensory fusion in Physarum polycephalum and implementing multi sensory functional computation
arXiv: Emerging Technologies, 2014Co-Authors: James G. H. Whiting, Ben Lacy Costello, Andrew AdamatzkyAbstract:Surface electrical potential and observational growth recordings were made of a protoplasmic tube of the slime mould Physarum polycephalum in response to a multitude of stimuli with regards to sensory fusion or multisensory integration. Each stimulus was tested alone and in combination in order to evaluate for the first time the effect that multiple stimuli have on the frequency of streaming oscillation. White light caused a decrease in frequency whilst increasing the temperature and applying a food source in the form of oat flakes both increased the frequency. Simultaneously stimulating P. polycephalum with light and oat flake produced no net change in frequency, while combined light and heat stimuli showed an increase in frequency smaller than that observed for heat alone. When the two positive stimuli, oat flakes and heat, were combined, there was a net increase in frequency similar to the cumulative increases caused by the individual stimuli. Boolean logic gates were derived from the measured frequency change.
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towards slime mould colour sensor recognition of colours by Physarum polycephalum
Organic Electronics, 2013Co-Authors: Andrew AdamatzkyAbstract:Abstract Acellular slime mould Physarum polycephalum is a popular now user-friendly living substrate for designing of future and emergent sensing and computing devices. P. polycephalum exhibits regular patterns of oscillations of its surface electrical potential. The oscillation patterns are changed when the slime mould is subjected to mechanical, chemical, electrical or optical stimuli. We evaluate feasibility of slime-mould based colour sensors by illuminating Physarum with red, green, blue and white colours and analysing patterns of the slime mould’s electrical potential oscillations. We define that the slime mould recognises a colour if it reacts to illumination with the colour by a unique changes in amplitude and periods of oscillatory activity. In laboratory experiments we found that the slime mould recognises red and blue colour. The slime mould does not differentiate between green and white colours. The slime mould also recognises when red colour is switched off. We also map colours to diversity of the oscillations: illumination with a white colour increases diversity of amplitudes and periods of oscillations, other colours studied increase diversity either of amplitude or period.
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on the internalisation intraplasmodial carriage and excretion of metallic nanoparticles in the slime mould Physarum polycephalum
arXiv: Emerging Technologies, 2013Co-Authors: Richard Mayne, Ben Lacy Costello, Andrew Adamatzky, David Patton, Rosemary Camilla PattonAbstract:The plasmodium of Physarum polycephalum is a large single cell visible with the naked eye. When inoculated on a substrate with attractants and repellents the plasmodium develops optimal networks of protoplasmic tubes which span sites of attractants (i.e. nutrients) yet avoid domains with a high nutrient concentration. It should therefore be possible to program the plasmodium towards deterministic adaptive transformation of internalised nano- and micro-scale materials. In laboratory experiments with magnetite nanoparticles and glass micro-spheres coated with silver metal we demonstrate that the plasmodium of P. polycephalum can propagate the nano-scale objects using a number of distinct mechanisms including endocytosis, transcytosis and dragging. The results of our experiments could be used in the development of novel techniques targeted towards the growth of metallised biological wires and hybrid nano- and micro-circuits.
Madeleine Beekman - One of the best experts on this subject based on the ideXlab platform.
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speed accuracy trade offs during foraging decisions in the acellular slime mould Physarum polycephalum
Proceedings of The Royal Society B: Biological Sciences, 2011Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:Speed–accuracy trade-offs (SATs) are thought to be a fundamental feature of biological information processing, yet most evidence of SATs comes from animals. Here, we examine SATs in the foraging decisions of an acellular, amoeboid organism: the slime mould Physarum polycephalum . Slime moulds were given a simple discrimination task: selecting the highest-quality food item from a set of three options. We investigated the effect of two stressors, light exposure and hunger, on the speed and accuracy of decision-making. We also examined the effect of task difficulty. When given a difficult discrimination task, stressed individuals tend to make faster decisions than non-stressed individuals. This effect was reversed in plasmodia given easy discrimination tasks, where stressed individuals made slower decisions than non-stressed individuals. We found evidence of SATs, such that individuals who made fast decisions were more likely to make costly errors by selecting the worst possible food option. Our results suggest that SATs occur in a wider range of taxa than previously considered.
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food quality affects search strategy in the acellular slime mould Physarum polycephalum
Behavioral Ecology, 2009Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:When searching for resources, organisms can increase the efficiency of search and exploitation behavior by using information about the quality of a current resource patch in their decision making. The search strategy used by an organism can in turn affect its performance in different landscapes. Here we examine the effect of resource quality on 2 foraging decisions: how much time to allocate to explore the environment for new resources and what search strategy to use during exploration. We used the slime mould Physarum polycephalum as our model system. Physarum polycephalum is an amoeboid organism that forages as a flowing mass of pseudopods. We quantified the search pattern of plasmodia after engulfment of food of 6 different qualities. Food quality had a significant, positive effect on how long plasmodia waited before resuming search behavior and on how long it took to abandon food disks. Food quality had a positive effect on fractal dimension, indicating that the amount of localized search performed by plasmodia increased with food quality. Our results suggest that increasing food quality results in a shift from extensive to intensive search. Next, we examined foraging performance in landscapes with different patch structures. Plasmodia in correlated landscapes (half the patches contained only high-quality food, half contained only low-quality food) gained more weight than plasmodia foraging in noncorrelated landscapes (patches contained both high- and low-quality food disks). Our results show that food quality affects exploitation and search behavior and that both behaviors influence foraging performance in different landscapes. Copyright 2009, Oxford University Press.
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food quality affects search strategy in the acellular slime mould Physarum polycephalum
Behavioral Ecology, 2009Co-Authors: Tanya Latty, Madeleine BeekmanAbstract:When searching for resources, organisms can increase the efficiency of search and exploitation behavior by using information about the quality of a current resource patch in their decision making. The search strategy used by an organism can in turn affect its performance in different landscapes. Here we examine the effect of resource quality on 2 foraging decisions: how much time to allocate to explore the environment for new resources and what search strategy to use during exploration. We used the slime mould Physarum polycephalum as our model system. Physarum polycephalum is an amoeboid organism that forages as a flowing mass of pseudopods. We quantified the search pattern of plasmodia after engulfment of food of 6 different qualities. Food quality had a significant, positive effect on how long plasmodia waited before resuming search behavior and on how long it took to abandon food disks. Food quality had a positive effect on fractal dimension, indicating that the amount of localized search performed by plasmodia increased with food quality. Our results suggest that increasing food quality results in a shift from extensive to intensive search. Next, we examined foraging performance in landscapes with different patch structures. Plasmodia in correlated landscapes (half the patches contained only high-quality food, half contained only low-quality food) gained more weight than plasmodia foraging in noncorrelated landscapes (patches contained both high- and low-quality food disks). Our results show that food quality affects exploitation and search behavior and that both behaviors influence foraging performance in different landscapes. Key words: amoeboid, area-restricted search, exploitation, exploration, foraging, myxomycophyta. [Behav Ecol]
Marcus J B Hauser - One of the best experts on this subject based on the ideXlab platform.
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oscillations and uniaxial mechanochemical waves in a model of an active poroelastic medium application to deformation patterns in protoplasmic droplets of Physarum polycephalum
Physica D: Nonlinear Phenomena, 2016Co-Authors: Sergio Alonso, Ulrike Strachauer, Markus Radszuweit, Markus Bar, Marcus J B HauserAbstract:Self-organization in cells often manifests itself in oscillations and waves. Here, we address deformation waves in protoplasmic droplets of the plasmodial slime mould Physarum polycephalum by modelling and experiments. In particular, we extend a one-dimensional model that considered the cell as a poroelastic medium, where active tension caused mechanochemical waves that were regulated by an inhibitor (Radszuweit et al., 2013). Our extension consists of a simple, qualitative chemical reaction–diffusion model (Brusselator) that describes the regulation of the inhibitor by another biochemical species. The biochemical reaction enhances the formation of mechanochemical waves if the reaction rates and input concentrations are near or inside an oscillatory regime. The period of the waves is found to be controlled by the characteristic oscillation period, whereas their wavelength is set by mechanical parameters. The model also allows for a systematic study of the chemical activity at the onset of mechanochemical waves. We also present examples for pattern formation in protoplasmic droplets of Physarum polycephalum including global oscillations where the central region of the droplets is in antiphase to the boundary zone, as well as travelling and standing wave-like uniaxial patterns. Finally, we apply our model to reproduce these experimental results by identifying the active tension inhibitor with the intracellular calcium concentration in the Physarum droplets and by using parameter values from mechanical experiments, respectively knowledge about the properties of calcium oscillations in Physarum. The simulation results are then found to be in good agreement with the experimental observations.
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functional organization of the vascular network of Physarum polycephalum
Physical Biology, 2013Co-Authors: Werner Baumgarten, Marcus J B HauserAbstract:The plasmodium of the slime mould Physarum polycephalum forms a transportation network of veins, in which protoplasm is transported due to peristaltic pumping. This network forms a planar, weighted, undirected graph that, for the first time, can be extracted automatically from photographs or movies. Thus, data from real transportation networks have now become available for the investigation of network properties. We determine the local drag of the vein segments and use these data to calculate the transport efficiency. We unravel which veins form the backbone of the transportation network by using a centrality measure from graph theory. The principal vein segments lie on relatively ample cycles of veins, and the most important segments are those that belong simultaneously to two of these principal cycles. Each principal cycle contains a series of smaller cycles of veins of lower transport efficiency, thus reflecting the hierarchical and self-similar structure of the transportation network. Finally, we calculate accessibility maps that show how easily different nodes of the network may be reached from a given reference node.
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plasmodial vein networks of the slime mold Physarum polycephalum form regular graphs
Physical Review E, 2010Co-Authors: Werner Baumgarten, Tetsuo Ueda, Marcus J B HauserAbstract:The morphology of a typical developing biological transportation network, the vein network of the plasmodium of the myxomycete Physarum polycephalum is analyzed during its free extension. The network forms a classical, regular graph, and has exclusively nodes of degree 3. This contrasts to most real-world transportation networks which show small-world or scale-free properties. The complexity of the vein network arises from the weighting of the lengths, widths, and areas of the vein segments. The lengths and areas follow exponential distributions, while the widths are distributed log-normally. These functional dependencies are robust during the entire evolution of the network, even though the exponents change with time due to the coarsening of the vein network.
Wolfgang Marwan - One of the best experts on this subject based on the ideXlab platform.
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Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks.
Scientific Reports, 2017Co-Authors: Gernot Glöckner, Wolfgang MarwanAbstract:Activation of a phytochrome photoreceptor triggers a program of Physarum polycephalum plasmodial cell differentiation through which a mitotic multinucleate protoplasmic mass synchronously develops into haploid spores formed by meiosis and rearrangement of cellular components. We have performed a transcriptome-wide RNAseq study of cellular reprogramming and developmental switching. RNAseq analysis revealed extensive remodeling of intracellular signaling and regulation in switching the expression of sets of genes encoding transcription factors, kinases, phosphatases, signal transduction proteins, RNA-binding proteins, ubiquitin ligases, regulators of the mitotic and meiotic cell cycle etc. in conjunction with the regulation of genes encoding metabolic enzymes and cytoskeletal proteins. About 15% of the differentially expressed genes shared similarity with members of the evolutionary conserved set of core developmental genes of social amoebae. Differential expression of genes encoding regulators that act at the transcriptional, translational, and post-translational level indicates the establishment of a new state of cellular function and reveals evolutionary deeply conserved molecular changes involved in cellular reprogramming and differentiation in a prototypical eukaryote.
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functional mapping of the branched signal transduction pathway that controls sporulation in Physarum polycephalum
Photochemistry and Photobiology, 2008Co-Authors: Christine Starostzik, Wolfgang MarwanAbstract:Abstract— Sporulation of starving plasmodia of Physarum polycephalum was found to be induced by far-red light, blue light or heat shock, each of which is perceived by a different input receptor system. The branched signal transduction pathway was mapped and the time-dependent formation of some of its components analyzed.
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reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical petri net modelling and simulation
Journal of Theoretical Biology, 2005Co-Authors: Wolfgang Marwan, Arumugam Sujatha, Christine StarostzikAbstract:Abstract We reconstruct the regulatory network controlling commitment and sporulation of Physarum polycephalum from experimental results using a hierarchical Petri Net-based modelling and simulation framework. The stochastic Petri Net consistently describes the structure and simulates the dynamics of the molecular network as analysed by genetic, biochemical and physiological experiments within a single coherent model. The Petri Net then is extended to simulate time-resolved somatic complementation experiments performed by mixing the cytoplasms of mutants altered in the sporulation response, to systematically explore the network structure and to probe its dynamics. This reverse engineering approach presumably can be employed to explore other molecular or genetic signalling systems where the activity of genes or their products can be experimentally controled in a time-resolved manner.
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a photoreceptor with characteristics of phytochrome triggers sporulation in the true slime mould Physarum polycephalum
FEBS Letters, 1995Co-Authors: Christine Starostzik, Wolfgang MarwanAbstract:Phytochrome is a ubiquitous photoreceptor in plants that controls a variety of responses to light, including gene expression, differential cell growth and intracellular movement of organelles. All phytochromes analysed so far are reversibly interconverted by light between an inactive and an active conformation, each of which has a different and characteristic absorbance spectrum. Based on photophysiological measurements we provide evidence, that a photoreceptor with these unique properties of phytochrome triggers sporulation in the true slime mould Physarum polycephalum.