Amoeboid organism solves complex nutritional challenges

Novel image-analytic approach reveals new insights in fine-tuning of slime mould network adaptation

This study introduces a novel methodology to explore the network dynamics of Physarum polycephalum, an organism celebrated for its remarkable adaptive capabilities. We used two innovative techniques to analyse its growth behaviour and network modifications under stress conditions, including starvation and differential epinephrine exposures. The first method provided a quantitative assessment of growth and exploration over time. The second method provided a detailed examination of vein diameter and contraction patterns, illuminating the physiological adjustments P. polycephalum undergoes in response to environmental challenges. By integrating these approaches, we were able to estimate the total network volume of the organism, with a focus on the normalized estimated volume, unveiling insightful aspects of its structural adaptations. While starvation reduced the volume, indicating a significant structural compromise, low and high epinephrine concentrations maintained a volume-to-area ratio comparable with the control. Determining the fractal dimension of the networks over time revealed a fine-tuning of the network complexity in response to environmental conditions, with significant reductions under stress indicating a constrained network adaptation strategy. These methods, novel in their application to P. polycephalum, provide a framework for future studies and a basis for exploring complex network behaviours with potential applications in bioengineering and adaptive network design.

Emergence of synchronized growth oscillations in filamentous fungi

Many species of soil fungi grow in the form of branched networks that enable long-range communication and mass flow of nutrient. These networks play important roles in the soil ecosystem as a major decomposer of organic materials. While there have been investigations on the branching of the fungal networks, their long-term growth dynamics in space and time is still not very well understood. In this study, we monitor the spatio-temporal growth dynamics of the plant-promoting filamentous fungus Serendipita indica for several days in a controlled environment within a microfluidic chamber. We find that S. indica cells display synchronized growth oscillations with the onset of sporulation and at a period of 3 h. Quantifying this experimental synchronization of oscillatory dynamics, we show that the synchronization can be recapitulated by the nearest neighbour Kuramoto model with a millimetre-scale cell-cell coupling. The microfluidic set-up presented in this work may aid the future characterization of the molecular mechanisms of the cell-cell communication, which could lead to biophysical approaches for controlling fungi growth and reproductive sporulation in soil and plant health management.

Increased intake of tree forage by moose is associated with intake of crops rich in nonstructural carbohydrates

Animals representing a wide range of taxonomic groups are known to select specific food combinations to achieve a nutritionally balanced diet. The nutrient balancing hypothesis suggests that, when given the opportunity, animals select foods to achieve a particular target nutrient balance, and that balancing occurs between meals and between days. For wild ruminants who inhabit landscapes dominated by human land use, nutritionally imbalanced diets can result from ingesting agricultural crops rich in starch and sugar (nonstructural carbohydrates [NCs]), which can be provided to them by people as supplementary feeds. Here, we test the nutrient balancing hypothesis by assessing potential effects that the ingestion of such crops by Alces alces (moose) may have on forage intake. We predicted that moose compensate for an imbalanced intake of excess NC by selecting tree forage with macro-nutritional content better suited for their rumen microbiome during wintertime. We applied DNA metabarcoding to identify plants in fecal and rumen content from the same moose during winter in Sweden. We found that the concentration of NC-rich crops in feces predicted the presence of Picea abies (Norway spruce) in rumen samples. The finding is consistent with the prediction that moose use tree forage as a nutritionally complementary resource to balance their intake of NC-rich foods, and that they ingested P. abies in particular (normally a forage rarely eaten by moose) because it was the most readily available tree. Our finding sheds new light on the foraging behavior of a model species in herbivore ecology, and on how habitat alterations by humans may change the behavior of wildlife.

Size-dependent self-avoidance enables superdiffusive migration in macroscopic unicellulars

Many cells face search problems, such as finding food, mates, or shelter, where their success depends on their search strategy. In contrast to other unicellular organisms, the slime mold Physarum polycephalum forms a giant network-shaped plasmodium while foraging for food. What is the advantage of the giant cell on the verge of multicellularity? We experimentally study and quantify the migration behavior of P. polycephalum plasmodia on the time scale of days in the absence and presence of food. We develop a model which successfully describes its migration in terms of ten data-derived parameters. Using the mechanistic insights provided by our data-driven model, we find that regardless of the absence or presence of food, P. polycephalum achieves superdiffusive migration by performing a self-avoiding run-and-tumble movement. In the presence of food, the run duration statistics change, only controlling the short-term migration dynamics. However, varying organism size, we find that the long-term superdiffusion arises from self-avoidance determined by cell size, highlighting the potential evolutionary advantage that this macroscopically large cell may have.

The paradox of plant preference: The malaria vectors Anopheles gambiae and Anopheles coluzzii select suboptimal food sources for their survival and reproduction

Anopheles gambiae and Anopheles coluzzii mosquitoes, two major malaria vectors in sub-Saharan Africa, exhibit selectivity among plant species as potential food sources. However, it remains unclear if their preference aligns with optimal nutrient intake and survival. Following an extensive screening of the effects of 31 plant species on An. coluzzii in Burkina Faso, we selected three species for their contrasting effects on mosquito survival, namely Ixora coccinea, Caesalpinia pulcherrima, and Combretum indicum. We assessed the sugar content of these plants and their impact on mosquito fructose positivity, survival, and insemination rate, using Anopheles coluzzii and Anopheles gambiae, with glucose 5% and water as controls. Plants displayed varying sugar content and differentially affected the survival, sugar intake, and insemination rate of mosquitoes. All three plants were more attractive to mosquitoes than controls, with An. gambiae being more responsive than An. coluzzii. Notably, C. indicum was the most attractive but had the lowest sugar content and offered the lowest survival, insemination rate, and fructose positivity. Our findings unveil a performance-preference mismatch in An. coluzzii and An. gambiae regarding plant food sources. Several possible reasons for this negative correlation between performance and preference are discussed.

Fungal infection alters collective nutritional intake of ant colonies

In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term-a form of collective self-medication.

The improved resistance of germinated spores to ultraviolet irradiation: Comparison with chlorine

Fungi outbreaks in water will include a series of processes, including spore aggregation, germination, biofilm, and finally present in a mixed state in the aquatic environment. More attention is paid to the control of dispersed fungal spores, however, there was little knowledge of the control of germinated spores. This study investigated the inactivation kinetics and mechanism of ultraviolet (UV) treatment for fungal spores with different germination percentages compared with dormant spores. The results indicated that the inactivation rate constants (k) of spores with 5%-45% germination were 0.0278-0.0299 cm2/mJ for Aspergillus niger and 0.0588-0.0647 cm2/mJ for Penicillium polonicum, which were lower than those of dormant spores. It suggested that germinated spores were more tolerant to UV irradiation than dormant spores, and it may be due to the defensive barrier (upregulated pigments) and some reductive substance (upregulated enoyl reductase) by absorbing UV or reacting with reactive oxygen species according to transcriptome analysis. Compared to dormant spores, the k-UV of germinated spores decreased by 18.17%-26.56% for Aspergillus niger, which was less than k-chlorine (62.33%-69.74%). A slighter decrease in k-UV showed UV irradiation can efficiently control fungi contamination, especially when dormant spores and germinated spores coexisted in actual water systems. This study indicates that more attention should be paid to germinated spores.

Principles of cognitive biology and the concept of biocivilisations

A range of studies published in the last few decades promotes the cognitive aspects of life: all organisms, from bacteria to mammals, are capable of sensing/perception, decision-making, problem-solving, learning, and other cognitive functions, including sentience and consciousness. In this paper I present a scientific and philosophical synthesis of these studies, leading to an integrated view of cognitive biology. This view is expressed through the four principles applicable to all living systems: (1) sentience and consciousness, (2) autopoiesis, (3) free energy principle and relational biology, and (4) cognitive repertoire. The principles are circular, and they reinforce themselves. The circularity is not rigid, meaning that hierarchical and heterarchical shifts are widespread in the biosphere. The above principles emerged at the dawn of life, with the first cells, bacteria and archaea. All biogenic forms and functions that emerged since then can be traced to the first cells - indivisible units of biological agency. Following these principles, I developed the concept of biocivilisations to explain various forms of social intelligence in different kingdoms of life. The term biociviloisations draws on the human interpretation of the concept of civilisation, which searches for non-human equivalents of communication, engineering, science, medicine, art, and agriculture, in all kingdoms of life by applying the principles of cognitive biology. Potential avenues for testing the concept of biocivilisations are highlighted.

Perspectives on Principles of Cellular Behavior from the Biophysics of Protists

Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles.

Toward reconciling the roles of FGF21 in protein appetite, sweet preference, and energy expenditure

Fibroblast growth factor 21 (FGF21), an endocrine signal robustly increased by protein restriction independently of an animal's energy status, exerts profound effects on feeding behavior and metabolism. Here, we demonstrate that considering the nutritional contexts within which FGF21 is elevated can help reconcile current controversies over its roles in mediating macronutrient preference, food intake, and energy expenditure. We show that FGF21 is primarily a driver of increased protein intake in mice and that the effect of FGF21 on sweet preference depends on the carbohydrate balance of the animal. Under no-choice feeding, FGF21 infusion either increased or decreased energy expenditure depending on whether the animal was fed a high- or low-energy diet, respectively. We show that while the role of FGF21 in mediating feeding behavior is complex, its role in promoting protein appetite is robust and that the effects on sweet preference and energy expenditure are macronutrient-state-dependent effects of FGF21.

Thoughts from the forest floor: a review of cognition in the slime mould Physarum polycephalum

Sensing, communication, navigation, decision-making, memory and learning are key components in a standard cognitive tool-kit that enhance an animal's ability to successfully survive and reproduce. However, these tools are not only useful for, or accessible to, animals-they evolved long ago in simpler organisms using mechanisms which may be either unique or widely conserved across diverse taxa. In this article, I review the recent research that demonstrates these key cognitive abilities in the plasmodial slime mould Physarum polycephalum, which has emerged as a model for non-animal cognition. I discuss the benefits and limitations of comparisons drawn between neural and non-neural systems, and the implications of common mechanisms across wide taxonomic divisions. I conclude by discussing future avenues of research that will draw the most benefit from a closer integration of Physarum and animal cognition research.

Protein appetite as an integrator in the obesity system: the protein leverage hypothesis

Despite the large volume and extensive range of obesity research, there is substantial disagreement on the causes and effective preventative strategies. We suggest the field will benefit from greater emphasis on integrative approaches that examine how various potential contributors interact, rather than regarding them as competing explanations. We demonstrate the application of nutritional geometry, a multi-nutrient integrative framework developed in the ecological sciences, to obesity research. Such studies have shown that humans, like many other species, regulate protein intake more strongly than other dietary components, and consequently if dietary protein is diluted there is a compensatory increase in food intake-a process called protein leverage. The protein leverage hypothesis (PLH) proposes that the dilution of protein in modern food supplies by fat and carbohydrate-rich highly processed foods has resulted in increased energy intake through protein leverage. We present evidence for the PLH from a variety of sources (mechanistic, experimental and observational), and show that this mechanism is compatible with many other findings and theories in obesity research. This article is part of a discussion meeting issue 'Causes of obesity: theories, conjectures and evidence (Part II)'.

Assessment of the diet of the critically endangered northern hairy-nosed wombat (Lasiorhinus krefftii) using DNA metabarcoding

Invasive buffel grass (Cenchrus ciliaris) is considered a threat to the critically endangered northern hairy-nosed wombat (Lasiorhinus krefftii; NHW). Buffel grass outcompetes native grasses, reducing availability of native food items for NHW, and causes more intense fires due to the large volumes of dead matter it produces. Previous studies suggested buffel grass was increasing in the diet; however, the diet of the NHW has not been reassessed for over two decades and was limited to Epping Forest National Park, with the population at Richard Underwood Nature Refuge having never been assessed. The recently released 2022 Recovery Action Plan for the species outlined objectives to assist its conservation and recommended the impact of buffel grass on the species' diet be investigated. This study aimed to determine: (1) which plant species are being consumed by the NHW; (2) the differences in the diet between sites; (3) differences between seasons; and (4) the abundance of buffel grass in the diet. The diet was assessed using DNA metabarcoding of scat samples collected from both sites from winter 2020 to spring 2021. Site and season significantly affected the diet of the NHW. Buffel grass dominated the diet and has increased in the diet since past assessments. The findings of this study will support population and habitat management of the critically endangered NHW. Enhanced knowledge of dietary items consumed at both sites will also assist efforts to locate additional sites suitable for translocation.

Diet and mitonuclear haplotype interactions affect growth rate in a slime mould

Trait expression in metazoans is strongly influenced by the balance of macronutrients (i.e. protein, carbohydrate and fat) in the diet. At the same time, an individual's genetic background seems to regulate the magnitude of phenotypic response to a particular diet. It needs to be better understood whether interactions between diet, genetic background and trait expression are found in unicellular eukaryotes. A protist-the slime mould, Physarum polycephalum can choose diets based on protein-to-carbohydrate (P:C) content to support optimal growth rate. Yet, the role of genetic background (variation in the mitochondrial and nuclear DNAs) in mediating growth rate response to dietary P:C ratios in the slime mould is unknown. Here, we studied the effects of interactions between mitochondrial and nuclear DNA haplotypes and diet (i.e. G × G × E interactions) on the growth rate of P. polycephalum. A genetic panel of six distinct strains of P. polycephalum that differ in their mitochondrial and nuclear DNA haplotypes was used to measure growth rate across five diets that varied in their P:C ratio and total calories. We first determined the strains' growth rate (total biomass and surface area) when grown on a set menu with access to a particular diet. We then assessed whether the growth rate of strains increased on a buffet menu with access to all diets. Our findings show that the growth rate of P. polycephalum is generally higher on diets containing more carbohydrates than protein and that total calories negatively affect the growth rate. Three-way interactions between mitochondrial, nuclear haplotypes and dietary P:C ratios affected the strains' surface area of growth but not biomass. Intriguingly, strains did not increase their surface area and biomass when they had access to all diets on the buffet menu. Our findings have broad implications for our understanding of the effect of mitonuclear interactions on trait expression across diverse eukaryotic lineages.

Network topology enables efficient response to environment inPhysarum polycephalum

The network-shaped body plan distinguishes the unicellular slime mouldPhysarum polycephalumin body architecture from other unicellular organisms. Yet, network-shaped body plans dominate branches of multi-cellular life such as in fungi. What survival advantage does a network structure provide when facing a dynamic environment with adverse conditions? Here, we probe how network topology impactsP. polycephalum's avoidance response to an adverse blue light. We stimulate either an elongated, I-shaped amoeboid or a Y-shaped networked specimen and subsequently quantify the evacuation process of the light-exposed body part. The result shows that Y-shaped specimen complete the avoidance retraction in a comparable time frame, even slightly faster than I-shaped organisms, yet, at a lower almost negligible increase in migration velocity. Contraction amplitude driving mass motion is further only locally increased in Y-shaped specimen compared to I-shaped-providing further evidence that Y-shaped's avoidance reaction is energetically more efficient than in I-shaped amoeboid organisms. The difference in the retraction behaviour suggests that the complexity of network topology provides a key advantage when encountering adverse environments. Our findings could lead to a better understanding of the transition from unicellular to multicellularity.

Behavioural changes in slime moulds over time

Changes in behaviour over the lifetime of single-cell organisms have primarily been investigated in response to environmental stressors. However, growing evidence suggests that unicellular organisms undergo behavioural changes throughout their lifetime independently of the external environment. Here we studied how behavioural performances across different tasks vary with age in the acellular slime mould Physarum polycephalum. We tested slime moulds aged from 1 week to 100 weeks. First, we showed that migration speed decreases with age in favourable and adverse environments. Second, we showed that decision making and learning abilities do not deteriorate with age. Third, we revealed that old slime moulds can recover temporarily their behavioural performances if they go throughout a dormant stage or if they fuse with a young congener. Last, we observed the response of slime mould facing a choice between cues released by clone mates of different age. We found that both old and young slime moulds are attracted preferentially toward cues left by young slime moulds. Although many studies have studied behaviour in unicellular organisms, few have taken the step of looking for changes in behaviour over the lifetime of individuals. This study extends our knowledge of the behavioural plasticity of single-celled organisms and establishes slime moulds as a promising model to investigate the effect of ageing on behaviour at the cellular level. This article is part of a discussion meeting issue 'Collective behaviour through time'.

G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum

In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.

From representations to servomechanisms to oscillators: my journey in the study of cognition

The study of comparative cognition bloomed in the 1970s and 1980s with a focus on representations in the heads of animals that undergird what animals can achieve. Even in action-packed domains such as navigation and spatial cognition, a focus on representations prevailed. In the 1990s, I suggested a conception of navigation in terms of navigational servomechanisms. A servomechanism can be said to aim for a goal, with deviations from the goal-directed path registering as an error. The error drives action to reduce the error in a negative-feedback loop. This loop, with the action reducing the very signal that drove action in the first place, is key to defining a servomechanism. Even though actions are crucial components of servomechanisms, my focus was on the representational component that encodes signals and evaluates errors. Recently, I modified and amplified this view in claiming that, in navigation, servomechanisms operate by modulating the performance of oscillators, endogenous units that produce periodic action. The pattern is found from bacteria travelling micrometres to sea turtles travelling thousands of kilometres. This pattern of servomechanisms working with oscillators is found in other realms of cognition and of life. I think that oscillators provide an effective way to organise an organism's own activities while servomechanisms provide an effective means to adjust to the organism's environment, including that of its own body.

A survey on physarum polycephalum intelligent foraging behaviour and bio-inspired applications

In recent years, research on Physarum polycephalum has become more popular after Nakagaki (AIR 407: 6803-470, 2000) performed their famous experiment showing that Physarum was able to find the shortest route through a maze. Subsequent researches have confirmed the ability of Physarum-inspired algorithms to solve a wide range of real-world applications. In contrast to previous reviews that either focus on biological aspects or bio-inspired applications, here we present a comprehensive review that highlights recent Physarum polycephalum biological aspects, mathematical models, and Physarum bio-inspired algorithms and their applications. The novelty of this review stems from our exploration of Physarum intelligent behaviour in competition settings. Further, we have presented our new model to simulate Physarum in competition, where multiple Physarum interact with each other and with their environments. The bio-inspired Physarum in competition algorithms proved to have great potentials for future research.

An integrative approach to dietary balance across the life course

Animals require specific blends of nutrients that vary across the life course and with circumstances, e.g., health and activity levels. Underpinning and complicating these requirements is that individual traits may be optimized on different dietary compositions leading to nutrition-mediated trade-offs among outcomes. Additionally, the food environment may constrain which nutrient mixtures are achievable. Natural selection has equipped animals for solving such multi-dimensional, dynamic challenges of nutrition, but little is understood about the details and their theoretical and practical implications. We present an integrative framework, nutritional geometry, which models complex nutritional interactions in the context of multiple nutrients and across levels of biological organization (e.g., cellular, individual, and population) and levels of analysis (e.g., mechanistic, developmental, ecological, and evolutionary). The framework is generalizable across different situations and taxa. We illustrate this using examples spanning insects to primates and settings (laboratory, and the wild), and demonstrate its relevance for human health.

Representing Stimulus Information in an Energy Metabolism Pathway

We explored a computational model of astrocytic energy metabolism and demonstrated the theoretical plausibility that this type of pathway might be capable of coding information about stimuli in addition to its known functions in cellular energy and carbon budgets. Simulation results indicate that glycogenolytic glycolysis triggered by activation of adrenergic receptors can capture the intensity and duration features of a neuromodulator waveform and can respond in a dose-dependent manner, including non-linear state changes that are analogous to action potentials. We show how this metabolic pathway can translate information about external stimuli to production profiles of energy-carrying molecules such as lactate with a precision beyond simple signal transduction or non-linear amplification. The results suggest the operation of a metabolic state-machine from the spatially discontiguous yet interdependent metabolite elements. Such metabolic pathways might be well-positioned to code an additional level of salient information about a cell's environmental demands to impact its function. Our hypothesis has implications for the computational power and energy efficiency of the brain.

Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium

In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleate syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters and if nuclei within the cell diversify into heterogeneous states. Here, we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleus cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

Stepwise slime mould growth as a template for urban design

The true slime mould, Physarum polycephalum, develops as a vascular network of protoplasm, connecting node-like sources of food in an effort to solve multi-objective transport problems. The organism first establishes a dense and continuous mesh, reinforcing optimal pathways over time through constructive feedbacks of protoplasmic streaming. Resolved vascular morphologies are the result of an evolutionarily-refined mechanism of computation, which can serve as a versatile biological model for network design at the urban scale. Existing digital Physarum models typically use positive reinforcement mechanisms to capture meshing and refinement behaviours simultaneously. While these automations generate accurate descriptions of sensory and constructive feedback, they limit stepwise design control, reducing flexibility and applicability. A model that decouples the two “phases” of Physarum behaviour would enable multistage control over network growth. Here we introduce such a system, first by producing a site-responsive mesh from a population of nutrient-attracted agents, and then by independently calculating from it a flexible, proximity-defined shortest-walk to produce a final network. We develop and map networks within existing urban environments that perform similarly to those biologically grown, establishing a versatile tool for bio-inspired urban network design.

Emergence of behaviour in a self-organized living matter network

What is the origin of behaviour? Although typically associated with a nervous system, simple organisms also show complex behaviours. Among them, the slime mold Physarum polycephalum, a giant single cell, is ideally suited to study emergence of behaviour. Here, we show how locomotion and morphological adaptation behaviour emerge from self-organized patterns of rhythmic contractions of the actomyosin lining of the tubes making up the network-shaped organism. We quantify the spatio-temporal contraction dynamics by decomposing experimentally recorded contraction patterns into spatial contraction modes. Notably, we find a continuous spectrum of modes, as opposed to a few dominant modes. Our data suggests that the continuous spectrum of modes allows for dynamic transitions between a plethora of specific behaviours with transitions marked by highly irregular contraction states. By mapping specific behaviours to states of active contractions, we provide the basis to understand behaviour’s complexity as a function of biomechanical dynamics.

Correspondence insights into the role of genes in cell functionality. Comments on "The gene: An appraisal" by K. Baverstock

One of the most important goals of the post-genomic era is to understand the different sources of molecular information that regulate the functional and structural architecture of cells. In this regard, Prof. K. Baverstock underscores in his recent article "The gene: An appraisal" (Baverstock, 2021) that genes are not the leading elements in cellular functionality, inheritance and evolution. As a consequence, the theory of evolution based on the Neo-Darwinian synthesis, is inadequate for today's scientific evidence. Conversely, the author contends that life processes viewed on the basis of thermodynamics, complex system dynamics and self-organization provide a new framework for the foundations of Biology. I consider it necessary to comment on some essential aspects of this relevant work, and here I present a short overview of the main non-genetic sources of biomolecular order and complexity that underline the molecular dynamics and functionality of cells. These sources generate different processes of complexity, which encompasses from the most elementary levels of molecular activity to the emergence of systemic behaviors, and the information necessary to sustain them is not contained in the genome.

The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant

Foraging trails of leafcutter colonies are iconic scenes in the Neotropics, with ants collecting freshly cut plant fragments to provision a fungal food crop. We hypothesised that the fungus‐cultivar's requirements for macronutrients and minerals govern the foraging niche breadth of Atta colombica leafcutter ants. Analyses of plant fragments carried by foragers showed how nutrients from fruits, flowers and leaves combine to maximise cultivar performance. While the most commonly foraged leaves delivered excess protein relative to the cultivar's needs, in vitro experiments showed that the minerals P, Al and Fe may expand the leafcutter foraging niche by enhancing the cultivar's tolerance to protein‐biased substrates. A suite of other minerals reduces cultivar performance in ways that may render plant fragments with optimal macronutrient blends unsuitable for provisioning. Our approach highlights how the nutritional challenges of provisioning a mutualist can govern the multidimensional realised niche available to a generalist insect herbivore.

Encoding memory in tube diameter hierarchy of living flow network

The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment-successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient's location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes' capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks' tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks' version of associative memory-very likely of relevance for the plethora of living flow networks as well as for bioinspired design.

Timing of Resource Addition Affects the Migration Behavior of Wood Decomposer Fungal Mycelia

Studies of fungal behavior are essential for a better understanding of fungal-driven ecological processes. Here, we evaluated the effects of timing of resource (bait) addition on the behavior of fungal mycelia when it remains in the inoculum and when it migrates from it towards a bait, using cord-forming basidiomycetes. Experiments allowed mycelium to grow from an inoculum wood across the surface of a soil microcosm, where it encountered a new wood bait 14 or 98 d after the start of growth. After the 42-d colonization of the bait, inoculum and bait were individually moved to a dish containing fresh soil to determine whether the mycelia were able to grow out. When the inoculum and bait of mycelia baited after 14 d were transferred to new soil, there was 100% regrowth from both inoculum and bait in Pholiota brunnescens and Phanerochaete velutina, indicating that no migration occurred. However, when mycelium was baited after 98 d, 3 and 4 out of 10 replicates of P. brunnescens and P. velutina, respectively, regrew only from bait and not from inoculum, indicating migration. These results suggest that prolonged periods without new resources alter the behavior of mycelium, probably due to the exhaustion of resources.

Macronutrient balancing in free-ranging populations of moose

At northern latitudes, large spatial and temporal variation in the nutritional composition of available foods poses challenges to wild herbivores trying to satisfy their nutrient requirements. Studies conducted in mostly captive settings have shown that animals from a variety of taxonomic groups deal with this challenge by adjusting the amounts and proportions of available food combinations to achieve a target nutrient balance. In this study, we used proportions-based nutritional geometry to analyze the nutritional composition of rumen samples collected in winter from 481 moose (Alces alces) in southern Sweden and examine whether free-ranging moose show comparable patterns of nutrient balancing. Our main hypothesis was that wild moose actively regulate their rumen nutrient composition to offset ecologically imposed variation in the nutritional composition of available foods. To test this, we assessed the macronutritional composition (protein, carbohydrates, and lipids) of rumen contents and commonly eaten foods, including supplementary feed, across populations with contrasting winter diets, spanning an area of approximately 10,000 km2. Our results suggest that moose balanced the macronutrient composition of their rumen, with the rumen contents having consistently similar proportional relationship between protein and nonstructural carbohydrates, despite differences in available (and eaten) foods. Furthermore, we found that rumen macronutrient balance was tightly related to ingested levels of dietary fiber (cellulose and hemicellulose), such that the greater the fiber content, the less protein was present in the rumen compared with nonstructural carbohydrates. Our results also suggest that moose benefit from access to a greater variety of trees, shrubs, herbs, and grasses, which provides them with a larger nutritional space to maneuver within. Our findings provide novel theoretical insights into a model species for ungulate nutritional ecology, while also generating data of direct relevance to wildlife and forest management, such as silvicultural or supplementary feeding practices.

Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior

One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.

Feeding and condition shifts after encountering a pathogen

Feeding behaviour is a dynamic process, especially if an individual is dealing with an infection. Here, we used Tenebrio molitor beetles to evaluate the effects of changes in diet macronutrients (protein:carbohydrate) on: (i) feeding behaviour before and after infection (using the entomopathogenic fungus Metarhizium robertsii) in males; and (ii) body condition, measured as the amount of proteins, carbohydrates, and lipids in the body, in males and females. Given that females also depend on the nutrients from the spermatophore, we also addressed the impact on female condition of using spermatophores from males whose diets differed in macronutrients whether they were confronting an infection. We found that males with different diets and regardless of their infection status, and females with different diets, all consumed less of the protein-rich diet but more of the carbohydrate-rich diet. In addition, infection in males produced anorexia. The infection resulted in males and the females they mated with, with fewer body proteins and lipids. This suggests that unlike studies in other insects, T. molitor does not consume large amounts of protein during the adult stage, even during an infection. Females’ condition depended strongly on that of their mates, improving even when paired with infected males. This implies that females may be using the nutrients that the males transfer during mating for maintenance.

Daily protein prioritization and long-term nutrient balancing in a dietary generalist, the blue monkey

Animals make dietary choices to achieve adequate nutrient intake; however, it is challenging to study such nutritional strategies in wild populations. We explored the nutritional strategy of a generalist social primate, the blue monkey (Cercopithecus mitis). We hypothesized that females balance intake of nutrients, specifically non-protein energy and protein, both on a daily and long-term basis. When balancing was not possible, we expected subjects to prioritize constant protein intake, allowing non-protein energy to vary more. To understand the ecology of nutrient balancing, we examined how habitat use, food availability, diet composition, social dominance rank, and reproductive demand influenced nutrient intake. Over 9 months, we conducted 371 all-day focal follows on 24 subjects in Kakamega Forest, Kenya. Females exhibited short- and long-term nutritional strategies. Daily, they balanced non-protein energy to protein intake but when balancing was impossible, monkeys prioritized protein intake. Longer term, they balanced non-protein energy:protein intake in a 3.8:1 ratio. The ratio related positively to fruit in the diet and negatively to time in near-natural forest, but we found no evidence that it related to food availability, reproductive demand, or dominance rank. Lower-ranked females had broader daily diets, however, which may reflect behavioral feeding strategies to cope with social constraints. Overall, females prioritized daily protein, allowing less variation in protein intake than other aspects such as non-protein energy:protein ratio and non-protein energy intake. The emerging pattern in primates suggests that diverse dietary strategies evolved to allow adherence to a nutrient balance of non-protein energy:protein despite various social and environmental constraints.

Adaptive behaviour and learning in slime moulds: the role of oscillations

The slime mould Physarum polycephalum, an aneural organism, uses information from previous experiences to adjust its behaviour, but the mechanisms by which this is accomplished remain unknown. This article examines the possible role of oscillations in learning and memory in slime moulds. Slime moulds share surprising similarities with the network of synaptic connections in animal brains. First, their topology derives from a network of interconnected, vein-like tubes in which signalling molecules are transported. Second, network motility, which generates slime mould behaviour, is driven by distinct oscillations that organize into spatio-temporal wave patterns. Likewise, neural activity in the brain is organized in a variety of oscillations characterized by different frequencies. Interestingly, the oscillating networks of slime moulds are not precursors of nervous systems but, rather, an alternative architecture. Here, we argue that comparable information-processing operations can be realized on different architectures sharing similar oscillatory properties. After describing learning abilities and oscillatory activities of P. polycephalum, we explore the relation between network oscillations and learning, and evaluate the organism's global architecture with respect to information-processing potential. We hypothesize that, as in the brain, modulation of spontaneous oscillations may sustain learning in slime mould. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.

Learning in single cell organisms

The survival of all species requires appropriate behavioral responses to environmental challenges. Learning is one of the key processes to acquire information about the environment and adapt to changing and uncertain conditions. Learning has long been acknowledged in animals from invertebrates to vertebrates but remains a subject of debate in non-animal systems such a plants and single cell organisms. In this review I will attempt to answer the following question: are single cell organisms capable of learning? I will first briefly discuss the concept of learning and argue that the ability to acquire and store information through learning is pervasive and may be found in single cell organisms. Second, by focusing on habituation, the simplest form of learning, I will review a series of experiments showing that single cell organisms such as slime molds and ciliates display habituation and follow most of the criteria adopted by neuroscientists to define habituation. Then I will discuss disputed evidence suggesting that single cell organisms might also undergo more sophisticated forms of learning such as associative learning. Finally, I will stress out that the challenge for the future is less about whether or not to single cell organisms fulfill the definition of learning established from extensive studies in animal systems and more about acknowledging and understanding the range of behavioral plasticity exhibited by such fascinating organisms.

Substrate and cell fusion influence on slime mold network dynamics

The acellular slime mold Physarum polycephalum provides an excellent model to study network formation, as its network is remodelled constantly in response to mass gain/loss and environmental conditions. How slime molds networks are built and fuse to allow for efficient exploration and adaptation to environmental conditions is still not fully understood. Here, we characterize the network organization of slime molds exploring homogeneous neutral, nutritive and adverse environments. We developed a fully automated image analysis method to extract the network topology and followed the slime molds before and after fusion. Our results show that: (1) slime molds build sparse networks with thin veins in a neutral environment and more compact networks with thicker veins in a nutritive or adverse environment; (2) slime molds construct long, efficient and resilient networks in neutral and adverse environments, whereas in nutritive environments, they build shorter and more centralized networks; and (3) slime molds fuse rapidly and establish multiple connections with their clone-mates in a neutral environment, whereas they display a late fusion with fewer connections in an adverse environment. Our study demonstrates that slime mold networks evolve continuously via pruning and reinforcement, adapting to different environmental conditions.

Nutritional niches reveal fundamental domestication trade-offs in fungus-farming ants

During crop domestication, human farmers traded greater productivity for higher crop vulnerability outside specialized cultivation conditions. We found a similar domestication tradeoff across the major co-evolutionary transitions in farming systems of attine ants. First, the fundamental nutritional niches (FNNs) of cultivars narrowed during ~ 60 million years of naturally selected domestication, and laboratory experiments showed that ant farmers representing subsequent domestication stages strictly regulate protein harvest relative to cultivar FNNs. Second, ants with different farming systems differed in their abilities to harvest the resources that best matched the nutritional needs of their fungal cultivars. This was assessed by quantifying realized nutritional niches (RNNs) from analyses of items collected from the mandibles of laden ant foragers in the field. Third, extensive field collections suggest that among-colony genetic diversity of cultivars in small-scale farms may offer population-wide resilience benefits that species with large-scale farming colonies achieve by more elaborate and demanding cultivation practices of less diverse crops. Our results underscore that naturally selected farming systems have potential to shed light on nutritional tradeoffs that shaped the course of culturally evolved human farming.

Enactive Pragmatism and Ecological Psychology

A widely cited roadblock to bridging ecological psychology and enactivism is that the former identifies with realism and the latter identifies with constructivism, which critics charge is subjectivist. A pragmatic reading, however, suggests non-mental forms of constructivism that simultaneously fit core tenets of enactivism and ecological realism. After advancing a pragmatic version of enactive constructivism that does not obviate realism, I reinforce the position with an empirical illustration: Physarum polycephalum, a communal unicellular organism that leaves slime trails that form chemical barriers that it avoids in foraging explorations. Here, environmental building and sensorimotor engagement are part of the same process with P. polycephalum coordinating around self-created, affordance-bearing geographies, which nonetheless exist independently in ways described by ecological realists. For ecological psychologists, affordances are values, meaning values are external to the perceiver. I argue that agent-enacted values have the same status and thus do not obviate ecological realism or generate subjectivism. The constructivist-realist debate organizes around the emphasis that enactivists and ecological theorists respectively place on the inner constitution of organisms vs. the structure of environments. Building on alimentary themes introduced in the P. polycephalum example and also in Gibson’s work, I go on to consider how environment, brain, visceral systems, and even bacteria within them enter perceptual loops. This highlights almost unfathomable degrees of mutually modulating internal and external synchronization. It also shows instances in which internal conditions alter worldly configurations and invert values, in Gibson’s sense of the term, albeit without implying subjectivism. My aim is to cut across the somatic focus of enactive constructivism and the external environment-oriented emphasis of ecological realism and show that enactivism can enrich ecological accounts of value.

Stress signalling in acellular slime moulds and its detection by conspecifics

Unicellular organisms live in unpredictable environments. Therefore, they need to continuously assess environmental conditions and respond appropriately to survive and thrive. When subjected to rapid changes in their environment or to cellular damages, unicellular organisms such as bacteria exhibit strong physiological reactions called stress responses that can be sensed by conspecifics. The ability to detect and use stress-related cues released by conspecifics to acquire information about the environment constitutes an adaptive survival response by prompting the organism to avoid potential dangers. Here, we investigate stress signalling and its detection by conspecifics in a unicellular organism, Physarum polycephalum. Slime moulds were subjected to either biotic (i.e. nutritional) or abiotic (i.e. chemical and light) stressors or left undisturbed while they were exploring a homogeneous environment. Then, we observed the responses of slime moulds facing a choice between cues released by stressed clone mates and cues released by undisturbed ones. We found that slime moulds actively avoided environments previously explored by stressed clone mates. These results suggest that slime moulds, like bacteria or social amoeba, exhibit physiological responses to biotic and abiotic stresses that can be sensed by conspecifics. Our results establish slime moulds as a promising new model to investigate the use of social information in unicellular organisms. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

Nutritional Dimensions of Invasive Success

Despite mounting calls for predictive ecological approaches rooted in physiological performance currencies, the field of invasive species biology has lagged behind. For instance, successful invaders are often predicted to consume diverse foods, but the nutritional complexity of foods often leaves food-level analyses short of physiological mechanisms. The emerging field of nutritional geometry (NG) provides new theory and empirical tools to predict invasive potential based on fundamental and realized nutritional niches. We review recent advances and synthesize NG predictions about behavioral traits that favor invasive establishment, and evolutionary dynamics that promote invasive spread. We also provide practical advice for applying NG approaches, and discuss the power of nutrition to achieve a more predictive invasion biology that explicitly integrates physiological mechanisms.

Liquid brains, solid brains

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

The brain: a concept in flux

One of the most important aspects of the scientific endeavour is the definition of specific concepts as precisely as possible. However, it is also important not to lose sight of two facts: (i) we divide the study of nature into manageable parts in order to better understand it owing to our limited cognitive capacities and (ii) definitions are inherently arbitrary and heavily influenced by cultural norms, language, the current political climate, and even personal preferences, among many other factors. As a consequence of these facts, clear-cut definitions, despite their evident importance, are oftentimes quite difficult to formulate. One of the most illustrative examples about the difficulty of articulating precise scientific definitions is trying to define the concept of a brain. Even though the current thinking about the brain is beginning to take into account a variety of organisms, a vertebrocentric bias still tends to dominate the scientific discourse about this concept. Here I will briefly explore the evolution of our 'thoughts about the brain', highlighting the difficulty of constructing a universally (or even a generally) accepted formal definition of it and using planarians as one of the earliest examples of organisms proposed to possess a 'traditional', vertebrate-style brain. I also suggest that the time is right to attempt to expand our view of what a brain is, going beyond exclusively structural and taxa-specific criteria. Thus, I propose a classification that could represent a starting point in an effort to expand our current definitions of the brain, hopefully to help initiate conversations leading to changes of perspective on how we think about this concept. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Memory inception and preservation in slime moulds: the quest for a common mechanism

Learning and memory are indisputably key features of animal success. Using information about past experiences is critical for optimal decision-making in a fluctuating environment. Those abilities are usually believed to be limited to organisms with a nervous system, precluding their existence in non-neural organisms. However, recent studies showed that the slime mould Physarum polycephalum, despite being unicellular, displays habituation, a simple form of learning. In this paper, we studied the possible substrate of both short- and long-term habituation in slime moulds. We habituated slime moulds to sodium, a known repellent, using a 6 day training and turned them into a dormant state named sclerotia. Those slime moulds were then revived and tested for habituation. We showed that information acquired during the training was preserved through the dormant stage as slime moulds still showed habituation after a one-month dormancy period. Chemical analyses indicated a continuous uptake of sodium during the process of habituation and showed that sodium was retained throughout the dormant stage. Lastly, we showed that memory inception via constrained absorption of sodium for 2 h elicited habituation. Our results suggest that slime moulds absorbed the repellent and used it as a 'circulating memory'. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Best behaviour: A proposal for a non-binary conceptualization of behaviour in biology

Behaviour is a widespread object of research in biology, yet it is often left undefined, and the variety of existing definitions have not led to a consensus. We argue that the fundamental problem in defining behaviour has been the assumption that the concept must be categorical: either a phenomenon is a behaviour or it is not. We propose instead that 'behaviour' is best understood as a spectrum concept. We have identified three major characteristics of phenomena which, we argue, fuel the intuitions of biologists regarding the classification of cases as behaviour. All are related to the mechanistic explanations put forth to account for the phenomena, and are (i) the complexity of the mechanism, (ii) the stability of the constitutive entities, and (iii) the quantity and significance of the inputs to the underlying mechanism. We illustrate this new conceptualisation through a three-dimensional behaviour-space which highlights the apparently different conceptualizations of behaviour attributed to humans, animals and plants, showing that they, in fact, all partake of a unified, malleable understanding of a single concept.

Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum

Terpene synthases (TPSs) are pivotal enzymes for the production of diverse terpenes, including monoterpenes, sesquiterpenes, and diterpenes. In our recent studies, dictyostelid social amoebae, also known as cellular slime molds, were found to contain TPS genes for making volatile terpenes. For comparison, here we investigated Physarum polycephalum, a plasmodial slime mold also known as acellular amoeba. Plasmodia of P. polycephalum grown on agar plates were found to release a mixture of volatile terpenoids consisting of four major sesquiterpenes (α-muurolene, (E)-β-caryophyllene, two unidentified sesquiterpenoids) and the monoterpene linalool. There were no qualitative differences in terpenoid composition at two stages of young plasmodia. To understand terpene biosynthesis, we analyzed the transcriptome and genome sequences of P. polycephalum and identified four TPS genes designated PpolyTPS1-PpolyTPS4. They share 28-73% of sequence identities. Full-length cDNAs for the four TPS genes were cloned and expressed in Escherichia coli to produce recombinant proteins, which were tested for sesquiterpene synthase and monoterpene synthase activities. While neither PpolyTPS2 nor PpolyTPS3 was active, PpolyTPS1 and PpolyTPS4 were able to produce sesquiterpenes and monoterpenes from the respective substrates farnesyl diphosphate and geranyl diphosphate. By comparing the volatile profile of P. polycephalum plasmodia and the in vitro products of PpolyTPS1 and PpolyTPS4, it was concluded that most sesquiterpenoids emitted from P. polycephalum were attributed to PpolyTPS4. Phylogenetic analysis placed the four PpolyTPSs genes into two groups: PpolyTPS1 and PpolyTPS4 being one group that was clustered with the TPSs from the dictyostelid social amoeba and PpolyTPS2 and PpolyTPS3 being the other group that showed closer relatedness to bacterial TPSs. The biological role of the volatile terpenoids produced by the plasmodia of P. polycephalum is discussed.

The role of active movement in fungal ecology and community assembly

Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth, mycelial translocations, or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus.

Mitochondrial numbers increase during glucose deprivation in the slime mold Physarum polycephalum

Glucose deprivation in the slime mold Physarum polycephalum leads to a specific morphotype, a highly motile mesoplasmodium. We investigated the ultrastructure of both mesoplasmodia and non-starved plasmodia and found significantly increased numbers of mitochondria in glucose-deprived mesoplasmodia. The volume of individual mitochondria was the same in both growth forms. We conjecture that the number of mitochondria correlates with the metabolic state of the cell: When glucose is absent, the slime mold is forced to switch to different metabolic pathways, which occur inside mitochondria. Furthermore, a catabolic cue (such as AMP-activated protein kinase (AMPK)) could stimulate mitochondrial biogenesis.

Substrate composition directs slime molds behavior

Cells, including unicellulars, are highly sensitive to external constraints from their environment. Amoeboid cells change their cell shape during locomotion and in response to external stimuli. Physarum polycephalum is a large multinucleated amoeboid cell that extends and develops pseudopods. In this paper, changes in cell behavior and shape were measured during the exploration of homogenous and non-homogenous environments that presented neutral, and nutritive and/or adverse substances. In the first place, we developed a fully automated image analysis method to measure quantitatively changes in both migration and shape. Then we measured various metrics that describe the area covered, the exploration dynamics, the migration rate and the slime mold shape. Our results show that: (1) Not only the nature, but also the spatial distribution of chemical substances affect the exploration behavior of slime molds; (2) Nutritive and adverse substances both slow down the exploration and prevent the formation of pseudopods; and (3) Slime mold placed in an adverse environment preferentially occupies previously explored areas rather than unexplored areas using mucus secretion as a buffer. Our results also show that slime molds migrate at a rate governed by the substrate up until they get within a critical distance to chemical substances.

The dark face of fructose as a tumor promoter

Fructose, an essential biomolecule and it is a major ingredient of the modern diet across the globe. Excess consumption of fructose may be a key driver of many serious diseases such as obesity, heart diseases, type 2 diabetes and cancer. Understanding the metabolism of fructose, molecular mechanisms of its toxic nature will aid in the treatment of various diseases including cancer.

Protein Leverage: Theoretical Foundations and Ten Points of Clarification

Much attention has been focused on fats and carbohydrates as the nutritional causes of energy overconsumption and obesity. In 2003, a model of intake regulation was proposed in which the third macronutrient, protein, is not only involved but is a primary driver of calorie intake via its interactions with carbohydrates and fats. This model, called protein leverage, posits that the strong regulation of protein intake causes the overconsumption of fats and carbohydrates (hence total energy) on diets with a low proportion of energy from protein and their underconsumption on diets with a high proportion of protein. Protein leverage has since been demonstrated in a range of animal studies and in several studies of human macronutrient regulation, and its potential role in contributing to the obesity epidemic is increasingly attracting discussion. Over recent years, however, several misconceptions about protein leverage have arisen. Our aim in this paper is to briefly outline some key aspects of the underlying theory and clarify 10 points of misunderstanding that have the potential to divert attention from the substantive issues.