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Scientific Reports Aug 2022This paper presents a novel biologically-inspired explore-and-fuse approach to solving a large array of problems. The inspiration comes from Physarum, a unicellular...
This paper presents a novel biologically-inspired explore-and-fuse approach to solving a large array of problems. The inspiration comes from Physarum, a unicellular slime mold capable of solving the traveling salesman and Steiner tree problems. Besides exhibiting individual intelligence, Physarum can also share information with other Physarum organisms through fusion. These characteristics of Physarum imply that spawning many such organisms we can explore the problem space in parallel, each individual gathering information and forming partial solutions pertaining to a local region of the problem space. When the organisms meet, they fuse and share information, eventually forming one organism which has a global view of the problem and can apply its intelligence to find an overall solution to the problem. This approach can be seen as a "softer" method of divide and conquer. We demonstrate this novel approach, developing the Physarum Steiner Algorithm which is capable of finding feasible solutions to the Euclidean Steiner tree problem. This algorithm is of particular interest due to its resemblance to Physarum polycephalum, ability to leverage parallel processing, avoid obstacles, and operate on various shapes and topological surfaces including the rectilinear grid.
Topics: Algorithms; Physarum polycephalum; Trees
PubMed: 36008426
DOI: 10.1038/s41598-022-18316-3 -
BMC Microbiology Dec 2022Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage....
BACKGROUND
Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage. Plasmodia are all found to be associated with bacteria. However, the information about bacteria diversity and composition in different plasmodia was limited. Therefore, this study aimed to investigate the bacterial diversity of plasmodia from different myxomycetes species and reveal the potential function of plasmodia-associated bacterial communities.
RESULTS
The bacterial communities associated with the plasmodia of six myxomycetes (Didymium iridis, Didymium squamulosum, Diderma hemisphaericum, Lepidoderma tigrinum, Fuligo leviderma, and Physarum melleum) were identified by 16S rRNA amplicon sequencing. The six plasmodia harbored 38 to 52 bacterial operational taxonomic units (OTUs) that belonged to 7 phyla, 16 classes, 23 orders, 40 families, and 53 genera. The dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria. Most OTUs were shared among the six myxomycetes, while unique bacteria in each species only accounted for a tiny proportion of the total OTUs.
CONCLUSIONS
Although each of the six myxomycetes plasmodia had different bacterial community compositions, a high similarity was observed in the plasmodia-associated bacterial communities' functional composition. The high enrichment for gram-negative (> 90%) and aerobic (> 99%) bacteria in plasmodia suggest that myxomycetes may positively recruit certain kinds of bacteria from the surrounding environment.
Topics: Humans; Myxomycetes; RNA, Ribosomal, 16S; Physarum; Bacteria; Plasmodium
PubMed: 36544088
DOI: 10.1186/s12866-022-02725-5 -
Philosophical Transactions of the Royal... Apr 2023Changes in behaviour over the lifetime of single-cell organisms have primarily been investigated in response to environmental stressors. However, growing evidence...
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 . 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'.
Topics: Humans; Infant, Newborn; Physarum polycephalum; Learning; Cues
PubMed: 36802777
DOI: 10.1098/rstb.2022.0063 -
AMB Express Jun 2021Given the emerging multidrug-resistant pathogens, the number of effective antimicrobial agents to deal with the threat of bacterial and fungal resistance has fallen... (Review)
Review
Given the emerging multidrug-resistant pathogens, the number of effective antimicrobial agents to deal with the threat of bacterial and fungal resistance has fallen dramatically. Therefore, the critical solution to deal with the missing effective antibiotics is to research new sources or new synthetic antibiotics. Natural products have different advantages to be considered antimicrobial agents. There are different natural sources for antimicrobial agents, such as bacteria, fungi, algae, slime molds, and plants. This article has focused on antibiotics from slime molds, especially Myxomycetes. The reason why slime molds have been chosen to be studied is their unique bioactive metabolites, especially over the past couple of decades. Some of those metabolites have been demonstrated to possess antibiotic activities. Hence, this article has focused on the potential of these creatures as an alternative source of antibiotics.
PubMed: 34160704
DOI: 10.1186/s13568-021-01251-3 -
BMC Biotechnology Mar 2021Microbial polysaccharides have been reported to possess remarkable bioactivities. Physarum polycephalum is a species of slime mold for which the microplasmodia are...
BACKGROUND
Microbial polysaccharides have been reported to possess remarkable bioactivities. Physarum polycephalum is a species of slime mold for which the microplasmodia are capable of rapid growth and can produce a significant amount of cell wall-less biomass. There has been a limited understanding of the polysaccharides produced by microplasmodia of slime molds, including P. polycephalum. Thus, the primary objectives of this research were first to chemically characterize the exopolysaccharides (EPS) and intracellular polysaccharides (IPS) of P. polycephalum microplasmodia and then to evaluate their cytotoxicity against several cancer cell lines.
RESULTS
The yields of the crude EPS (4.43 ± 0.44 g/l) and partially purified (deproteinated) EPS (2.95 ± 0.85 g/l) were comparable (p > 0.05) with the respective crude IPS (3.46 ± 0.36 g/l) and partially purified IPS (2.45 ± 0.36 g/l). The average molecular weight of the EPS and IPS were 14,762 kDa and 1788 kDa. The major monomer of the EPS was galactose (80.22%), while that of the IPS was glucose (84.46%). Both crude and purified IPS samples showed significantly higher cytotoxicity toward Hela cells, especially the purified sample and none of the IPSs inhibited normal cells. Only 38.42 ± 2.84% Hela cells remained viable when treated with the partially purified IPS (1 mg/ml). However, although only 34.76 ± 6.58% MCF-7 cells were viable when exposed to the crude IPS, but the partially purified IPS displayed non-toxicity to MCF-7 cells. This suggested that the cytotoxicity toward MCF-7 would come from some component associated with the crude IPS sample (e.g. proteins, peptides or ion metals) and the purification process would have either completely removed or reduced amount of that component. Cell cycle analysis by flow cytometry suggested that the mechanism of the toxicity of the crude IPS toward MCF-7 and the partially purified IPS toward Hela cells was due to apoptosis.
CONCLUSIONS
The EPS and IPS of P. polycephalum microplasmodia had different chemical properties including carbohydrate, protein and total sulfate group contents, monosaccharide composition and molecular weights, which led to different cytotoxicity activities. The crude and partially purified IPSs would be potential materials for further study relating to cancer treatment.
Topics: Antineoplastic Agents; HeLa Cells; Humans; MCF-7 Cells; Molecular Weight; Physarum polycephalum; Polysaccharides
PubMed: 33773573
DOI: 10.1186/s12896-021-00688-5 -
ELife Feb 2022In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic...
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 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 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.
Topics: Gene Expression Regulation; Giant Cells; Physarum polycephalum; RNA-Seq; Single-Cell Analysis; Transcriptome
PubMed: 35195068
DOI: 10.7554/eLife.69745 -
International Journal of Molecular... Jan 2023The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone...
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in . However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.
Topics: Animals; Histones; Physarum polycephalum; Histone Chaperones; Saccharomyces cerevisiae; Chromatin; Molecular Chaperones
PubMed: 36674565
DOI: 10.3390/ijms24021051 -
Persoonia Jun 2023The class consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic...
The class consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order , with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, , , and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family is paraphyletic to the rest of . Within s.lat., the recent reinstatement of the genus for most species traditionally ascribed to , except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus in and s.str. () in (Prikhodko et al. 2023). Additionally, the genus is redefined to include some species previously treated in ( spp. with true columella). Within the monophyletic family , most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, , is proposed for a major clade containing and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) is resurrected for the clade containing . Additionally, is suggested as the correct name for the clade containing . The taxonomy and nomenclature of some provisional genera, currently synonymous with and , are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided. : García-Martín JM, Zamora JC, Lado C. 2023. Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. Persoonia 51: 89-124. doi: 10.3767/persoonia.2023.51.02.
PubMed: 38665983
DOI: 10.3767/persoonia.2023.51.02 -
Microscopy Research and Technique Mar 2022The habit of feeding on slime moulds (Myxomycetes) commonly present in litter or dead wood requires specific morphological adaptations of the mouthparts and sensory...
The habit of feeding on slime moulds (Myxomycetes) commonly present in litter or dead wood requires specific morphological adaptations of the mouthparts and sensory structures involved in the search for habitat and food. In this study, the external morphology of antenna and its sensilla were studied using scanning electron microscopy in the saproxylic beetle, Clinidium canaliculatum, Costa 1839 (Coleoptera, Rhysodidae). Their moniliform antennae consist of a scape, pedicel, and nine flagellomeres. We identified seven different types of sensilla, according to their morphological characteristics: two types of sensilla chaetica (sc1 and 2), two types of sensilla basiconica (sb1 and 2), one type of sensilla campaniformia, one type of sensilla coeloconica, and Böhm sensilla. No sexual dimorphism was found regarding antennal morphology and sensilla type and distribution, except for the sensilla coeloconica. The functional role of these sensilla was discussed in relation to their external structure and distribution, and compared with the current knowledge on coleopteran sense organs. Results are basic information for further physiological and behavioral studies to identify their role in the selection of habitat, food, mates and oviposition sites.
Topics: Animals; Arthropod Antennae; Coleoptera; Microscopy, Electron, Scanning; Sensilla; Wood
PubMed: 34676944
DOI: 10.1002/jemt.23969 -
Scientific Reports Jun 2022In order to solve the inverse kinematics (IK) of complex manipulators efficiently, a hybrid equilibrium optimizer slime mould algorithm (EOSMA) is proposed. Firstly, the...
In order to solve the inverse kinematics (IK) of complex manipulators efficiently, a hybrid equilibrium optimizer slime mould algorithm (EOSMA) is proposed. Firstly, the concentration update operator of the equilibrium optimizer is used to guide the anisotropic search of the slime mould algorithm to improve the search efficiency. Then, the greedy strategy is used to update the individual and global historical optimal to accelerate the algorithm's convergence. Finally, the random difference mutation operator is added to EOSMA to increase the probability of escaping from the local optimum. On this basis, a multi-objective EOSMA (MOEOSMA) is proposed. Then, EOSMA and MOEOSMA are applied to the IK of the 7 degrees of freedom manipulator in two scenarios and compared with 15 single-objective and 9 multi-objective algorithms. The results show that EOSMA has higher accuracy and shorter computation time than previous studies. In two scenarios, the average convergence accuracy of EOSMA is 10e-17 and 10e-18, and the average solution time is 0.05 s and 0.36 s, respectively.
Topics: Algorithms; Biomechanical Phenomena; Physarum polycephalum; Robotic Surgical Procedures; Robotics
PubMed: 35676308
DOI: 10.1038/s41598-022-13516-3