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Current Biology : CB Apr 2021Interview with Audrey Dussutour, who uses slime molds and ant colonies to study collective behavior and cognition at the Center for Integrative Biology in Toulouse.
Interview with Audrey Dussutour, who uses slime molds and ant colonies to study collective behavior and cognition at the Center for Integrative Biology in Toulouse.
Topics: Animals; Cognition; Communication; History, 21st Century; Learning; Mentors; Myxomycetes; Research Support as Topic; Sexism; Writing
PubMed: 33905686
DOI: 10.1016/j.cub.2021.03.033 -
Current Biology : CB Dec 2013
Topics: Physarum polycephalum; Signal Transduction
PubMed: 24355778
DOI: 10.1016/j.cub.2013.09.040 -
Journal of the Royal Society, Interface Apr 2022is a unicellular slime mould that has been intensely studied owing to its ability to solve mazes, find shortest paths, generate Steiner trees, share knowledge and...
is a unicellular slime mould that has been intensely studied owing to its ability to solve mazes, find shortest paths, generate Steiner trees, share knowledge and remember past events and the implied applications to unconventional computing. The CELL model is a cellular automaton introduced in Gunji . (Gunji 2008 , 659-667 (doi:10.1016/j.jtbi.2008.04.017)) that models 's amoeboid motion, tentacle formation, maze solving and network creation. In the present paper, we extend the CELL model by spawning multiple CELLs, allowing us to understand the interactions between multiple cells and, in particular, their mobility, merge speed and cytoplasm mixing. We conclude the paper with some notes about applications of our work to modelling the rise of present-day civilization from the early nomadic humans and the spread of trends and information around the world. Our study of the interactions of this unicellular organism should further the understanding of how communicates and shares information.
Topics: Cell Fusion; Humans; Physarum polycephalum
PubMed: 35472268
DOI: 10.1098/rsif.2022.0054 -
Journal of Bacteriology Nov 1962Daniel, John W. (University of Wisconsin, Madison), Jacqueline Kelley, and Harold P. Rusch. Hematin-requiring plasmodial myxomycete. J. Bacteriol. 84:1104-1110....
Daniel, John W. (University of Wisconsin, Madison), Jacqueline Kelley, and Harold P. Rusch. Hematin-requiring plasmodial myxomycete. J. Bacteriol. 84:1104-1110. 1962.-The myxomycete Physarum polycephalum, previously shown to require chick embryo extract for growth on a partially defined, soluble medium, grows as well if hematin or certain hemoproteins are substituted for the embryo extract. Hematin is also required as a growth factor if the organism is grown on a synthetic medium. Of the variety of porphyrins tested only iron protoporphyrin IX is utilized for growth by P. polycephalum. Protoporphyrin IX is inactive. Protein-bound iron porphyrin is active at one-tenth the concentration of free hematin. Although hematin completely replaces embryo extract, the extract activity has properties not characteristic of hematin or the hemoproteins tested: ladility to light and rapid plasmodial uptake.
Topics: Animals; Chick Embryo; Culture Media; Heme; Hemeproteins; Hemin; Myxomycetes; Porphyrins; Protoporphyrins
PubMed: 14024912
DOI: 10.1128/jb.84.5.1104-1110.1962 -
Genes Mar 2023The mtDNA of the myxomycete can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are... (Review)
Review
The mtDNA of the myxomycete can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes are cryptogenes that require a unique type of RNA editing (MICOTREM). A second category of gene is putative protein-coding genes represented by 26 significant open reading frames. However, these genes do not appear to be transcribed during the growth of the plasmodium and are currently unassigned since they do not have any apparent similarity to other classical mitochondrial protein-coding genes. The third category of gene is found in the mtDNA of some strains of . These genes derive from a linear mitochondrial plasmid with nine significant, but unassigned, open reading frames which can integrate into the mitochondrial DNA by recombination. Here, we review the mechanism and evolution of the RNA editing necessary for cryptogene expression, discuss possible origins for the 26 unassigned open reading frames based on tentative identification of their protein product, and discuss the implications to mtDNA structure and replication of the integration of the linear mitochondrial plasmid.
Topics: Physarum polycephalum; DNA, Mitochondrial; Base Sequence; Mitochondria; Genetic Variation
PubMed: 36980901
DOI: 10.3390/genes14030628 -
Bio Systems Feb 2016Left-right patterning and lateralised behaviour is an ubiquitous aspect of plants and animals. The mechanisms linking cellular chirality to the large-scale asymmetry of...
Left-right patterning and lateralised behaviour is an ubiquitous aspect of plants and animals. The mechanisms linking cellular chirality to the large-scale asymmetry of multicellular structures are incompletely understood, and it has been suggested that the chirality of living cells is hardwired in their cytoskeleton. We examined the question of biased asymmetry in a unique organism: the slime mould Physarum polycephalum, which is unicellular yet possesses macroscopic, complex structure and behaviour. In laboratory experiment using a T-shape, we found that Physarum turns right in more than 74% of trials. The results are in agreement with previously published studies on asymmetric movement of muscle cells, neutrophils, liver cells and growing neural filaments, and for the first time reveal the presence of consistently-biased laterality in the fungi kingdom. Exact mechanisms of the slime mould's direction preference remain unknown.
Topics: Body Patterning; Cell Movement; Computer Simulation; Models, Biological; Models, Statistical; Myxomycetes; Physarum polycephalum
PubMed: 26747637
DOI: 10.1016/j.biosystems.2015.12.008 -
Animal Cognition Nov 2023Sensing, communication, navigation, decision-making, memory and learning are key components in a standard cognitive tool-kit that enhance an animal's ability to... (Review)
Review
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.
Topics: Animals; Physarum polycephalum; Cognition; Learning
PubMed: 37166523
DOI: 10.1007/s10071-023-01782-1 -
Methods in Molecular Biology (Clifton,... 2022Physarum polycephalum is a protist slime mould that exhibits a high degree of responsiveness to its environment through a complex network of tubes and cytoskeletal...
Physarum polycephalum is a protist slime mould that exhibits a high degree of responsiveness to its environment through a complex network of tubes and cytoskeletal components that coordinate behavior across its unicellular, multinucleated body. Physarum has been used to study decision making, problem solving, and mechanosensation in aneural biological systems. The robust generative and repair capacities of Physarum also enable the study of whole-body regeneration within a relatively simple model system. Here we describe methods for growing, imaging, quantifying, and sampling Physarum that are adapted for investigating regeneration and repair.
Topics: Adaptation, Physiological; Models, Biological; Physarum polycephalum
PubMed: 35359302
DOI: 10.1007/978-1-0716-2172-1_3 -
Genes May 2022Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic...
Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar group I introns. We analyzed and compared 75 group I introns at position 516 in the small subunit ribosomal DNA from diverse and distantly related myxomycete taxa. A consensus secondary structure revealed a conserved group IC1 ribozyme core, but with a surprising RNA sequence complexity in the peripheral regions. Five S516 group I introns possess a twintron organization, where a His-Cys homing endonuclease gene insertion was interrupted by a small spliceosomal intron. Eleven S516 introns contained direct repeat arrays with varying lengths of the repeated motif, a varying copy number, and different structural organizations. Phylogenetic analyses of S516 introns and the corresponding host genes revealed a complex inheritance pattern, with both vertical and horizontal transfers. Finally, we reconstructed the evolutionary history of S516 nucleolar group I introns from insertion of mobile-type introns at unoccupied cognate sites, through homing endonuclease gene degradation and loss, and finally to the complete loss of introns. We conclude that myxomycete S516 introns represent a family of genetic elements with surprisingly dynamic structures despite a common function in RNA self-splicing.
Topics: DNA, Ribosomal; Endonucleases; Eukaryota; Introns; Myxomycetes; Phylogeny; RNA, Catalytic
PubMed: 35741706
DOI: 10.3390/genes13060944 -
IUBMB Life 2003'RNA editing' describes the programmed alteration of the nucleotide sequence of an RNA species, relative to the sequence of the encoding DNA. The phenomenon encompasses... (Review)
Review
'RNA editing' describes the programmed alteration of the nucleotide sequence of an RNA species, relative to the sequence of the encoding DNA. The phenomenon encompasses two generic patterns of nucleotide change, 'insertion/deletion' and 'substitution', defined on the basis of whether the sequence of the edited RNA is colinear with the DNA sequence that encodes it. RNA editing is mediated by a variety of pathways that are mechanistically and evolutionarily unrelated. Messenger, ribosomal, transfer and viral RNAs all undergo editing in different systems, but well-documented cases of this phenomenon have so far been described only in eukaryotes, and most often in mitochondria. Editing of mRNA changes the identity of encoded amino acids and may create translation initiation and termination codons. The existence of RNA editing violates one of the long-accepted tenets of genetic information flow, namely, that the amino acid sequence of a protein can be directly predicted from the corresponding gene sequence. Particular RNA editing systems display a narrow phylogenetic distribution, which argues that such systems are derived within specific eukaryotic lineages, rather than representing traits that ultimately trace to a common ancestor of eukaryotes, or even further back in evolution. The derived nature of RNA editing raises intriguing questions about how and why RNA editing systems arise, and how they become fixed as additional, essential steps in genetic information transfer.
Topics: Amino Acid Sequence; Animals; Dinoflagellida; Evolution, Molecular; Kinetoplastida; Molecular Sequence Data; Myxomycetes; Phylogeny; RNA; RNA Editing; RNA, Mitochondrial
PubMed: 12880203
DOI: 10.1080/1521654031000119425