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International Journal of Molecular... Mar 2023Propofol belongs to a class of molecules that are known to block learning and memory in mammals, including rodents and humans. Interestingly, learning and memory are not...
Propofol belongs to a class of molecules that are known to block learning and memory in mammals, including rodents and humans. Interestingly, learning and memory are not tied to the presence of a nervous system. There are several lines of evidence indicating that single-celled organisms also have the capacity for learning and memory which may be considered as basal intelligence. Here, we introduce a new experimental model for testing the learning ability of , a model organism frequently used to study single-celled "intelligence". In this study, the impact of propofol on 's "intelligence" was tested. The model consists of a labyrinth of subsequent bifurcations in which food (oat flakes soaked with coconut oil-derived medium chain triglycerides [MCT] and soybean oil-derived long chain triglycerides [LCT]) or propofol in MCT/LCT) is placed in one of each Y-branch. In this setting, it was tested whether memorized the rewarding branch. We saw that was a quick learner when capturing the first bifurcations of the maze; thereafter, the effect decreased, perhaps due to reaching a state of satiety. In contrast, when oat flakes were soaked with propofol, 's preference for oat flakes declined significantly. Several possible actions, including the blocking of gamma-aminobutyric acid (GABA) receptor signaling, are suggested to account for this behavior, many of which can be tested in our new model.
Topics: Humans; Propofol; Anesthetics, Intravenous; Physarum polycephalum; Pain; Triglycerides
PubMed: 37047260
DOI: 10.3390/ijms24076287 -
Proceedings of the National Academy of... Mar 2021The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past...
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 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.
Topics: Cytoplasm; Models, Biological; Physarum polycephalum
PubMed: 33619174
DOI: 10.1073/pnas.2007815118 -
Biochimica Et Biophysica Acta. General... Jun 2023Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze...
BACKGROUND
Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze chitin, an important structural component of the cell walls in fungi and in the exoskeleton of insects and crustaceans.
METHODS
Low stringency sequence signature search in transcriptomes was used to identify GH18 sequences related to chitinases. Identified sequences were expressed in E. coli and corresponding structures modelled. Synthetic substrates and in some cases colloidal chitin were used to characterize activities.
RESULTS
Catalytically functional hits were sorted and their predicted structures compared. All share the TIM barrel structure of the GH18 chitinase catalytic domain, optionally fused to binding motifs, such as CBM50, CBM18, and CBM14, involved in sugar recognition. Assessment of the enzymatic activities following deletion of the C-terminal CBM14 domain of the most active clone evidenced a significant contribution of this extension to the chitinase activity. A classification based on module organization, functional and structural criteria of characterized enzymes was proposed.
CONCLUSIONS
Physarum polycephalum sequences encompassing a chitinase like GH18 signature share a modular structure involving a structurally conserved catalytic TIM barrels decorated or not by a chitin insertion domain and optionally surrounded by additional sugar binding domains. One of them plays a clear role in enhancing activities toward natural chitin.
GENERAL SIGNIFICANCE
Myxomycete enzymes are currently poorly characterized and constitute a potential source for new catalysts. Among them glycosyl hydrolases have a strong potential for valorization of industrial waste as well as in therapeutic field.
Topics: Chitinases; Physarum polycephalum; Myxomycetes; Escherichia coli; Chitin; Sugars
PubMed: 36933625
DOI: 10.1016/j.bbagen.2023.130343 -
Molecular Phylogenetics and Evolution Dec 2022Early phylogenetic studies refuted most previous assumptions concerning the evolution of the morphological traits in the fruiting bodies of the order Trichiales and did...
Early phylogenetic studies refuted most previous assumptions concerning the evolution of the morphological traits in the fruiting bodies of the order Trichiales and did not detect discernible evolutionary patterns, yet they were based on a limited number of species. We infer a new Trichiales phylogeny based on three independently inherited genetic regions (nuclear and mitochondrial), with a fair taxonomic sampling encompassing its broad diversity. Besides, we study the evolutionary history of some key morphological characters. According to the new phylogeny, most fruiting body traits in Trichiales systematics do not represent exclusive synapomorphies or autapomorphies for most monophyletic groups. Instead, the evolution of the features derived from the peridium, stalk, capillitium, and spores showed intricate patterns, and character state transitions occurred rather within- than between clades. Thus, we should consider other evolutionary scenarios instead of assuming the homology of some characters. According to these results, we propose a new classification of Trichiales, including the creation of a new genus, Gulielmina, the resurrection of the family Dictydiaethaliaceae and the genus Ophiotheca, and the proposal of 13 new combinations for species of the genera Arcyria (1), Hemitrichia (2), Ophiotheca (2), Oligonema (4), Gulielmina (3), and Perichaena (1).
Topics: Amoeba; Amoebozoa; Ascomycota; Myxomycetes; Phylogeny
PubMed: 35963588
DOI: 10.1016/j.ympev.2022.107609 -
Philosophical Transactions of the Royal... Jul 2020Unicellular organisms live in unpredictable environments. Therefore, they need to continuously assess environmental conditions and respond appropriately to survive and...
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, . 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'.
Topics: Cues; Physarum polycephalum; Signal Transduction; Stress, Physiological
PubMed: 32420856
DOI: 10.1098/rstb.2019.0470 -
Non-coding RNA Jul 2021Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in...
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.
PubMed: 34449660
DOI: 10.3390/ncrna7030043 -
Journal of Fungi (Basel, Switzerland) Feb 2021Structural color occurs by the interaction of light with regular structures and so generates colors by completely different optical mechanisms to dyes and pigments....
Structural color occurs by the interaction of light with regular structures and so generates colors by completely different optical mechanisms to dyes and pigments. Structural color is found throughout the tree of life but has not, to date, been reported in the fungi. Here we give an overview of structural color across the tree of life and provide a brief guide aimed at stimulating the search for this phenomenon in fungi.
PubMed: 33669274
DOI: 10.3390/jof7020141 -
Nanotoxicology May 2021Carbon nanotubes (CNTs) offer attractive opportunities due to their physical, electrical, mechanical, optical, and thermal properties. They are used in a wide range of...
Carbon nanotubes (CNTs) offer attractive opportunities due to their physical, electrical, mechanical, optical, and thermal properties. They are used in a wide range of applications and are found in numerous consumer products. On the downside, their increasing presence in the environment poses potential threats to living organisms and ecosystems. The aim of this study was to evaluate the toxicity of double-walled carbon nanotubes (DWCNTs) on a new model system: the acellular slime mold Despite its ecological significance, its simplicity of organization, and its behavioral complexity, exposure of such organisms to nanoparticles has been poorly investigated. Slime molds were exposed to DWCNTs using three routes of exposure (topical, food, environment). We first demonstrated that DWCNTs were rapidly internalized by slime molds especially when DWCNTs were mixed with the food or spread out in the environment. Secondly, we showed that a 6-week exposure to DWCNTs did not lead to bioaccumulation nor did it lead to persistence in the slime molds when they entered a resting stage. Thirdly, we revealed that 2 days following exposure, DWCNTs were almost entirely excreted from the slime molds. Lastly, we uncovered that DWCNTs exposure altered the migration speed, the pseudopods formation, and the expansion rate of the slime molds. Our results extend our current knowledge of CNTs cytotoxicity and introduce as an ideal organism for nanotoxicology.
Topics: Ecosystem; Nanotubes, Carbon; Physarum polycephalum
PubMed: 33705250
DOI: 10.1080/17435390.2021.1894615 -
Current Biology : CB Jul 2021Spliceosomal introns interrupt nuclear genes and are removed from RNA transcripts ("spliced") by machinery called spliceosomes. Although the vast majority of...
Spliceosomal introns interrupt nuclear genes and are removed from RNA transcripts ("spliced") by machinery called spliceosomes. Although the vast majority of spliceosomal introns are removed by the so-called major (or "U2") spliceosome, diverse eukaryotes also contain a rare second form, the minor ("U12") spliceosome, and associated ("U12-type") introns. In all characterized species, U12-type introns are distinguished by several features, including being rare in the genome (∼0.5% of all introns), containing extended evolutionarily conserved splicing motifs, being generally ancient, and being inefficiently spliced. Here, we report a remarkable exception in the slime mold Physarum polycephalum. The P. polycephalum genome contains >20,000 U12-type introns-25 times more than any other species-enriched in a diversity of non-canonical splice boundaries as well as transformed splicing signals that appear to have co-evolved with the spliceosome due to massive gain of efficiently spliced U12-type introns. These results reveal an unappreciated dynamism of minor spliceosomal introns and spliceosomal introns in general.
Topics: Introns; Physarum polycephalum; RNA Splicing; RNA, Small Nuclear; Spliceosomes
PubMed: 34015249
DOI: 10.1016/j.cub.2021.04.050 -
MycoKeys 2020Macrofungi are considered as organisms that form large fruiting bodies above or below the ground that are visible without the aid of a microscope. These fungi include...
Macrofungi are considered as organisms that form large fruiting bodies above or below the ground that are visible without the aid of a microscope. These fungi include most basidiomycetes and a small number of ascomycetes. Macrofungi have different ecological roles and uses, where some are edible, medicinal, poisonous, decomposers, saprotrophs, predators and pathogens, and they are often used for innovative biotechnological, medicinal and ecological applications. However, comprehensive checklists, and compilations on the diversity and distribution of mushrooms are lacking for South Africa, which makes regulation, conservation and inclusion in national biodiversity initiatives difficult. In this review, we compiled a checklist of macrofungi for the first time (excluding lichens). Data were compiled based on available literature in journals, books and fungorium records from the National Collection of Fungi. Even if the list is not complete due to numerous unreported species present in South Africa, it still represents an overview of the current knowledge of the macromycetes of South Africa. The list of names enables the assessment of gaps in collections and knowledge on the fungal biodiversity of South Africa, and downstream applications such as defining residency status of species. It provides a foundation for new names to be added in future towards developing a list that will be as complete as possible, and that can be used by a wide audience including scientists, authorities and the public.
PubMed: 32089638
DOI: 10.3897/mycokeys.63.36566