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Scientific Reports Feb 2022The maternal/uniparental inheritance of mitochondria is controlled by the selective elimination of paternal/uniparental mitochondria and digestion of their mitochondrial...
The maternal/uniparental inheritance of mitochondria is controlled by the selective elimination of paternal/uniparental mitochondria and digestion of their mitochondrial DNA (mtDNA). In isogamy, the selective digestion of mtDNA in uniparental mitochondria is initiated after mating and is completed prior to the elimination of mitochondria, but the molecular mechanism of the digestion of uniparental mtDNA remains unknown. In this study, we developed a semi-in vitro assay for DNase, wherein the digestion of mitochondrial nucleoids (mt-nucleoids) was microscopically observed using isolated mitochondria from Physarum polycephalum and the DNase involved in uniparental inheritance was characterized. When myxamoebae of AI35 and DP246 are crossed, mtDNA and mt-nucleoid from only the DP246 parent are digested. The digestion of mt-nucleoids was observed in zygotes 3 h after plating for mating. During the digestion of mt-nucleoids, mitochondrial membrane integrity was maintained. In the semi-in vitro assay, the digestion of mt-nucleoids was only observed in the presence of Mg at pH 7.5-9.0. Moreover, such Mg-dependent DNase activity was specifically detected in mitochondria isolated from zygotes 3 h after plating for mating. Therefore, Mg-dependent DNase is potentially involved in uniparental inheritance. Our findings provide insights into the DNase involved in uniparental inheritance and its regulatory mechanism.
Topics: DNA, Mitochondrial; Deoxyribonucleases; Hydrogen-Ion Concentration; Magnesium; Mitochondria; Mitochondrial Membranes; Physarum polycephalum; Zygote
PubMed: 35194142
DOI: 10.1038/s41598-022-06920-2 -
Nucleic Acids Research Mar 2022DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic...
DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic information. The integrity of the epigenome is, in part, insured by the recycling of parental histones and de novo deposition of newly synthesized histones. While the histone variants have revealed important functions in epigenetic regulations, the deposition in chromatin during S-phase of newly synthesized histone variants remains unclear. The identification of histone variants of H3 and unique features of Physarum polycephalum provides a powerful system for investigating de novo deposition of newly synthesized histones by tracking the incorporation of exogenous histones within cells. The analyses revealed that the rate of deposition of H3.1 and H3.3 is anticorrelated as S-phase progresses, H3.3 is predominately produced and utilized in early S and dropped throughout S-phase, while H3.1 behaved in the opposite way. Disturbing the expression of H3 variants by siRNAs revealed mutual compensation of histone transcripts. Interestingly, the incorporation of pre-formed constrained histone complexes showed that tetramers of H3/H4 are more efficiently utilized by the cell than dimers. These results support the model whereby the histone variant distribution is established upon replication and new histone deposition.
Topics: Cell Cycle; Chromatin; DNA Replication; Histones; Nucleosomes; Physarum polycephalum
PubMed: 35137186
DOI: 10.1093/nar/gkac060 -
ELife Jan 2022What is the origin of behaviour? Although typically associated with a nervous system, simple organisms also show complex behaviours. Among them, the slime mold , a giant...
What is the origin of behaviour? Although typically associated with a nervous system, simple organisms also show complex behaviours. Among them, the slime mold , 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.
Topics: Actomyosin; Biomechanical Phenomena; Cell Physiological Phenomena; Locomotion; Physarum polycephalum
PubMed: 35060901
DOI: 10.7554/eLife.62863 -
Artificial Life Jun 2022We present Monte Carlo Physarum Machine (MCPM): a computational model suitable for reconstructing continuous transport networks from sparse 2D and 3D data. MCPM is a...
We present Monte Carlo Physarum Machine (MCPM): a computational model suitable for reconstructing continuous transport networks from sparse 2D and 3D data. MCPM is a probabilistic generalization of Jones's (2010) agent-based model for simulating the growth of Physarum polycephalum (slime mold). We compare MCPM to Jones's work on theoretical grounds, and describe a task-specific variant designed for reconstructing the large-scale distribution of gas and dark matter in the Universe known as the cosmic web. To analyze the new model, we first explore MCPM's self-patterning behavior, showing a wide range of continuous network-like morphologies-called polyphorms-that the model produces from geometrically intuitive parameters. Applying MCPM to both simulated and observational cosmological data sets, we then evaluate its ability to produce consistent 3D density maps of the cosmic web. Finally, we examine other possible tasks where MCPM could be useful, along with several examples of fitting to domain-specific data as proofs of concept.
Topics: Physarum; Physarum polycephalum
PubMed: 34905603
DOI: 10.1162/artl_a_00351 -
PeerJ 2021Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and...
Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape of large numbers of spherical bodies, such as spores or pollen, by using inexpensive equipment. A spore suspension mounted on a slide is treated with a low-cost, high-vibration device to distribute spores uniformly in a single layer without overlap. Subsequently, 10,000 to 50,000 objects per slide are measured by automated image analysis. The workflow involves (1) slide preparation, (2) automated image acquisition by light microscopy, (3) filtering to separate high-density clusters, (4) image segmentation by applying a machine learning software, Waikato Environment for Knowledge Analysis (WEKA), and (5) statistical evaluation of the results. The technique produced consistent results and compared favorably with manual measurements in terms of precision. Moreover, measuring spore size distribution yields information not obtained by manual microscopic analyses, as shown for the myxomycete . The exact size distribution of spores revealed irregularities in spore formation resulting from the influence of environmental conditions on spore maturation. A comparison of the spore size distribution within and between sporocarp colonies showed large environmental and likely genetic variation. In addition, the comparison identified specimens with spores roughly twice the normal size. The successful implementation of the presented method for analyzing myxomycete spores also suggests potential for other applications.
PubMed: 34820196
DOI: 10.7717/peerj.12471 -
Zootaxa Sep 2021Two species of the genus Metatrichia Coquillett, from South America, are described as new to science: Metatrichia barbata sp. nov. and Metatrichia brunneipennis sp. nov....
Two species of the genus Metatrichia Coquillett, from South America, are described as new to science: Metatrichia barbata sp. nov. and Metatrichia brunneipennis sp. nov. Their relationships with related species are discussed. Metatrichia bulbosa (Osten Sacken, 1877) is registered to Brazil for the first time. A key to New World species of Metatrichia is presented.
Topics: Animal Distribution; Animals; Diptera; Myxomycetes
PubMed: 34811095
DOI: 10.11646/zootaxa.5039.1.5 -
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 -
Molecular Ecology Jan 2022Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding...
Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.
Topics: Amoebozoa; Base Sequence; Genetic Variation; Genotype; Phylogeny; Physarum
PubMed: 34676941
DOI: 10.1111/mec.16239 -
European Journal of Protistology Oct 2021Spores are the dispersal and reproductive units in Myxomycetes, and their ornamentation, usually at the light microscopy resolution limit, is taxonomically meaningful....
Spores are the dispersal and reproductive units in Myxomycetes, and their ornamentation, usually at the light microscopy resolution limit, is taxonomically meaningful. Here, we analyze with scanning and transmission electron microscopy the spore ultrastructural features in Trichiales, one of the most morphologically diverse orders. In Trichiales, the spore wall consists of two layers, an outer one, including the ornamentation, and an inner layer subdivided into two sections. The diversity of ornamental elements includes verrucae, bacula, pila, muri, and cristae, the two latter creating reticulate patterns. Each of these elements defines a broadly recognized ornamentation type except cristae, from which we differentiate for the first time the cristate reticulate and patched subtypes. Besides, our results point out a previous incorrect classification of the spores of the species Trichia decipiens and T. scabra. Advances in Trichiales phylogeny showed that the capillitium ornamental elements, such as the spirals, do not reflect phylogenetic relationships among the species. The same seems to apply to some of spore ornamentation types, e.g., baculate. Consequently, we may consider the need to combine multiple characters, like the spore and capillitium ornamentation, so that Trichiales systematics better reflect the still cryptic phylogenetic affinities.
Topics: Amoebozoa; Microscopy, Electron, Scanning; Myxomycetes; Phylogeny; Spores, Protozoan
PubMed: 34624792
DOI: 10.1016/j.ejop.2021.125839 -
Mycologia 2021A new nivicolous myxomycete is described as a result of a comprehensive study of collections from the entire range of its occurrence. Statistical analysis of 12...
A new nivicolous myxomycete is described as a result of a comprehensive study of collections from the entire range of its occurrence. Statistical analysis of 12 morphological characters, phylogenetic analyses of nuc 18S rDNA and elongation factor 1-alpha gene (), and a delimitation method (automatic barcode gap diversity) have been applied to corroborate the identity of the new species. A preliminary morphological analysis of revealed high variability of South American populations where four types of spore ornamentation were noted. However, results of molecular study and statistical analysis of morphological characters did not support recognition of these four forms but the distinction of two morphotypes. Consequently, two species have been recognized: and the newly proposed . The new species can be distinguished from by distinctly larger and mostly plasmodiocarpic sporophores, which are scattered to gregarious, paler spores, and by the paler, more delicate and more elastic capillitium. Spore ornamentation of is uniform and can be described as distinctly spiny (pilate under scanning electron microscope [SEM]), whereas those of is more variable, where spines (pilae under SEM) are delicate, distinct, or conspicuous. Additionally, whereas is a species distributed worldwide, occurs only in the austral Andes of Argentina and Chile.
Topics: Argentina; DNA, Ribosomal; Myxomycetes; Phylogeny; Physarida
PubMed: 34533412
DOI: 10.1080/00275514.2021.1961068