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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 -
Journal of Fungi (Basel, Switzerland) Jun 2022To address international food security concerns and sustain a growing global population, global agricultural output needs to increase by 70% by the year 2050. Current...
To address international food security concerns and sustain a growing global population, global agricultural output needs to increase by 70% by the year 2050. Current agricultural techniques to increase crop yields, specifically the application of chemicals, have resulted in a wide range of negative impacts on the environment and human health. The maintenance of good quality soil organic matter, a key concern in tropical countries such as India, requires a steady input of organic residues to maintain soil fertility. A tree with many uses, , has attracted much attention over the past decades. As per our literature review, no research has been conducted examining leaves for their fungal decomposition and their use as green manure. A study of the fungal colonization of leaves at various stages of decomposition was conducted to get an insight into which fungi play a critical role in the decomposition process. In total, fifty-two different species of fungi were isolated. There was an increase in the percentage of fungus occurrences as the leaves senesced and then finally decomposed. Almost all decomposition stages were characterized by a higher percentage occurrence of Deuteromycetes (75.47%) and by a lower rate of Ascomycetes (9.43%). A gradual increase of basidiomycetes such as unidentified sclerotia and was seen as the leaves senesced and finally decomposed. In the moist chamber, was the only Myxomycete isolated from completely decomposed leaves. In the present study, on average, there were more fungi in wet seasons than in the dry seasons.
PubMed: 35736090
DOI: 10.3390/jof8060608 -
Mycologia 2022A new species of the genus (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and...
A new species of the genus (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and phylogenetic data, are provided. At first glance, the new species shares some morphological similarities with both , type of the genus, and , but it strikingly differs from all other species of its genus by combining a short dark stalk, with a reticulate columella, and clustered spores. Moreover, it seems to be the only species of exclusively associated with tropical forests at elevations above 3500 m. Apart from a comprehensive morphological study of 31 specimens, we here provide phylogenetic evidence to confirm the inclusion of this species in the genus . Specifically, our phylogenetic analyses of the nuclear 18S rDNA (18S), mitochondrial 17S rDNA (17S), and elongation factor-1 alpha () genes show that the new species is related to and . The remarkably different morphological characters distinguishing the new from all other species of its genus, along with its particular ecological preferences and geographic distribution, indicate that it is a distinct entity deserving recognition as an independent species.
Topics: DNA, Ribosomal; Forests; Myxomycetes; Peru; Phylogeny
PubMed: 35695815
DOI: 10.1080/00275514.2022.2072140 -
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 -
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 -
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 -
Mycoscience 2022The bark of live trees provides an important microhabitat for corticolous myxomycetes. However, the association between the presence of myxomycetes and health of host...
The bark of live trees provides an important microhabitat for corticolous myxomycetes. However, the association between the presence of myxomycetes and health of host trees has not been studied in detail. In this study, we aimed to investigate the relationship between tree vitality and myxomycetes on the bark of trees in a montane forest in western Japan. The vitality of trees was categorized into four grades based on the visual assessment of tree shape and leaf density in the upper branches. Myxomycetes on the bark surface were examined using the moist chamber culture method. A decline in tree vitality increased bark pH and decreased electrical conductivity of the bark exudates. Seventeen myxomycete species were recorded in 74 trees. The structure of myxomycete communities varied between healthy and unhealthy trees, and species diversity increased as the vitality declined. The relative abundance of decreased as the vitality declined, while that of increased. The results showed that acidophilic myxomycetes grew on healthy bark, but changes in bark pH associated with vitality decline led to the weakening of acidity and shifted the community structure; thus, corticolous myxomycete diversity was enhanced as tree vitality decline.
PubMed: 37092009
DOI: 10.47371/mycosci.2022.01.001 -
Proceedings of the National Academy of... Mar 2022Multiple modes of asexual reproduction are observed among microbial organisms in natural populations. These modes are not only subject to evolution, but may drive...
Multiple modes of asexual reproduction are observed among microbial organisms in natural populations. These modes are not only subject to evolution, but may drive evolutionary competition directly through their impact on population growth rates. The most prominent transition between two such modes is the one from unicellularity to multicellularity. We present a model of the evolution of reproduction modes, where a parent organism fragments into smaller parts. While the size of an organism at fragmentation, the number of offspring, and their sizes may vary a lot, the combined mass of fragments is limited by the mass of the parent organism. We found that mass conservation can fundamentally limit the number of possible reproduction modes. This has important direct implications for microbial life: For unicellular species, the interplay between cell shape and kinetics of the cell growth implies that the largest and the smallest possible cells should be rod shaped rather than spherical. For primitive multicellular species, these considerations can explain why rosette cell colonies evolved a mechanistically complex binary split reproduction. Finally, we show that the loss of organism mass during sporulation can explain the macroscopic sizes of the formally unicellular microorganism Myxomycetes plasmodium. Our findings demonstrate that a number of seemingly unconnected phenomena observed in unrelated species may be different manifestations of the same underlying process.
Topics: Bacteria; Reproduction
PubMed: 35294281
DOI: 10.1073/pnas.2122197119 -
Scientific Reports Mar 2022Biogenic amorphous calcium carbonate (ACC) is typically metastable and can rapidly transform through aging, dehydration, and/or heating to crystalline calcium carbonate....
Biogenic amorphous calcium carbonate (ACC) is typically metastable and can rapidly transform through aging, dehydration, and/or heating to crystalline calcium carbonate. Gaining insight into its structure and properties is typically hampered by its tendency to crystallize over short time periods once isolated from the host organism, and also by the small quantities that are usually available for study. Here we describe an exceptionally stable hydrated ACC (HACC) precipitated by the cosmopolitan slime mold Fuligo septica (L.) F.H. Wigg. (1780). A single slime mold can precipitate up to a gram of HACC over the course of one night. Powder x-ray diffraction (XRD) patterns, transmission electron microscopy images, infrared absorption spectra, together with the lack of optical birefringence are consistent with an amorphous material. XRD simulations, supported by thermogravimetric and evolved gas analysis data, are consistent with an intimate association of organic matter with ~ 1-nm-sized ACC units that have monohydrocalcite- and calcite-like nano-structural properties. It is postulated that this association imparts the extreme stability of the slime mold HACC by inhibiting loss of HO and subsequent crystallization. The composition, structure, and thermal behavior of the HACC precipitated by F. septica collected over 8000 km apart and in markedly different environments, suggests a common structure, as well as similar biochemical and biomineralization mechanisms.
Topics: Animals; Calcium Carbonate; Chemical Phenomena; Crystallization; Dogs; Myxomycetes; Physarida; X-Ray Diffraction
PubMed: 35256681
DOI: 10.1038/s41598-022-07648-9 -
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