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Scientific Reports Nov 2022This study presents the Slime Mold Algorithm (SMA) to solve the time-cost-quality trade-off problem in a construction project. The proposed SMA is a flexible and...
This study presents the Slime Mold Algorithm (SMA) to solve the time-cost-quality trade-off problem in a construction project. The proposed SMA is a flexible and efficient algorithm in exploration and exploitation to reach the best optimal solution to process the input model's data. This paper aims to discuss and solve the optimization problem and compare the evaluation with other algorithms such as Opposition-based Multiple Objective Differential Evolution, Non-dominated sorting genetic algorithm, Multiple objective particle swarm optimization, Multiple objective differential evolution and Chaotic initialized multiple objective differential evolution (CAMODE) to verify the efficiency and potential of the proposed algorithm. According to the analysis results, the SMA model generated a diversification measure for case studies, producing superior outcomes to those of previous algorithms.
Topics: Artificial Intelligence; Problem Solving; Algorithms; Physarum polycephalum; Cell Movement
PubMed: 36418454
DOI: 10.1038/s41598-022-24668-7 -
Mycologia 2023is one of the most widely known myxomycete species and the first-ever discovered representative of this group. Using 687 original DNA sequences from 330 herbarium...
is one of the most widely known myxomycete species and the first-ever discovered representative of this group. Using 687 original DNA sequences from 330 herbarium specimens from Europe, Asia, North and Central America, and Australia, we constructed the first detailed phylogenies of the genus , based on two independently inherited genetic markers, the ribosome small subunit 18S rRNA nuclear gene (18S rDNA) and the mitochondrial cytochrome oxidase subunit I gene (COI). In both phylogenies, appeared to be a polyphyletic group, represented by numerous clades. The four other recognized species of the genus (, and ) are scattered between branches corresponding to . A barcode gap analysis revealed 60 18S rDNA phylogroups of , which are distant from each other not less than from other species of the genus . For 18 of these phylogroups with both 18S rDNA and COI sequences available, recombination patterns were analyzed to test for reproductive isolation. In contrast to the results of a simulation assuming panmixis, no crossing between ribosomal and mitochondrial phylogroups was found, thus allowing the conclusion that all tested phylogroups represent biospecies. More than one third (39.6%) of the studied specimens share a single 18S rDNA phylogroup, which we consider to be s. str. This group displays the broadest geographic distribution and the highest intraspecific genetic variability. Nearly all (93.3%) of the remaining non-singleton 18S rDNA phylogroups are restricted to certain continents or even regions. At the same time, various reproductively isolated phylogroups occur sympatric at a given location.
Topics: Sequence Analysis, DNA; Myxomycetes; Genetic Markers; RNA, Ribosomal, 18S; DNA, Ribosomal; Phylogeny
PubMed: 36399690
DOI: 10.1080/00275514.2022.2133526 -
Marine Drugs Sep 2022The marine environment is important yet generally underexplored. It contains new sources of functional constituents that can affect various pathways in food processing,... (Review)
Review
The marine environment is important yet generally underexplored. It contains new sources of functional constituents that can affect various pathways in food processing, storage, and fortification. Bioactive secondary metabolites produced by marine microorganisms may have significant potential applications for humans. Various components isolated from disparate marine microorganisms, including fungi, microalgae, bacteria, and myxomycetes, showed considerable biological effects, such as anticancer, antioxidant, antiviral, antibacterial, and neuroprotective activities. Growing studies are revealing that potential anticancer effects of marine agents could be achieved through the modulation of several organelles. Mitochondria are known organelles that influence growth, differentiation, and death of cells via influencing the biosynthetic, bioenergetic, and various signaling pathways related to oxidative stress and cellular metabolism. Consequently, mitochondria play an essential role in tumorigenesis and cancer treatments by adapting to alterations in environmental and cellular conditions. The growing interest in marine-derived anticancer agents, combined with the development and progression of novel technology in the extraction and cultures of marine life, led to revelations of new compounds with meaningful pharmacological applications. This is the first critical review on marine-derived anticancer agents that have the potential for targeting mitochondrial function during tumorigenesis. This study aims to provide promising strategies in cancer prevention and treatment.
Topics: Humans; Antioxidants; Mitochondria; Antineoplastic Agents; Anti-Bacterial Agents; Antiviral Agents; Neoplasms; Carcinogenesis; Biological Products; Aquatic Organisms
PubMed: 36286449
DOI: 10.3390/md20100625 -
Mobile DNA Oct 2022Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion....
BACKGROUND
Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes.
RESULTS
A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3' polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3' overhang at the intron insertion site.
CONCLUSIONS
The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.
PubMed: 36209098
DOI: 10.1186/s13100-022-00280-4 -
Neuroscience Letters Nov 2022The inhibition hypothesis advocated by Ekman (1985) states when an emotion is concealed or masked, the true emotion is manifested as a micro-expression (ME) which is a...
The inhibition hypothesis advocated by Ekman (1985) states when an emotion is concealed or masked, the true emotion is manifested as a micro-expression (ME) which is a fleeting expression lasting for 40 to 500 ms. However, research about the inhibition hypothesis of ME from the perspective of electrophysiology is lacking. Here, we report the electrophysiological evidence obtained from an electroencephalography (EEG) data analysis method. Specifically, we designed an ME elicitation paradigm to collect data of MEs of positive emotions and EEG from 70 subjects, and proposed a method based on tensor component analysis (TCA) combined with the Physarum network (PN) algorithm to characterize the spatial, temporal, and spectral signatures of dynamic EEG data of MEs. The proposed TCA-PN methods revealed two pathways involving dorsal and ventral streams in functional brain networks of MEs, which reflected the inhibition processing and emotion arousal of MEs. The results provide evidence for the inhibition hypothesis from an electrophysiological standpoint, which allows us to better understand the neural mechanism of MEs.
Topics: Humans; Brain Mapping; Physarum; Electroencephalography; Brain; Algorithms
PubMed: 36195299
DOI: 10.1016/j.neulet.2022.136897 -
Mycologia 2022Type specimens of four species of (Myxomycetes, Amoebozoa)-, and have been studied using an integrative approach including application of traditional taxonomy methods,...
Importance of type specimen study for understanding genus boundaries-taxonomic clarifications in based on integrative taxonomy approach leading to resurrection of the old genus .
Type specimens of four species of (Myxomycetes, Amoebozoa)-, and have been studied using an integrative approach including application of traditional taxonomy methods, i.e., morphological study under stereoscopic and compound microscopes, detailed analysis of micromorphological characters using scanning electron microscopy, and molecular analysis by way of Sanger sequencing of molecular markers (nuc 18S rDNA and elongation factor 1-alpha gene, ). Results of the study revealed that is conspecific with is a malformed specimen of , whereas and represent two well-defined morphologically and genetically separate species. Phylogeny of Physarales shows the polyphyletic character of the genus . The type species of clusters together with , whereas other representatives of this genus form a monophyletic, well-supported clade. The species from this clade are proposed to belong to the genus described by A. Corda in 1842 that is resurrected and emended here. Nine species of are transferred to . A new key to Didymiaceae including is provided.
Topics: Myxomycetes; DNA, Ribosomal; Phylogeny
PubMed: 36166209
DOI: 10.1080/00275514.2022.2109914 -
Protist Oct 2022Spore size enables dispersal in plasmodial slime molds (Myxomycetes) and is an important taxonomic character. We recorded size and the number of nuclei per spore for 39...
Spore size enables dispersal in plasmodial slime molds (Myxomycetes) and is an important taxonomic character. We recorded size and the number of nuclei per spore for 39 specimens (colonies of 50-1000 sporocarps) of the nivicolous myxomycete Physarum albescens, a morphologically defined taxon with several biological species. For each colony, three sporocarps were analyzed from the same spore mount under brightfield and DAPI-fluorescence, recording ca. 14,000 spores per item. Diagrams for spore size distribution showed narrow peaks of mostly uninucleate spores. Size was highly variable within morphospecies (10.6-13.5 µm, 11-13%), biospecies (3-13%), even within spatially separated colonies of one clone (ca. 8%); but fairly constant for a colony (mean variation 0.4 µm, ca. 1.5%). ANOVA explains most of this variation by the factor locality (within all colonies: 32.7%; within a region: 21.4%), less by biospecies (13.5%), whereas the contribution of intra-colony variation was negligible (<0.1%). Two rare aberrations occur: 1) multinucleate spores and 2) oversized spores with a double or triple volume of normal spores. Both are not related to each other or limited to certain biospecies. Spore size shows high phenotypic plasticity, but the low variation within a colony points to a strong genetic background.
Topics: Myxomycetes; Physarum; Spores, Protozoan; Cell Nucleus
PubMed: 36037769
DOI: 10.1016/j.protis.2022.125904 -
Theory in Biosciences = Theorie in Den... Sep 2022Fifty years ago, the enigmatic Brazilian myxomycete-species Didymium aquatile was described and analyzed with respect to the structure of the plasmodium and its spores....
Fifty years ago, the enigmatic Brazilian myxomycete-species Didymium aquatile was described and analyzed with respect to the structure of the plasmodium and its spores. In this study, we compare this rare plasmodial slime mold with another, temporarily aquatic taxon from Europe, Didymium nigripes. Phenotypic plasticity of D. nigripes was investigated under various environmental conditions. Large changes in the morphology of the plasmodia were observed. For species identification, characteristics of the fruiting bodies are key features. However, Didymium aquatile was only characterized by its "abnormal" plasmodia, but no molecular data were available. Here, we analyzed DNA-sequences of 22 species of the genera Didymium and Diderma with a focus on this South American taxon via molecular genetics. A comparison of 18S-rDNA-sequences from D. aquatile and 21 other Didymium (and Diderma)-species indicates that D. aquatile is a reproductively isolated morpho-species. Phenotypic plasticity of D. nigripes is documented with respect to plasmodium morphology and the formation of fruiting bodies, as an example of an adaptation of a terrestrial species to aquatic environments.
Topics: Adaptation, Physiological; Myxomycetes; Phylogeny
PubMed: 36029433
DOI: 10.1007/s12064-022-00375-9 -
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 -
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