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At least 19 recordsLinked to original sources

Species richness and ecological characterization of myxomycetes and myxomycete-like organisms in the canopy of a temperate deciduous forest.

The ecological community of myxomycetes and myxomycete-like organisms (MMLO) in the canopy of living deciduous trees was studied in a riparian deciduous forest at Leipzig, Germany. A systematic survey carried out with a total of 146 moist chamber cultures resulted in 386 records of 37 taxa, with 32 myxomycetes, two myxobacteria, two protostelids and the fruit body forming ciliate Sorogena stoianovitchae, the latter recorded for the first time for Europe. With 94% of all cultures positive for MMLO, these organisms are present consistently in the investigated sections of white-rotten twigs attached to living trees at 10-30 m above the ground. Our sampling recovered a majority of the likely species, with 37 out of the 42-45 predicted according to a species-accumulation curve and two other estimators of species richness. Nonmetric multidimensional scaling revealed pH, water-holding capacity and stage of decay to explain most of the variation in species distribution. Arcyria cinerea and Perichaena depressa as the most common species occurred in 32% and 29% of all samples, respectively. Viewing the sampled twigs as habitat islands and a single spore as sufficient to establish a population, a simulation program assuming a random spore rain estimated an average of 0.4 and 0.35 spore hits per twig as necessary to explain the observed frequencies. This is matched by the potential productivity of the substrate. All fruit bodies from the cultured twigs would be able to create a spore rain of 86 (A. cinerea) or 40 (P. depressa) spore hits per twig when dispersed evenly over the plot. The terminal fall velocity of spores was measured, revealing that it took about 5 h for a spore to land (30 m) in still air and indicating high dispersal ability for canopy-inhabiting MMLO.

Animals↗

Isolation of bioactive natural products from myxomycetes.

The Myxomycetes (true slime molds) are an unusual group of primitive organisms that may be assigned to one of the lowest classes of eukaryotes. As their fruit bodies are very small and it is very difficult to collect much quantity of slime molds, few studies have been made on the chemistry of myxomycetes. Cultivation of the plasmodium of myxomycetes in a practical scale for natural products chemistry studies is known only for very limited species. Here is described a review on the recent results on isolation of bioactive natural products from myxomycetes obtained in these two years in the laboratories. Spore germination experiments were studied of hundreds of field-collected myxomycetes collected in Japan and succeeded in laboratory culture of plasmodia of several myxomycetes in a practical scale for natural products chemistry studies. As a result, pyrroloiminoquinones, polyene yellow pigments, and a peptide lactone from cultured plasmodia of Didymium iridis, Physarum rigidum and P. melleum, respectively were isolated. New naphthoquinone pigments, cycloanthranilylprolines, tyrosine-kinase inhibitory bisindoles, and a cytotoxic triterpenoid aldehyde lactone were also isolated from field-collected fruit bodies of Cribraria purpurea, Fuligo candida, Tubifera casparyi, and Tubifera dimorphotheca, respectively.

Animals↗

Observations on an ATP-sensitive protein system from the plasmodia of a myxomycete.

1. Extracts of the plasmodia of the myxomycete, Physarum polycephalum, exhibit reversible decreases in viscosity in response to the addition of ATP under appropriate conditions. The protoplasm material prepared by extraction with KCl solution can apparently exist in either a high or a low viscosity state. As prepared, it is in the low viscosity condition. Rapid and extensive increases in viscosity of the extract are brought about by addition of AMP, inorganic phosphate, or, under certain conditions, of ATP. Only after the high viscosity state has been attained does addition of appropriate quantities of ATP cause a reversible decrease in viscosity. 2. The active principle of crude plasmodial extracts may be concentrated by fractional precipitation with ammonium sulfate and is found in the fraction precipitated between 30 and 40 per cent saturation. This material possesses a higher viscosity than does the original crude extract and is apparently in the high viscosity state since the addition of ATP causes an immediate reversible decrease in viscosity. 3. The ATP-sensitive fraction of myxomycete plasmodia possesses a viscosity which is dependent upon its previous thermal treatment. Extracts incubated at 0 degrees for a period of a few hours increase greatly in viscosity when they are returned to 24.5 degrees . This increased viscosity is structural in nature, is destroyed by mechanical agitation of the solution, and may be reversibly destroyed by addition of ATP. 4. It is suggested that the ATP-responsive protein of myxomycete plasmodia may be related to sol-gel transformations which have been observed in intact plasmodia and may participate in the protoplasmic streaming of the intact organism. This suggestion is based upon the following facts: (a) the protoplasmic streaming of myxomycete plasmodia is increased by microinjection of ATP; (b) the gel portion of the cytoplasm at the site of the microinjection of ATP is extensively converted to the sol state. The changes in structure of the intact cytoplasm are thus similar in nature to the changes exhibited in response to ATP by the purified ATP-sensitive protein. 5. The ATP-sensitive protein of myxomycete plasmodia appears to undergo reversible aggregation to form a high viscosity state. The function of ATP is to break down the aggregates thus formed. Since a specific ATPase activity is associated with the purified material, added ATP is gradually destroyed and recovery of viscosity attends the spontaneous reconstitution of aggregates.

Adenosine Triphosphate↗

Short-read genome skimming enables molecular barcoding of old myxomycete collections.

This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. We successfully retrieved partial sequences of the standard marker gene (nucSSU) in all cases, as well as additional markers (mtSSU, EF1a, and COI) for certain collections. Altogether, 28 genes were recognized in the studied material. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming confirmedly (matching sequences in the NCBI nucleotide database) or potentially (no-hit fraction) from myxomycetes, regardless of specimen age. In addition to target DNA, we revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. Thus, even in old collections, metagenomic data still carry information regarding the substrate upon which the myxomycete developed. The results demonstrate that short-read genome skimming may help to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method overcomes the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.

Amoebozoa↗

Structure and evolution of myxomycete nuclear group I introns: a model for horizontal transfer by intron homing.

We have examined five nuclear group I introns, located at three different positions in the large subunit ribosomal RNA (LSU rRNA) gene of the two myxomycete species, Didymium iridis and Physarum polycephalum. Structural models of intron RNAs, including secondary and tertiary interactions, are proposed. This analysis revealed that the Physarum intron 2 contains an unusual core region that lacks the P8 segment, as well as several of the base-triples known to be conserved among group I introns. Structural and evolutionary comparisons suggest that the corresponding introns 1 and 2 were present in a common ancestor of Didymium and Physarum, and that the five introns in LSU rRNA genes of these myxomycetes were acquired in three different events. Evolutionary relationships, inferred from the sequence analysis of several different nuclear group I introns and the ribosomal RNA genes of the intron-harbouring organisms, strongly support horizontal transfer of introns in the course of evolution. We propose a model that may explain how myxomycetes in natural environments obtained their nuclear group I introns.

Animals↗

Evolution of four types of RNA editing in myxomycetes.

The myxomycete Physarum polycephalum requires extensive RNA editing to create functional mitochondrial transcripts. The cytochrome c oxidase subunit 1 (col) transcript exhibits a combination of editing forms not found together in any other eukaryotic RNA: 66 insertions of ribonucleotides (59 Cs, a single U, and three mixed dinucleotides) as well as base conversion of four Cs to Us (Gott et al., J Biol Chem, 1993, 268:25483-25486). Through a phylogenetic survey of col DNA genes and RNA transcripts in representative myxomycetes, we have decoupled the four types of editing in this lineage. Some myxomycetes share insertional editing with P. polycephalum, yet lack C--> U conversion, consistent with previous reports of separation of insertional and base conversion editing in P. polycephalum extracts (Visomirski-Robic & Gott, RNA, 1995, 3:821-837). Most remarkably, we detect unique evolutionary histories of the three different types of insertional editing, though these have been indistinguishable in vitro. For example, Clastoderma debaryanum exhibits insertions of Us, but not Cs or dinucleotides.

Amino Acid Sequence↗

Myxomycetes from upper Egypt.

The results of the first inventory of Myxomycetes from the subtropical region Upper Egypt are reported. The substrates were wood, bark of living and dead tree and leaf litter. 20 species belonging to 17 genera of Myxomycetes were identified. Wood was the best substrate for Myxomycetes colonization. Ceratiomyxa fruticulosa, Didymiun melanospermum, Licea biforis and Lycogala epidendrum were the most common species. Brief description and classification of species are provided.

Egypt↗

The molecular evolution and structural organization of self-splicing group I introns at position 516 in nuclear SSU rDNA of myxomycetes.

Group I introns are relatively common within nuclear ribosomal DNA of eukaryotic microorganisms, especially in myxomycetes. Introns at position S516 in the small subunit ribosomal RNA gene are particularly common, but have a sporadic occurrence in myxomycetes. Fuligo septica, Badhamia gracilis, and Physarum flavicomum, all members of the family Physaraceae, contain related group IC1 introns at this site. The F. septica intron was studied at the molecular level and found to self-splice as naked RNA and to generate full-length intron RNA circles during incubation. Group I introns at position S516 appear to have a particularly widespread distribution among protists and fungi. Secondary structural analysis of more than 140 S516 group I introns available in the database revealed five different types of organization, including IC1 introns with and without His-Cys homing endonuclease genes, complex twin-ribozyme introns, IE introns, and degenerate group I-like introns. Both intron structural and phylogenetic analyses indicate a multiple origin of the S516 introns during evolution. The myxomycete introns are related to S516 introns in the more distantly related brown algae and Acanthamoeba species. Possible mechanisms of intron transfer both at the RNA- and DNA-levels are discussed in order to explain the observed widespread, but scattered, phylogenetic distribution.

DNA, Ribosomal↗

RNA reprogramming of alpha-mannosidase mRNA sequences in vitro by myxomycete group IC1 and IE ribozymes.

Trans-splicing group I ribozymes have been introduced in order to mediate RNA reprogramming (including RNA repair) of therapeutically relevant RNA transcripts. Efficient RNA reprogramming depends on the appropriate efficiency of the reaction, and several attempts, including optimization of target recognition and ribozyme catalysis, have been performed. In most studies, the Tetrahymena group IC1 ribozyme has been applied. Here we investigate the potential of group IC1 and group IE intron ribozymes, derived from the myxomycetes Didymium and Fuligo, in addition to the Tetrahymena ribozyme, for RNA reprogramming of a mutated alpha-mannosidase mRNA sequence. Randomized internal guide sequences were introduced for all four ribozymes and used to select accessible sites within isolated mutant alpha-mannosidase mRNA from mammalian COS-7 cells. Two accessible sites common to all the group I ribozymes were identified and further investigated in RNA reprogramming by trans-splicing analyses. All the myxomycete ribozymes performed the trans-splicing reaction with high fidelity, resulting in the conversion of mutated alpha-mannosidase RNA into wild-type sequence. RNA protection analysis revealed that the myxomycete ribozymes perform trans-splicing at approximately similar efficiencies as the Tetrahymena ribozyme. Interestingly, the relative efficiency among the ribozymes tested correlates with structural features of the P4-P6-folding domain, consistent with the fact that efficient folding is essential for group I intron trans-splicing.

Animals↗

The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster.

The genus Schenella has proven difficult to classify since its description as a new genus in 1911. Macbride placed it with the Myxomycetes but it was unclear with which myxomycete, if any, it should be grouped. Recent identification of abundant samples of Schenella has aided a re-evaluation of its classification as a myxomycete. Morphological evidence based on light and scanning electron microscopy of recently collected specimens and on the type specimen of Macbride suggested that it might be synonymous with the gasteromycete Pyrenogaster Analysis of DNA sequences from freshly isolated samples indicates that the genus Schenella is related closely to an anciently diverged, monophyletic group of fungi that includes several gasteromycete genera, among them Geastrum, Sphaerobolus and Pseudocolus. Comparisons of the morphology and DNA sequences of authentically identified specimens of Pyrenogaster atrogleba indicate that it is synonymous with Schenella simplex. The nomenclatural implications of this discovery are discussed.

Abies↗

Hematin--requiring plasmodial myxomycete.

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.

Animals↗

Group I twintrons: genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs.

Protists are unicellular eukaryotes which represent a significant fraction of the global biodiversity. The myxomycete Didymium and the schizopyrenid amoeboflagellate Naegleria are distantly related protists. However, we have noted several striking similarities in life cycle, cell morphology, and ribosomal DNA organization between these organisms. Both have multicopy nuclear extrachromosomal ribosomal DNAs. Here the small subunit ribosomal RNA genes are interrupted by an optional group I twintron, a novel category among the group I introns. Group I twintrons are mobile self-splicing introns of 1.3-1.4 kb in size, with a complex organization at the RNA level. A group I twintron consists of two distinct ribozymes (catalytic RNAs) with different functions in RNA processing, and an open reading frame encoding a functional homing endonuclease--all with prospects of application as molecular tools in biotechnology. Updated RNA secondary structure models of group I twintrons, as well as an example of in vitro ribozyme activity, are presented. We suggest that the group I twintrons have been independently established in myxomycetes and schizopyrenid amoeboflagellates by horizontal gene transfer due to a combination of the phagocytotic behavior in natural environments and the extrachromosomal multicopy nature of ribosomal DNA.

Animals↗

Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes.

RNA editing has a major impact on the genes and genomes that it modifies. Editing by insertion, deletion and base conversion exists in nuclear, mitochondrial and viral genomes throughout the eukaryotic lineage. Editing was first discovered in kinetoplastids, and recent work has resulted in the characterization of some components of the editing machinery. Two proteins with ligase activity have been identified in Trypanosoma brucei, and other proteins in the editosome complex are yielding to the probe of research. A second group of protists, myxomycetes, are unique in their use of four different types of editing within a single transcript. Phylogenetic analysis of editing in representative myxomycetes revealed a different history of the four types of editing in this lineage. Development of a soluble in vitro editing system has provided further support for the co-transcriptional nature of editing in Physarum polycephalum, and will certainly provide future opportunities for understanding this mysterious process.

Cytidine↗

Laboratory culture of the myxomycetes: formation of fruiting bodies of Didymium bahiense and its plasmodial production of Makaluvamine A.

Laboratory cultures of more than 100 strains of myxomycetes were investigated, and the spore germinations of six strains were observed. The plasmodium of the myxomycete Didymium bahiense was cultured on oatmeal agar plates in a laboratory. The formation of fruiting bodies was observed in a plate culture. From the cultured organisms, a marine sponge metabolite, makaluvamine A (1), was isolated and identified on the basis of spectral data.

Animals↗

Dihydrolindbladiones, three new naphthoquinone pigments from a myxomycete Lindbladia tubulina.

Three new naphthoquinone pigments, 6,7-dimethoxydihydrolindbladione (1), dihydrolindbladione (2), and 6-methoxydihydrolindbladione (3), have been isolated from a myxomycete Lindbladia tubulina, and their structures were elucidated by spectral data. Compound 3 appreciably exhibited a reversal effect of multidrug resistance. Lindbladione (4), the major pigment of this myxomycete, was also isolated from Cribraria intricata.

Drug Resistance, Multiple↗

Methionine metabolism of the myxomycete Physarum polycephalum.

Daniel, John W. (University of Wisconsin, Madison), and Karlee Babcock. Methionine metabolism of the myxomycete Physarum polycephalum. J. Bacteriol. 92:1028-1035. 1966.-Previous studies have shown that Physarum polycephalum requires exogenous methionine for growth, but not cysteine, folic acid, or vitamin B(12). Methionine can also serve as the sole source of sulfur for all cellular requirements, without limiting the growth rate. S-methyl-l-cysteine, 2-hydroxy-4-methiol butyric acid, S-adenosyl-l-methionine, and methionine peptides were the only compounds supporting growth, when substituted for methionine. Other methionine analogues, methyl donors in combination with homocysteine, and intermediates of the cystathionine pathway were not active. Ethionine and S-ethyl cysteine were good methionine antagonists. This myxomycete is apparently unable to synthesize the methyl or S-methyl group, although it still appears able to transmethylate, at least from S-methyl cysteine, and probably from S-adenosyl methionine, which can also serve as a source of adenine.

Adenine↗

A simple rapid procedure for obtaining axenic cultures from monoxenic cultures of myxomycete plasmodia.

Axenic culture of myxomycete plasmodia has been attempted from time to time by various authors, but with very little success. From over 500 known species of myxomycetes, fewer than 20 species have been reported in axenic culture to date, including axenic myxamoebal cultures. In these cultures, the plasmodia required either complex media, or a killed bacterial supplement for growth. Furthermore, the time required for attaining the axenic state varied from several months to years. In the present study, a simple, rapid procedure has been developed to render monoxenic plasmodial cultures axenic. This procedure is based on our discovery that plasmodia have certain unusual substrate preferences that are inhibitory to the associated bacteria using Physarella oblonga as a model. The presence or absence of the bacteria could be ascertained through incubation in four different bacteriological media and by the use of a differential staining technique.

Animals↗

Cycloanthranilylproline-derived constituents from a myxomycete Fuligo candida.

Cycloanthranilylproline (1) and its derivatives (2--4) were isolated from field-collected fruit-bodies of a myxomycete Fuligo candida and their structures were elucidated by spectral data. Compound 4, which was contained in the water-soluble fraction of the extract of this myxomycete, was unstable and quite susceptible to decarboxylation to yield compound 2, which was a major constituent of the EtOAc-soluble fraction of this extract.

Isatis↗