RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Regions of the Didymium iridis mitochondrial genome were identified with similarity to typical mitochondrial genes; however, these regions contained numerous stop codons. We used RT-PCR and DNA sequencing to determine whether, through RNA editing, these regions were transcribed into mRNAs that could encode functional proteins. Ten putative gene regions were examined: atp1, atp6, atp8, atp9, cox1, cox2, cytb, nad4L, nad6, and nad7. The cDNA sequences of each gene could encode a functional mitochondrial protein that was highly conserved compared with homologous genes. The type of editing events and editing sequence features were very similar to those observed in the homologous genes of Physarum polycephalum, though the actual editing locations showed a variable degree of conservation. Edited sites were compared with encoded sites in D. iridis and P. polycephalum for all 10 genes. Edited sequence for a portion of the cox1 gene was available for six myxomycetes, which, when compared, showed a high degree of conservation at the protein level. Different types of editing events showed varying degrees of site conservation with C-to-U base changes being the least conserved. Several aspects of single C insertion editing events led to the preferential creation of hydrophobic amino acid codons that may help to minimize adverse effects on the resulting protein structure.     

Phylogenetic position of Dictyostelium inferred from multiple protein data sets

The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.Correspondence to: T. Miyata     

Isolation and Characterization of the Putative Photoreceptor for Phototaxis in Amoebae of the Cellular Slime Mold,Dictyostelium discoideum

Amoebae of the cellular slime mold Dictyostelium discoideum (strain AX2) produce a pigment with an absorption spectrum that closely resembles the action spectrum for phototaxis. The protein-pigment complex was isolated and purified by sucrose gradient centrifugation, fast protein liquid chromatography (FPLC) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). It is tightly membrane-bound and the bulk of it is located in the mitochondrial membrane fraction, while a small part is located in the cytoplasmic membrane fraction, as indicated by marker enzyme tests (succinate dehydrogenase for mitochondria and alkaline phosphatase for the cytoplasmic membrane). It is speculated that the pigment bound to the cytoplasmic membrane acts as photoreceptor and that bound to the mitochondria operates as a shading pigment in the light direction perception mechanism of Dictyostelium amoebae.     

Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

ABSTRACT. The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages—amoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark‐spored (i.e. Stemonitida and Physarida) Myxogastria (including a new “Hyperamoeba”/Didymium sequence) and a ～400‐bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.     

Dental Mold: A Novel Formulation to Treat Common Dental Disorders

Oral administration of antibiotics to treat dental problems mostly yields slow actions due to slow onset and hepatic “first-pass.” Again, commonly used dental paints are generally washed out by saliva within few hours of application. To overcome the challenges, polymeric molds to be placed on an affected tooth (during carries and gum problems) were prepared and evaluated in vitro for sustained drug release for prolonged local action. Here, amoxicillin trihydrate and lidocaine hydrochloride were used as model drugs. Dental molds were prepared using corn zein, carbopol 934 P, gum karaya powder, and poloxamer 407 by mixing and solvent evaporation technique. Different physicochemical evaluation studies such as tooth adhesion test, surface pH, swelling index, and drug-distribution pattern were carried out. Percentage swelling varied from 56% to 93%. Average tooth adhesion strength and mean initial surface pH of the formulations were 50 g and 6.5, respectively. As assessed by scanning electron microscopy, drug distribution was uniform throughout the matrix. Cumulative percentage release of lidocaine hydrochloride and amoxicillin trihydrate in simulated saliva were 98% and 50%, respectively. In vitro drug-release studies revealed the sustained-release patterns of the drugs in simulated saliva at least for 24 h. The stability study shows that the drugs were stable in the formulations following the conditions as per ICH guideline. The formulation is a novel approach to deliver the drug(s) for a prolonged period for local action upon its application on an affected tooth.     

Patterns of occurrence of corticolous myxomycetes on white oak trees of two different size classes

Data were obtained on the assemblages of corticolous myxomycetes (plasmodial slime moulds or myxogastrids) associated with the bark surface of living white oak (Quercus alba) trees from two different size classes. Bark samples obtained from larger trees were characterized by higher values for both species richness and diversity when compared to those collected from smaller trees. This might have been expected since the former possess a larger surface area and presumably have persisted over a longer period of time. However, the myxomycete assemblage associated with smaller trees was appreciably different and did not simply represent a depauperate version of the assemblage associated with larger trees. This suggests that the differences observed between size classes cannot be simply attributed to size alone.     

Microbial Communities Associated with Tree Bark Foliose Lichens: A Perspective on their Microecology

Tree‐bark, foliose lichens occur widely on a global scale. In some locales, such as forests, they contribute a substantial amount of biomass. However, there are few research reports on microbial communities including eukaryotic microbes associated with foliose lichens. Lichens collected from tree bark at 11 locations (Florida, New York State, Germany, Australia, and the Arctic) were examined to determine the density and C‐biomass of bacteria and some eukaryotic microbes, i.e. heterotrophic nanoflagellates (HNF) and amoeboid protists. A rich microbial diversity was found, including large plasmodial slime molds, in some cases exceeding 100 μm in size. The densities of HNF and amoeboid protists were each positively correlated with densities of bacteria, r = 0.84 and 0.80, respectively (p < 0.01, N = 11 for each analysis) indicating a likely bacterial‐based food web. Microbial densities (number/g lichen dry weight) varied markedly across the geographic sampling sites: bacteria (0.7–13.1 × 10⁸), HNF (0.2–6.8 × 10⁶) and amoeboid protists (0.4–4.6 × 10³). The ranges in C‐biomass (μg/g lichen dry weight) across the 11 sites were: bacteria (8.8–158.5), HNF (0.03–0.85), and amoeboid protists (0.08–540), the latter broad range was due particularly to absence or presence of large slime mold plasmodia.     

簇生岐柄菌的超微形态学研究

为揭示网柄细胞状黏菌的超微结构特征,对簇生岐柄菌Cavendericfasciculata生活史过程中的孢子、黏变形体和柄细胞3种类型的细胞超微结构进行系统观察,并与目前仅知的3种网柄细胞状黏菌的超微结构进行比较.结果表明:簇生岐柄菌C.fasciculata的孢子、黏变形体和柄细胞内均有线粒体结构,随着细胞分化,线粒...     

Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa)

Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark‐spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter‐ and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless‐modified Echinosteliales. We discuss possible evolutionary pathways in dark‐spored Myxomycetes and propose a taxonomic update.     

First Records and Microhabitat Assessment of Protostelids in the Aberdare Region, Central Kenya

ABSTRACT. A rapid assessment survey on the occurrence and distribution of protosteloid amoebae was carried out in central Kenya. Samples of dead plant materials were collected from 46 study sites (each 20 × 20 m) situated along an elevation gradient (1,785–3,396 m) that encompassed five major land use/cover types. Twenty-four species and subspecific taxa were recovered and included 23 protostelids and one minute myxomycete, often included in surveys for protostelids. All of these were the first records for Kenya, and six were new for Africa. Numbers of taxa were highest in ground litter and aerial litter microhabitats (20 taxa each) and lowest on aerial bark (10) and ground bark (7). Relative species abundance was greatest in aerial litter, moderate in ground litter, and low on aerial and ground bark microhabitats. The most frequently occurring species on ground litter were Schizoplasmodiopsis pseudoendospora, Schizoplasmodiopsis amoeboidea , and Protostelium mycophaga var. mycophaga , whereas the most common species on aerial litter were P. mycophaga var. mycophaga and Soliformovum irregularis . Species richness and abundance decreased with increasing elevation.