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Amoebae
Kinds of Amoebae Terms modified by Amoebae Selected AbstractsPolarizable atomic multipole X-ray refinement: application to peptide crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Michael J. Schnieders Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA,IAS model lowered Rfree by 20,40% relative to the original spherically symmetric scattering model. [source] The SSU rDNA Coding Region of a Filose Amoeba Contains a Group I Intron Lacking the Universally Conserved G at the 3,-Terminus,THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2000DEBASHISH BHATTACHARYA ABSTRACT. We sequenced small subunit ribosomal DNA (rDNA) PCR-fragments of sizes 2.3 kb and 2.9 kb isolated from a culture of the red alga, Porphyru spiralis var. spiralis. Phylogenetic analysis of the 2.3-kb fragment showed that it encoded the sequence of a contaminant filose amoeba. The Nuclearia -like amoeba (named strain N-Por) was identified with scanning electron microscopy. Its rDNA sequence was positioned with strong bootstrap support within a diverse protist assemblage that includes filose amoebae, chlor-arachniophytes, cercomonads, and Plasmodiophora brussicae. The rDNA of N-Por contained a group I intron at the conserved 943 position that remarkably, had a U at the 3,-terminus rather than the universally conserved G. [source] Influence of Environmental Heterogeneity on the Structure of Testate Amoebae (Protozoa, Rhizopoda) Assemblages in the Plankton of the Upper Paraná River Floodplain, BrazilINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 2 2003Luiz Felipe Machado Velho Abstract In freshwater environments, testate amoebae are usually found associated with macrophytes and sediments and many studies have suggested that their occurrence in plankton samples is accidental. This implies that predictable patterns detected in planktonic assemblages should not be observed in testate amoebae assemblages. This hypothesis was tested in this study. Plankton samples were collected from different environments in the Upper Paraná River floodplain. Results show that patterns in species composition and abundance of testate amoebae are predictable, and that dominant species tend to present characteristic shell morphology in hydrologically different environments. We suggest that testate amoebae must be routinely included in plankton ecology studies, at least in floodplain environments. [source] Studies on amoebae and cysts associated with the isolation of Spongospora subterranea f.sp. subterranea in vitroPLANT PATHOLOGY, Issue 4 2001X.-S. Qu New evidence is presented to support the contention that the amoeba/cyst colonies isolated from surface-sterilized Spongospora subterranea f.sp. subterranea -infected potato tubers and spore balls have a saprophytic phase but are contaminants and not S. subterranea. Amoebae isolated from infected tissues and spore balls formed colonies associated with bacteria on 1% water agar at 18°C and encysted after 5,7 days. These cysts were morphologically distinct from the resting spores of S. subterranea and were formed singly or in a layer, unlike the spore ball (cystosorus) of S. subterranea. Amoebae, cysts and mixtures of amoebae and cysts in primary, secondary and tertiary subcultures failed to infect tomato roots. PCR amplification of DNA from amoebae, cysts and spore balls using the S. subterranea -specific primer pair SsF/R generated a 434-bp product from S. subterranea spore balls only and not from amoebae or cysts. When an amoeba/cyst-specific primer pair AmF/R was designed and used for PCR amplification, a single 411-bp product was generated from DNA of amoebae and cysts, but not from DNA of S. subterranea spore balls. These results are discussed in relation to earlier reports claiming the successful isolation of S. subterranea and other plasmodiophorids in vitro. [source] Effects of Altered Temperature and Precipitation on Desert Protozoa Associated with Biological Soil CrustsTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2006BRIAN J. DARBY ABSTRACT. Biological soil crusts are diverse assemblages of bacteria, cyanobacteria, algae, fungi, lichens, and mosses that cover much of arid land soils. The objective of this study was to quantify protozoa associated with biological soil crusts and test the response of protozoa to increased temperature and precipitation as is predicted by some global climate models. Protozoa were more abundant when associated with cyanobacteria/lichen crusts than with cyanobacteria crusts alone. Amoebae, flagellates, and ciliates originating from the Colorado Plateau desert (cool desert, primarily winter precipitation) declined 50-, 10-, and 100-fold, respectively, when moved in field mesocosms to the Chihuahuan Desert (hot desert, primarily summer rain). However, this was not observed in protozoa collected from the Chihuahuan Desert and moved to the Sonoran desert (hot desert, also summer rain, but warmer than Chihuahuan Desert). Protozoa in culture began to encyst at 37°C. Cysts survived the upper end of daily temperatures (37,55°C), and could be stimulated to excyst if temperatures were reduced to 15°C or lower. Results from this study suggest that cool desert protozoa are influenced negatively by increased summer precipitation during excessive summer temperatures, and that desert protozoa may be adapted to a specific desert's temperature and precipitation regime. [source] Korotnevella hemistylolepis N. Sp. and Korotnevella monacantholepis N. Sp. (Paramoebidae), Two New Scale-covered Mesohaline AmoebaeTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2001CHARLES J. O'KELLY ABSTRACT. Two new species of KorotnevellaGoodkov, 1988, Korotnevella hemistylolepis n. sp. and Korotnevella monacantholepis n. sp., are described from mesohaline ecosystems. The amoebae are characterized on the basis of light and electron microscopy with special emphasis on the structure of the basket scales, which have species-specific architecture. The two new species are the second and third ones recovered from environments other than freshwater. In terms of scale morphology they most closely resemble a freshwater species, Korotnevella bulla (Schaeffer, 1926) Goodkov, 1988. Two genus names, DactylamoebaKorotnev, 1880 and KorotnevellaGoodkov, 1988, are in current use. The latter name is preferred, pending rediscovery and characterization of Dactylamoeba elongataKorotnev, 1880, the type species of the genus. Korotnevella species can be divided into three groups on the basis of scale morphology, suggesting that the genus may not be monophyletic. A key to species is provided. [source] High Numbers of Naked Amoebae in the Planktonic Waters of a Mangrove Stand in Southern Florida, USATHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2000ANDREW ROGERSON ABSTRACT. This is the first study to examine the abundance of naked amoebae in the water column of a mangrove stand. A total of 37 different morphotypes was noted and at least 13 of these are probably new species. Over a one-year sampling interval, amoebae averaged 35,400 cells liter,1 (range 2,000,104,000) by an indirect enrichment cultivation method. Densities in the upper end of this range arc the highest ever reported for any planktonic habitat. Variation between samples was related to the quantity of suspended aggregates (floes) in the water column emphasizing that amoebae are usually floc-associated. The study also showed that it is essential to disrupt floc material prior to withdrawing sample aliquots for the indirect counting method since several amoebae can occupy the interstices of aggregates. There is concern that indirect enumeration methods that require organisms to be cultured in the laboratory seriously underestimate the true count. A direct counting method using acridine orange staining and epifluorescence microscopy was attempted to assess the possible magnitude of the error associated with indirect counting. While this direct method had limitations, notably the difficulty of unambiguously differentiating between small amoebae and nanoflagellates, the results suggested that the indirect method gave estimates that were close to the true count (within a factor of two). Mangrove waters are rich in heterotrophic protozoa (,3 × 106 liter1) and while the heterotrophic flagellates are by far the dominant group, naked amoebae outnumber ciliates some 20-foid. The ecological consequences of high numbers of amoebae, particularly the common small forms less than 10 ,m in length, need to be examined for these important coastal sites. [source] A methane-driven microbial food web in a wetland rice soilENVIRONMENTAL MICROBIOLOGY, Issue 12 2007Jun Murase Summary Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and 13C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria -related sequences were obtained from the ,heavy' rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the ,heavy' rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability. [source] Community development along a proglacial chronosequence: are above-ground and below-ground community structure controlled more by biotic than abiotic factors?JOURNAL OF ECOLOGY, Issue 5 2010Matthew L. Carlson Summary 1.,We studied vascular plant and soil-dwelling testate amoeba communities in deglaciated sites across a range of substrate ages in Kenai Fjords, Alaska, USA to test four hypotheses. (i) Patterns of community assembly are similar for vascular plants and testate amoebae. (ii) Vascular plant and testate amoeba communities are more strongly correlated to abiotic variables than to each other, since these communities are not directly linked trophically. (iii) Plant community structure becomes less associated with abiotic condition in succession relative to testate amoebae, as species replacement is believed to be more common for plants than testate amoebae. (iv) Above- and below-ground communities become more strongly linked over the succession, due a shift from predominantly allogenic to autogenic forces. 2.,We assessed relationships among biotic communities and abiotic site variables across the chronosequence using multiple factor analysis, redundancy analysis (RDA) and a moving-window analysis. 3.,The diversity patterns and the communities' response to site and soil variables differed between groups. The composition of both communities was significantly explained by bedrock type and moisture regime. The vascular plant community, however, was more influenced by distance from the glacier. 4.,Testate amoeba and vascular plant community patterns were significantly linked to each other and to location and physical conditions. The moving-window RDA indicates the variation explained by the physical and chemical environment tended to slightly decrease through the chronosequence for testate amoebae, while a bell-shape response was evidenced for vascular plants. The variation of the microbial community explained by the plant community was very low in the early stages of the succession and became higher than the variation explained by the environmental variables later in the chronosequence. 5.,Synthesis. These results suggest that vascular plants and testate amoebae are as linked or more in ecosystem development than either community is to changes in site condition. Furthermore, the strength of interactions varies along the succession. Thus, ecological links may be more important than macro-scale abiotic site condition is to community development, even between communities without direct trophic interactions. [source] LIPID COMPOSITION OF CHLORARACHNIOPHYTES (CHLORARACHNIOPHYCEAE) FROM THE GENERA BIGELOWIELLA, GYMNOCHLORA, AND LOTHARELLA,JOURNAL OF PHYCOLOGY, Issue 2 2005Jeffrey D. Leblond The Chlorarachniophyceae are unicellular eukaryotic algae characterized by an amoeboid morphology that may be the result of secondary endosymbiosis of a green alga by a nonphotosynthetic amoeba or amoeboflagellate. Whereas much is known about the phylogeny of chlorarachniophytes, little is known about their physiology, particularly that of their lipids. In an initial effort to characterize the lipids of this algal class, four organisms from three genera were examined for their fatty acid and sterol composition. Fatty acids from lipid fractions containing chloroplast-associated glycolipids, storage triglycerides, and cytoplasmic membrane-associated polar lipids were characterized. Glycolipid-associated fatty acids were of limited composition, principally eicosapentaenoic acid [20:5(n-3)] and hexadecanoic acid (16:0). Triglyceride-associated fatty acids, although minor, were found to be similar in composition. The polar lipid fraction was dominated by lipids that did not contain phosphorus and had a more variable fatty acid composition with 16:0 and docosapentaenoic acid [22:5(n-3)] dominant along with a number of minor C18 and C20 fatty acids. Crinosterol and one of the epimeric pair poriferasterol/stigmasterol were the sole sterols. Several genes required for synthesis of these sterols were computationally identified in Bigelowiella natans Moestrup. One sterol biosynthesis gene showed the greatest similarity to SMT1 of the green alga, Chlamydomonas reinhardtii. However, homologues to other species, mostly green plant species, were also found. Further, the method used for identification suggested that the sequences were transferred to a genetic compartment other than the likely original location, the nucleomorph nucleus. [source] 28 Lipid composition of members of the algal class chlorarachniophyceaeJOURNAL OF PHYCOLOGY, Issue 2003J. L. Dahmen The algal class Chlorarachniophyceae is comprised of a small group of unicellular eukaryotic algae that are often characterized by an unusual amoeboid morphology. This morphology is hypothesized to be the result of a secondary endosymbiosis in which a green alga was engulfed as prey by a nonphotosynthetic amoeba or amoebaflagellate. Whereas much is known about the phylogenetic relationships of individual chlorarachniophytes to one another, and to possible ancestral host organisms in the genera Cercomonas and Heteromita, little is known about their physiology, particularly that of their lipids. In an initial effort to characterize the lipids of this algal class, seven organisms were examined for their fatty acid and sterol composition. These included Bigelowiella natans, Chlorarachnion globusum, Chlorarachnion reptans, Gymnochlora stellata, Lotharella amoeboformis, Lotharella globosa, and Lotharella sp. Fatty acids associated with chloroplast-associated glycolipids, cytoplasmic membrane-associated phospholipids, and storage triglycerides were characterized. Glycolipid fatty acids were found to be of limited composition, containing principally eicosapentaenoic acid [20:5(n-3)] and hexadecanoic acid (16:0), which ranged in relative percentage from 67,90% and 10,29%, respectively, in these seven organisms. Triglyceride-associated fatty acids were found to be similar. Phospholipid fatty acid composition was more variable. The principal phospholipid fatty acids, 16:0 (25,32%) and a compound tentatively identified as docosapentaenoic acid [22:5(n-3)] (26,35%), were found along with a number of C18 and C20 fatty acids. All organisms contained two sterols as free sterols. These were tentatively identified as 24-ethylcholesta-5,22E-dien-3b-ol (stigmasterol; 70,95%) and 24-methylcholesta-5,22E-dien-3b-ol (brassicasterol; 5,30%). [source] Discovery of a large clonal patch of a social amoeba: implications for social evolutionMOLECULAR ECOLOGY, Issue 6 2009OWEN M GILBERT Abstract Studies of genetic population structures of clonally reproducing macro-organisms have revealed large areas where only one clone is found. These areas, referred to as clonal patches, have not been shown to occur in free-living microbes until now. In free-living microbes, high genetic diversity at local scales is usually maintained by high rates of dispersal. We report, however, a highly dense, 12-m clonal patch of the social amoeba Dictyostelium discoideum in a cattle pasture located in a Texas Gulf Coast prairie. We confirm the presence of only one clone by the analysis of 65 samples and amplification of 10 polymorphic microsatellite loci. Samplings of additional cattle pastures nearby showed higher clonal diversity, but with a density of D. discoideum isolates lower than in the clonal patch. These findings show that high rates of microbial dispersal do not always produce genetic diversity at local scales, contrary to the findings of previous studies. The existence of clonal patches may be particularly important for microbial social evolution. [source] Co-occurrence in nature of different clones of the social amoeba, Dictyostelium discoideumMOLECULAR ECOLOGY, Issue 4 2003A. Fortunato Abstract The social amoeba, Dictyostelium discoideum, produces a multicellular fruiting body and has become a model system for cell,cell interactions such as signalling, adhesion and development. However, unlike most multicellular organisms, it forms by aggregation of cells and, in the laboratory, forms genetic chimeras where there may be competition among clones. Here we show that chimera formation is also likely in nature, because different clones commonly co-occur on a very small scale. This suggests that D. discoideum will likely have evolved strategies for competing in chimeras, and that the function of some developmental genes will be competitive. Natural chimerism also makes D. discoideum a good model organism for the investigation of issues relating to coexistence and conflict between cells. [source] Ultrastructural Study of Encystation and Excystation in Acanthamoeba castellaniiTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005BIBIANA CHÁVEZ-MUNGUÍA Abstract. Encystation and excystation of Acanthamoeba castellanii were studied by transmission electron microscopy. The differentiation process was induced in asynchronous cultures grown axenically. Cytoplasmic vesicles containing a dense fibrous material very similar in appearance to the cyst wall were observed in trophozoites induced to encyst. When these trophozoites were incubated with calcofluor white m2r, fluorescence was observed in cytoplasmic vesicles, suggesting that the material contained in these vesicles corresponded to cyst wall precursors. Semithin cryosections of mature cysts with the same treatment showed fluorescence in the ectocyst and a less intense fluorescence in the endocyst, suggesting the presence of cellulose in both structures of the cyst wall. In mature cysts induced to excystation, small structures very similar to electron-dense granules (EDG) previously described in other amoebae were frequently observed. The EDGs were either sparsely distributed in the cytoplasm or associated with the cytoplasmic face of the plasma membrane. Many of them were located near the ostiole. In advanced phases of excystation, endocytic activity was suggested by the formation of endocytic structures and the presence of vacuoles with fibrous content similar to that of the cyst wall. Electron-dense granules in the process of dissolution were also observed in these vacuoles. Furthermore, the formation of a pseudopod suggests a displacement of the amoeba toward the ostiole. [source] Isolation of a Thermotolerant Paravahlkampfia sp. from Lizard Intestine: Biology and Molecular IdentificationTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 5 2003FREDERICK L. SCHUSTER ABSTRACT. An amoeba was isolated from the intestines of several moribund pink-tongued skinks (lizards), Hemisphaeriodon ger-rardi Unusual features of this isolate were its ability to grow at temperatures of , 37 °C, and its inability to use Escherichia coli as a food source or to grow axenically on a variety of enriched culture media suitable for other soil amoeba isolates. Growth was abundant, however, on tissue culture cells, with amoebae clearing cell monolayers in ,48 h at 37 °C. Trophozoites had a vahlkampfiid-like morphology, moving by means of an anterior eruptive pseudopod. Cysts, round to slightly ovoid and lacking exit pores, were formed in culture. Tests for enflagellation of trophic amoebae were negative. Indirect immunofluorescence staining was negative for Naegleria fowleri and Willaertia sp. The isolate was sensitive to azithromycin, but not to amphotericin B, pentamidine isethionate, fluconazole, 5-fluorocytosine, and sulfadiazine. Phylogenetic analysis based on the PCR-amplified small subunit ribosomal DNA, identified the organism as Paravahlkampfia ustiana, an amoeba not previously isolated from either poikilothermic or homeothermic hosts. No evidence of pathology was seen in stained sections of lizard intestine, suggesting that the ameba was part of the normal fauna of the lizard gut. Its diet in the lizard intestine is unknown and the organism may have unusual growth requirements. Thus, P. ustiana joins other soil amoebae that have been isolated from mammals, amphibia, fish, and reptiles, which have the potential of becoming opportunistic pathogens. [source] The SSU rDNA Coding Region of a Filose Amoeba Contains a Group I Intron Lacking the Universally Conserved G at the 3,-Terminus,THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2000DEBASHISH BHATTACHARYA ABSTRACT. We sequenced small subunit ribosomal DNA (rDNA) PCR-fragments of sizes 2.3 kb and 2.9 kb isolated from a culture of the red alga, Porphyru spiralis var. spiralis. Phylogenetic analysis of the 2.3-kb fragment showed that it encoded the sequence of a contaminant filose amoeba. The Nuclearia -like amoeba (named strain N-Por) was identified with scanning electron microscopy. Its rDNA sequence was positioned with strong bootstrap support within a diverse protist assemblage that includes filose amoebae, chlor-arachniophytes, cercomonads, and Plasmodiophora brussicae. The rDNA of N-Por contained a group I intron at the conserved 943 position that remarkably, had a U at the 3,-terminus rather than the universally conserved G. [source] Signalization and cytoskeleton activity through myosin IB during the early steps of phagocytosis in Entamoeba histolytica: a proteomic approachCELLULAR MICROBIOLOGY, Issue 10 2005Sabrina Marion Summary Phagocytosis of human cells is a crucial activity for the virulence of the human parasite Entamoeba histolytica. This protozoan invades and destroys the intestine by killing and phagocytosing epithelial cells, erythrocytes and cells from the immune system. In this study, we used magnetic beads covered with proteins from human serum as a model system to study the early events involved in phagocytosis by E. histolytica. We validated the system showing that the beads uptake triggered the activation of the actin-myosin cytoskeleton and involved a PI3-kinase as previously described for erythrophagocytosis. We purified early phagosomes from wild-type (WT) amoeba and from parasites that overproduced myosin IB (MyoIB+), the unique unconventional myosin of E. histolytica. The MyoIB+ cells exhibit a slower and more synchronized uptake process than the WT strain. Proteomic analysis by liquid chromatography and tandem mass spectroscopy (LC-MS/MS) of the WT and MyoIB+ phagosomes allowed us to identify, for the first time, molecular actors involved in the early step of the uptake process. These include proteins involved in cytoskeleton activity, signalling, endocytosis, lytic activity and cell surface proteins. Interestingly, the proteins that we found specifically recruited on the phagosomes from the MyoIB+ strain were previously described in other eukarytotic cells, as involved in the regulation of cortical F-actin dynamics, such as ,-actinin and formins. This proteomics approach allows a step further towards the understanding of the molecular mechanisms involved in phagocytosis in E. histolytica that revealed some interesting differences compared with phagocytosis in macrophages or Dictyostelium discoideum, and allowed to identify putative candidates for proteins linked to myosin IB activity during the phagocytic process [source] Analysis of Sir2E in the cellular slime mold Dictyostelium discoideum: Cellular localization, spatial expression and overexpressionDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 8 2008Takahiro Katayama It has been reported that Dictyostelium discoideum encodes four silent information regulator 2 (Sir2) proteins (Sir2A,D) showing sequence similarity to human homologues of Sir2 (SIRT1,3). Further screening in a database revealed that D. discoideum encodes an additional Sir2 homologue (Sir2E). The amino acid sequence of Sir2E is not similar to those of SIRTs but is similar to those of proteins encoded by Giardia lamblia, Cryptosporidium hominis and Cryptosporidium parvum. Fluorescence of Sir2E-green fluorescent protein fusion protein was detected in the D. discoideum nucleus, indicating that Sir2E is a nuclear localizing protein. Reverse transcription,polymerase chain reaction and whole-mount in situ hybridization analyses showed that D. discoideum expressed sir2E in amoebae in the growth phase and in prestalk cells in the developmental phase. D. discoideum overexpressing sir2E grew faster than the wild type. These results indicate that Sir2E plays important roles both in the growth phase and developmental phase of D. discoideum. [source] Modeling the model organism Dictyostelium discoideumDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 6 2000Seido Nagano The cellular slime mold Dictyostelium discoideum is a fascinating organism, not only for biologists, but also for physicists. Since the Belousov,Zhabotinskii reaction pattern, a well-known non-linear phenomenon in chemistry, was observed during aggregation of Dictyostelium amoebae, Dictyostelium has been one of the major subjects of non-linear dynamics studies. Macroscopic theory, such as continuous cell density approximation, has been a common approach to studying pattern formation since the pioneering work of Turing. Recently, promising microscopic approaches, such as the cellular dynamics method, have emerged. They have shown that Dictyostelium is useful as a model system in biology. The synchronization mechanism of oscillatory production of cyclic adenosine 3,,5,-monophosphate in Dictyostelium is discussed in detail to show how it is a universal feature that can explain synchronization in other organisms. [source] Effects of co-culture of amoebae with indoor microbes on their cytotoxic and proinflammatory potentialENVIRONMENTAL TOXICOLOGY, Issue 4 2007Terhi Yli-Pirilä Abstract Free-living amoebae are ubiquitous environmental protozoa found in both natural and man-made environments, including moisture-damaged buildings. Furthermore, the interaction between amoebae and bacteria has been shown to enhance the virulence and pathogenicity of some bacteria. While the inhabitants of moisture damaged buildings are known to be at risk of suffering adverse health effects, the exact causative agents and mechanisms are still obscure. To examine the possible role of amoebae in the health effects associated with moisture damages, the effects of amoebae on the cytotoxicity and proinflammatory potential of nonpathogenic microbes common in moisture-damaged buildings were investigated. First, two bacterial and three fungal strains were cultured both individually and in coculture with Acanthamoeba polyphaga. Then, mouse RAW264.7 macrophages were exposed to the cocultures as well as the individually grown bacteria, fungi, and amoebae. Finally, cell viability and production of proinflammatory mediators, i.e., nitric oxide (NO), tumor necrosis factor , (TNF-,), and interleukin 6 (IL-6), were measured in macrophages after the exposure. The results revealed that cocultivation with amoebae increased the cytotoxicity of the bacterium Streptomyces californicus and the fungus Penicillium spinulosum. Moreover, the macrophages produced up to 10 times higher concentrations of NO after the exposure to these cocultures than after the exposure to individually grown microbes. Finally, the production of the cytokines was up to two orders of magnitude higher (IL-6) and up to four times higher (TNF-,) after exposure to the cocultures when compared to individually grown microbes. We conclude that amoebae are able to potentiate the cytotoxicity and proinflammatory properties of certain microbes associated with moisture damages. © 2007 Wiley Periodicals, Inc. Environ Toxicol 22: 357,367, 2007. [source] Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen speciesFEBS JOURNAL, Issue 13 2008Hideki Sumimoto NADPH oxidases of the Nox family exist in various supergroups of eukaryotes but not in prokaryotes, and play crucial roles in a variety of biological processes, such as host defense, signal transduction, and hormone synthesis. In conjunction with NADPH oxidation, Nox enzymes reduce molecular oxygen to superoxide as a primary product, and this is further converted to various reactive oxygen species. The electron-transferring system in Nox is composed of the C-terminal cytoplasmic region homologous to the prokaryotic (and organelle) enzyme ferredoxin reductase and the N-terminal six transmembrane segments containing two hemes, a structure similar to that of cytochrome b of the mitochondrial bc1 complex. During the course of eukaryote evolution, Nox enzymes have developed regulatory mechanisms, depending on their functions, by inserting a regulatory domain (or motif) into their own sequences or by obtaining a tightly associated protein as a regulatory subunit. For example, one to four Ca2+ -binding EF-hand motifs are present at the N-termini in several subfamilies, such as the respiratory burst oxidase homolog (Rboh) subfamily in land plants (the supergroup Plantae), the NoxC subfamily in social amoebae (the Amoebozoa), and the Nox5 and dual oxidase (Duox) subfamilies in animals (the Opisthokonta), whereas an SH3 domain is inserted into the ferredoxin,NADP+ reductase region of two Nox enzymes in Naegleria gruberi, a unicellular organism that belongs to the supergroup Excavata. Members of the Nox1,4 subfamily in animals form a stable heterodimer with the membrane protein p22phox, which functions as a docking site for the SH3 domain-containing regulatory proteins p47phox, p67phox, and p40phox; the small GTPase Rac binds to p67phox (or its homologous protein), which serves as a switch for Nox activation. Similarly, Rac activates the fungal NoxA via binding to the p67phox -like protein Nox regulator (NoxR). In plants, on the other hand, this GTPase directly interacts with the N-terminus of Rboh, leading to superoxide production. Here I describe the regulation of Nox-family oxidases on the basis of three-dimensional structures and evolutionary conservation. [source] Viability of Listeria monocytogenes in co-culture with Acanthamoeba spp.FEMS MICROBIOLOGY ECOLOGY, Issue 1 2009Alisha Akya Abstract Listeria monocytogenes is a human pathogen, ubiquitous in the environment, and can grow and survive under a wide range of environmental conditions. It contaminates foods via raw materials or food-processing environments. However, the current knowledge of its ecology and, in particular, the mode of environmental survival and transmission of this intracellular pathogen remains limited. Research has shown that several intracellular pathogens are able to survive or replicate within free-living amoebae. To examine the viability of L. monocytogenes in interaction with Acanthamoeba spp., bacteria were co-cultured with three freshly isolated amoebae, namely Acanthamoeba polyphaga, Acanthamoeba castellanii and Acanthamoeba lenticulata. The survival of bacteria and amoebae was determined using culture techniques and microscopy. Under the experimental conditions used, all amoebae were able to eliminate bacteria irrespective of the hly gene. Bacteria did not survive or replicate within amoeba cells. However, extra-amoebic bacteria grew saprophytically on materials released from amoebae, which may play an important role in the survival of bacteria under extreme environmental conditions. [source] Amoebal pathogens as emerging causal agents of pneumoniaFEMS MICROBIOLOGY REVIEWS, Issue 3 2010Frédéric Lamoth Abstract Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella -like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.). [source] Genome analysis of microorganisms living in amoebae reveals a melting pot of evolutionFEMS MICROBIOLOGY REVIEWS, Issue 3 2010Claire Moliner Abstract Amoebae-resistant microorganisms exhibit a specific lifestyle. Unlike allopatric specialized intracellular pathogens, they have not specialized because they infect the amoebae via amoebal attack and present a sympatric lifestyle with species from different phyla. In this review, we compare the genomes from bacteria (Legionella pneumophila, Legionella drancourtii, Candidatus,Protochlamydia amoebophila,'Rickettsia bellii, Candidatus,Amoebophilus asiaticus') and a virus (mimivirus) that multiply naturally in amoebae. The objective is to highlight the genomic traits characterizing these microorganisms and their niche by comparison with other specialized pathogens. The genome of intra-amoebal microorganisms is significantly larger than that of their relatives, contradicting the genome reduction theory mostly accepted for intracellular pathogens. This is probably due to the fact that they are not specialized and therefore maintain their genome size. Moreover, the presence of many horizontally transferred genes and mobilomes in their genomes suggests that these microorganisms acquired genetic material from their neighbors and amoebal host, thus increasing their genome size. Important features involved in gene transfer and pathogenicity were thus acquired. These characteristics suggest that amoebae constitute a gene melting pot, allowing diverse microorganisms to evolve by the same pathway characterized by gene acquisition, and then either adapt to the intra-amoebal lifestyle or create new pathogens. [source] Influence of Environmental Heterogeneity on the Structure of Testate Amoebae (Protozoa, Rhizopoda) Assemblages in the Plankton of the Upper Paraná River Floodplain, BrazilINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 2 2003Luiz Felipe Machado Velho Abstract In freshwater environments, testate amoebae are usually found associated with macrophytes and sediments and many studies have suggested that their occurrence in plankton samples is accidental. This implies that predictable patterns detected in planktonic assemblages should not be observed in testate amoebae assemblages. This hypothesis was tested in this study. Plankton samples were collected from different environments in the Upper Paraná River floodplain. Results show that patterns in species composition and abundance of testate amoebae are predictable, and that dominant species tend to present characteristic shell morphology in hydrologically different environments. We suggest that testate amoebae must be routinely included in plankton ecology studies, at least in floodplain environments. [source] Isolation and identification of Acanthamoeba species related to amoebic encephalitis and nonpathogenic free-living amoeba species from the rice fieldJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010S.-Y. Liang Abstract Aims:, Isolation and characterization of the clinically relevant amphizoic amoebas in vegetated farmlands, which may present a risk to farmers' health. Methods and Results:,Acanthamoeba species was isolated and characterized via morphological and molecular means in the rice field where the patient was exposed to rice paddy water which most probably was the point of infection. An Acanthamoeba sp. abundant in the rice field was identified. Genotyping showed the strain to be genotype T4, which was identical to the amoebic parasite found in patient's cerebrospinal fluid. During the course of the study, three nonpathogenic free-living amoeba species were also isolated and characterized for the first time in Taiwan. Conclusions:, This study successfully located a possible source of granulomatous amoebic encephalitis in a patient and provided the first evidence that Acanthamoeba genotype T4 may be a potential pathogen in Taiwan. Significance and Impact of the Study:, The integration of field survey, clinical data and morphological and genetic examination represents a sound strategy for investigation of the possible role of free-living amoebae in causing human diseases. Future work should include investigating the potential contributory role of other nonpathogenic free-living protozoa in disease of livestock or even human. [source] Heterogeneity in chlorine susceptibility for Legionella pneumophila released from Acanthamoeba and HartmannellaJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009C.-W. Chang Abstract Aims:, To assess chlorine susceptibility of Legionella pneumophila grown from two amoebic hosts, Acanthamoeba castellanii and Hartmannella vermiformis. Methods and Results:, After being released from amoebae, Leg. pneumophila were chlorinated at 2 and 5 mg l,1 for 5 min,24 h. Bacterial culturability and cytoplasmic membrane deterioration were quantified by culture assay on BCYE, agar and BacLight stains coupled with a fluorescent microscope, respectively. Chlorination reduced the culturability of Leg. pneumophila by 2·93,4·59 log CFU ml,1 and damaged cellular membrane by 53·8,99·2%. Moreover, cells released from H. vermiformis exhibited significantly lower degrees in culturability reduction (P = 0·0008) and membrane deterioration (P < 0·0001) when compared with those from A. castellanii. The amoebic genus is the most significant parameter affecting cytoplasmic membrane integrity of chlorinated Legionella (P < 0·0001), followed by free chlorine concentration (P = 0·042). Conclusions:,Legionella pneumophila replicated from H. vermiformis possess greater chlorine resistance than the cells from A. castellanii. Significance and Impact of the Study:, This study shows the heterogeneity of amoebae-grown Leg. pneumophila in chlorine susceptibility, which should be considered in the control of legionellae proliferation, particularly in the systems where H. vermiformis is dominant, e.g. hot water plumbing. [source] Community development along a proglacial chronosequence: are above-ground and below-ground community structure controlled more by biotic than abiotic factors?JOURNAL OF ECOLOGY, Issue 5 2010Matthew L. Carlson Summary 1.,We studied vascular plant and soil-dwelling testate amoeba communities in deglaciated sites across a range of substrate ages in Kenai Fjords, Alaska, USA to test four hypotheses. (i) Patterns of community assembly are similar for vascular plants and testate amoebae. (ii) Vascular plant and testate amoeba communities are more strongly correlated to abiotic variables than to each other, since these communities are not directly linked trophically. (iii) Plant community structure becomes less associated with abiotic condition in succession relative to testate amoebae, as species replacement is believed to be more common for plants than testate amoebae. (iv) Above- and below-ground communities become more strongly linked over the succession, due a shift from predominantly allogenic to autogenic forces. 2.,We assessed relationships among biotic communities and abiotic site variables across the chronosequence using multiple factor analysis, redundancy analysis (RDA) and a moving-window analysis. 3.,The diversity patterns and the communities' response to site and soil variables differed between groups. The composition of both communities was significantly explained by bedrock type and moisture regime. The vascular plant community, however, was more influenced by distance from the glacier. 4.,Testate amoeba and vascular plant community patterns were significantly linked to each other and to location and physical conditions. The moving-window RDA indicates the variation explained by the physical and chemical environment tended to slightly decrease through the chronosequence for testate amoebae, while a bell-shape response was evidenced for vascular plants. The variation of the microbial community explained by the plant community was very low in the early stages of the succession and became higher than the variation explained by the environmental variables later in the chronosequence. 5.,Synthesis. These results suggest that vascular plants and testate amoebae are as linked or more in ecosystem development than either community is to changes in site condition. Furthermore, the strength of interactions varies along the succession. Thus, ecological links may be more important than macro-scale abiotic site condition is to community development, even between communities without direct trophic interactions. [source] Mechatronic Design and Locomotion of Amoebot,A Metamorphic Underwater VehicleJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 6 2003I-Ming Chen The Metamorphic Underwater Vehicle (MUV) is a vehicle that propels in the water by continuously changing the shape of its body similar to the motion of the microorganism amoebae. In this article, we describe the basic design of Amoebot, a plastic MUV that achieves shape-changing capability through the inflation and deflation of water-filled balloons. A sequence of inflation and deflation procedures can be taken to produce cyclic swimming shapes that propel the MUV. Swimming shapes similar to the microorganism amoebae have been successfully reproduced by present Amoebot. The mechanical system designed proves to be very reliable and flexible in producing desired body shapes. The physical shape of the Amoebot is analyzed numerically and its variation in time during the swim can be expressed explicitly. By formulating sets of idealized swimming rules based on the changing shape, simulations are carried out to predict the trajectory and study the pseudo dynamics of the swimming of Amoebot. Possible applications of this type of underwater vehicle are discussed. © 2003 Wiley Periodicals, Inc. [source] Experimental exposure of zebrafish, Danio rerio (Hamilton), to Mycobacterium marinum and Mycobacterium peregrinum reveals the gastrointestinal tract as the primary route of infection: a potential model for environmental mycobacterial infectionJOURNAL OF FISH DISEASES, Issue 10 2007M J Harriff Abstract The natural route by which fish become infected with mycobacteria is unknown. Danio rerio (Hamilton) were exposed by bath immersion and intubation to Mycobacterium marinum and Mycobacterium peregrinum isolates obtained from diseased zebrafish. Exposed fish were collected over the course of 8 weeks and examined for the presence of mycobacteriosis. Mycobacteria were consistently cultured from the intestines, and often from the livers and spleens of fish exposed by both methods. Mycobacteria were not observed in the gills. Histological analysis revealed that fish infected with M. marinum often developed granulomas accompanied by clinical signs of mycobacteriosis, while infection with M. peregrinum infrequently led to clinical signs of disease. Passage of the bacteria through environmental amoebae (Acanthamoeba castellani) was associated with increased growth of M. peregrinum over the course of 8 weeks, when compared to infection with the bacteria not passed through amoebae. The results provide evidence that zebrafish acquire mycobacteria primarily through the intestinal tract, resulting in mycobacterial dissemination. [source] | ||||||||||||||||||||||||||||||||||