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Microbiological Reviews Sep 1982
Comparative Study Review
Topics: Amoeba; Animals; Apicomplexa; Aspartic Acid Endopeptidases; Ciliophora; Cysteine Endopeptidases; Endopeptidases; Eukaryota; Food-Processing Industry; Fungi; Indicators and Reagents; Metalloendopeptidases; Myxomycetes; Peptide Hydrolases; Protease Inhibitors; Protein Processing, Post-Translational; Proteins; Serine Endopeptidases; Virulence
PubMed: 6813664
DOI: 10.1128/mr.46.3.308-340.1982 -
Proceedings. Biological Sciences Nov 2015Historically, research has focused on the mean and often neglected the variance. However, variability in nature is observable at all scales: among cells within an...
Historically, research has focused on the mean and often neglected the variance. However, variability in nature is observable at all scales: among cells within an individual, among individuals within a population and among populations within a species. A fundamental quest in biology now is to find the mechanisms that underlie variability. Here, we investigated behavioural variability in a unique unicellular organism, Physarum polycephalum. We combined experiments and models to show that variability in cell signalling contributes to major differences in behaviour underpinning some aspects of social interactions. First, following thousands of cells under various contexts, we identified distinct behavioural phenotypes: 'slow-regular-social', 'fast-regular-social' and 'fast-irregular-asocial'. Second, coupling chemical analysis and behavioural assays we found that calcium signalling is responsible for these behavioural phenotypes. Finally, we show that differences in signalling and behaviour led to alternative social strategies. Our results have considerable implications for our understanding of the emergence of variability in living organisms.
Topics: Calcium Signaling; Genetic Variation; Models, Biological; Phenotype; Physarum polycephalum; Social Behavior
PubMed: 26609088
DOI: 10.1098/rspb.2015.2322 -
The Journal of Biological Chemistry Oct 1979An improved purification procedure for the carbohydrate-binding proteins (lectins) of cohesive Polysphondylium pallidum cells has been devised. The procedure uses...
An improved purification procedure for the carbohydrate-binding proteins (lectins) of cohesive Polysphondylium pallidum cells has been devised. The procedure uses extraction of cells with lactose-containing buffer followed by ammonium sulfate precipitation and affinity chromatography of the redissolved precipitate on a column of acid-treated Sepharose 6B. All hemagglutination activity is adsorbed to the column and recoveries are about 70% of the activity of the starting cell lysate. Sodium dodecyl sulfate-gel electrophoresis of the protein obtained with this procedure resolved three subunits with molecular weights of 26,500 (A), 26,000 (B), and 25,000 (C). Three species are resolved by isoelectric focusing with apparent pI values of 6.4 (I), 7.3 (II), and 7.5 (III) which contain Subunits A, B, and C in the following ratios: I, B:C at 2:1; II, A:B at 2:1, and III, A:B at 1:2. All three isoforms agglutinate rabbit and human type O erythrocytes and are thus isolectins. Isoforms II and III are separated from Isoform I by galactose-gradient elution of the Sepharose 6B column. Isoforms II and III aggregate extensively (nonamers and multiples thereof), but reduction with 2-mercaptoethanol reverses this process yielding a single species of Mr = 73,000 (trimer). Isoform I exists as trimers and hexamers and reduction has no effect on this distribution. Amino acid compositions and tryptic peptide maps of S-[14C]carboxymethyl-isolectins indicate that Subunits A and B are very similar and may represent the same peptide chain, while Subunit C is a peptide quite distinct from A and B.
Topics: Amino Acids; Animals; Carbohydrates; Cell Adhesion; Hemagglutination Tests; Hexosamines; Humans; Lectins; Molecular Weight; Myxomycetes; Peptide Fragments; Rabbits; alpha-Fetoproteins
PubMed: 90676
DOI: No ID Found -
Chemical & Pharmaceutical Bulletin Aug 2002Lindbladione (1), 7-methoxylindbladione (2), and 6, 7-dimethoxylindbladione (3) have been isolated from a myxomycete Lindbladia tubulina and their structures were...
Lindbladione (1), 7-methoxylindbladione (2), and 6, 7-dimethoxylindbladione (3) have been isolated from a myxomycete Lindbladia tubulina and their structures were elucidated by spectral data.
Topics: Myxomycetes; Naphthoquinones; Pigments, Biological
PubMed: 12192152
DOI: 10.1248/cpb.50.1126 -
Proceedings of the National Academy of... Aug 2013Individuals can function as integrated organisms only when information and resources are shared across a body. Signals and substrates are commonly moved using fluids,...
Individuals can function as integrated organisms only when information and resources are shared across a body. Signals and substrates are commonly moved using fluids, often channeled through a network of tubes. Peristalsis is one mechanism for fluid transport and is caused by a wave of cross-sectional contractions along a tube. We extend the concept of peristalsis from the canonical case of one tube to a random network. Transport is maximized within the network when the wavelength of the peristaltic wave is of the order of the size of the network. The slime mold Physarum polycephalum grows as a random network of tubes, and our experiments confirm peristalsis is used by the slime mold to drive internal cytoplasmic flows. Comparisons of theoretically generated contraction patterns with the patterns exhibited by individuals of P. polycephalum demonstrate that individuals maximize internal flows by adapting patterns of contraction to size, thus optimizing transport throughout an organism. This control of fluid flow may be the key to coordinating growth and behavior, including the dynamic changes in network architecture seen over time in an individual.
Topics: Computer Simulation; Cytoplasm; Hydrodynamics; Microscopy; Models, Biological; Peristalsis; Physarum polycephalum
PubMed: 23898203
DOI: 10.1073/pnas.1305049110 -
Biophysical Journal Aug 1975The microelectrode system described in the accompanying paper was used to investigate properties of fields of Dictyostelium discoideum amoebae in late interphase. Cells...
The microelectrode system described in the accompanying paper was used to investigate properties of fields of Dictyostelium discoideum amoebae in late interphase. Cells in the fields were competent to respond chemotactically to, and to relay, a c-AMP signal, but not to produce an aggregative signal autonomously. The experimental results are generally consistent with c-AMP being the sole compound required for chemotaxis and signal relaying. A periodic signal from the microelectrode can initiate and control aggregation and can complete with spontaneously arising aggregates. The electrode was used to measure the refractory period for relaying which decreases from 9 min or more to between 2 and 3 min with increasing developmental age, and to measure thresholds for chemotaxis and signal relaying. The results are discussed in relation to models for the control of aggregation in D. discoideum.
Topics: Cyclic AMP; Dictyostelium; Dose-Response Relationship, Drug; Electrochemistry; Microelectrodes; Myxomycetes; Time Factors
PubMed: 167879
DOI: 10.1016/S0006-3495(75)85853-X -
Development, Growth & Differentiation Jun 2017Vein networks span the whole body of the amoeboid organism in the plasmodial slime mould Physarum polycephalum, and the network topology is rearranged within an hour in...
Vein networks span the whole body of the amoeboid organism in the plasmodial slime mould Physarum polycephalum, and the network topology is rearranged within an hour in response to spatio-temporal variations of the environment. It has been reported that this tube morphogenesis is capable of solving mazes, and a mathematical model, named the 'current reinforcement rule', was proposed based on the adaptability of the veins. Although it is known that this model works well for reproducing some key characters of the organism's maze-solving behaviour, one important issue is still open: In the real organism, the thick veins tend to trace the shortest possible route by cutting the corners at the turn of corridors, following a center-in-center trajectory, but it has not yet been examined whether this feature also appears in the mathematical model, using corridors of finite width. In this report, we confirm that the mathematical model reproduces the center-in-center trajectory of veins around corners observed in the maze-solving experiment.
Topics: Models, Biological; Physarum polycephalum
PubMed: 28707306
DOI: 10.1111/dgd.12384 -
The Biochemical Journal Jan 1977Eight exo-glycosidase activities were detected in the axenic culture medium of the myxomycete, Physarum polycephalum. The secretion of each enzyme examined followed the...
Eight exo-glycosidase activities were detected in the axenic culture medium of the myxomycete, Physarum polycephalum. The secretion of each enzyme examined followed the growth curve and continued during the stationary phase after the cessation of growth. Two or more forms of each enzyme were detected after electrophoretic separation. The beta-N-acetyl-D-hexosaminidase activity was readily separated into its two electrophoretic forms, X and Y, which were purified 145- and 306-fold respectively. These beta-N-acetyl-D-hexosaminidases had several similar characteristics. Evidence is presented that the major electrophoretic form of alpha-D-galactosidase is heterogeneous. The possible functions of extracellular glycosidases in teir occurrence and properties.
Topics: Culture Media; Electrophoresis, Starch Gel; Galactosidases; Glycoside Hydrolases; Hexosaminidases; Hydrogen-Ion Concentration; Kinetics; Myxomycetes; Physarum
PubMed: 15539
DOI: 10.1042/bj1610149 -
PLoS Computational Biology 2012RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high... (Comparative Study)
Comparative Study
RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails.
Topics: Algorithms; Binding Sites; Codon; Computational Biology; Computers; Conserved Sequence; DNA, Mitochondrial; Genome; Models, Biological; Models, Statistical; Mutation; Myxomycetes; Nucleotides; Physarum; Probability; RNA Editing
PubMed: 22383871
DOI: 10.1371/journal.pcbi.1002400 -
Journal of Bacteriology Nov 1968The process of spore germination in Dictyostelium discoideum consists of three sequential stages: activation of dormant spores, swelling of activated spores, and...
The process of spore germination in Dictyostelium discoideum consists of three sequential stages: activation of dormant spores, swelling of activated spores, and emergence of myxamoebae from swollen spores. Dormant and activated spores are resistant to heating, freezing, or drying. Drying and freezing, moreover, may maintain the activated state until the spores are returned to normal conditions. Low temperature incubation after heat shock or the presence of an autoinhibitor will return activated spores to the dormant state. The entire spore germination process is aerobic, being inhibited at any point by oxygen deprivation or respiratory poisons. Each spore of this social organism appears to germinate at its own rate and independent of the other spores in the suspension.
Topics: Hot Temperature; Myxomycetes; Oxygen Consumption; Spores
PubMed: 5749769
DOI: 10.1128/jb.96.5.1680-1689.1968