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Eberhard Bodenschatz - One of the best experts on this subject based on the ideXlab platform.
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influence of fast advective flows on pattern formation of Dictyostelium discoideum
PLOS ONE, 2018Co-Authors: Torsten Eckstein, Vladimir S Zykov, Eberhard Bodenschatz, Albert Bae, Estefania Vidalhenriquez, Azam GholamiAbstract:We report experimental and numerical results on pattern formation of self-organizing Dictyostelium discoideum cells in a microfluidic setup under a constant buffer flow. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. At high flow velocities, elongated cAMP waves are formed that cover the whole length of the channel and propagate both parallel and perpendicular to the flow direction. While the wave period and transverse propagation velocity are constant, parallel wave velocity and the wave width increase linearly with the imposed flow. We also observe that the acquired wave shape is highly dependent on the wave generation site and the strength of the imposed flow. We compared the wave shape and velocity with numerical simulations performed using a reaction-diffusion model and found excellent agreement. These results are expected to play an important role in understanding the process of pattern formation and aggregation of D. discoideum that may experience fluid flows in its natural habitat.
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flow driven two dimensional waves in colonies of Dictyostelium discoideum
New Journal of Physics, 2015Co-Authors: Azam Gholami, Oliver Steinbock, Vladimir S Zykov, Eberhard BodenschatzAbstract:Dictyostelium discoideum (D.d.) is a valuable model organism to study self-organization and pattern formation in biology. Recently we reported flow-driven waves in experiments with uniformly distributed populations of signaling amobae, D.d., and carried out a theoretical study in a one-dimensional model. In this work, we perform two-dimensional numerical simulations using the well-known Martiel–Golbeter model to study the effect of the flow profile and intrinsic noise on the flow-driven waves. We show that, in the presence of flow, a persistence noise due to spontaneous cell firing events can lead to sustained structures that fill the whole length of the system. We also show that external periodic stimuli of cyclic adenosine monophosphate can induce 1:1 and 2:1 entrainments which are in agreement with our experimental observations.
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flow driven instabilities during pattern formation of Dictyostelium discoideum
New Journal of Physics, 2015Co-Authors: Azam Gholami, Oliver Steinbock, Vladimir S Zykov, Eberhard BodenschatzAbstract:The slime mold Dictyostelium discoideum is a well known model system for the study of biological pattern formation. In the natural environment, aggregating populations of starving Dictyostelium discoideum cells may experience fluid flows that can profoundly change the underlying wave generation process. Here we study the effect of advection on the pattern formation in a colony of homogeneously distributed Dictyostelium discoideum cells described by the standard Martiel–Goldbeter model. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. The evolution of small perturbations in cAMP concentrations is studied analytically in the linear regime and by corresponding numerical simulations. We show that flow can significantly influence the dynamics of the system and lead to a flow-driven instability that initiate downstream traveling cAMP waves. We also show that boundary conditions have a significant effect on the observed patterns and can lead to a new kind of instability.
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flow driven waves and phase locked self organization in quasi one dimensional colonies of Dictyostelium discoideum
Physical Review Letters, 2015Co-Authors: Azam Gholami, Oliver Steinbock, Vladimir S Zykov, Eberhard BodenschatzAbstract:We report experiments on flow-driven waves in a microfluidic channel containing the signaling slime mold Dictyostelium discoideum. The observed cyclic adenosine monophosphate (cAMP) wave trains developed spontaneously in the presence of flow and propagated with the velocity proportional to the imposed flow velocity. The period of the wave trains was independent of the flow velocity. Perturbations of flow-driven waves via external periodic pulses of the signaling agent cAMP induced 1∶1, 2∶1, 3∶1, and 1∶2 frequency responses, reminiscent of Arnold tongues in forced oscillatory systems. We expect our observations to be generic to active media governed by reaction-diffusion-advection dynamics, where spatially bound autocatalytic processes occur under flow conditions.
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scanning x ray nanodiffraction on Dictyostelium discoideum
Biophysical Journal, 2014Co-Authors: Marius Priebe, Eberhard Bodenschatz, Marco Tarantola, Marten Bernhardt, Christoph Blum, Tim SaldittAbstract:We have performed scanning x-ray nanobeam diffraction experiments on single cells of the amoeba Dictyostelium discoideum. Cells have been investigated in 1), freeze-dried, 2), frozen-hydrated (vitrified), and 3), initially alive states. The spatially resolved small-angle x-ray scattering signal shows characteristic streaklike patterns in reciprocal space, which we attribute to fiber bundles of the actomyosin network. From the intensity distributions, an anisotropy parameter can be derived that indicates pronounced local variations within the cell. In addition to nanobeam small-angle x-ray scattering, we have evaluated the x-ray differential phase contrast in view of the projected electron density. Different experimental aspects of the x-ray experiment, sample preparation, and data analysis are discussed. Finally, the x-ray results are correlated with optical microscopy (differential phase contrast and confocal microscopy of mutant strains with fluorescently labeled actin and myosin II), which have been carried out in live and fixed states, including optical microscopy under cryogenic conditions.
Ernst Heinz - One of the best experts on this subject based on the ideXlab platform.
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cloning and functional expression of ugt genes encoding sterol glucosyltransferases from saccharomyces cerevisiae candida albicans pichia pastoris and Dictyostelium discoideum
Journal of Biological Chemistry, 1999Co-Authors: Dirk Warnecke, Ulrich Zähringer, Ralf Erdmann, Annette Fahl, Bernhard Hube, Frank Muller, Thorsten Zank, Ernst HeinzAbstract:Next Section Abstract Sterol glucosides, typical membrane-bound lipids of many eukaryotes, are biosynthesized by a UDP-glucose:sterol glucosyltransferase (EC 2.4.1.173). We cloned genes from three different yeasts and from Dictyostelium discoideum, the deduced amino acid sequences of which all showed similarities with plant sterol glucosyltransferases (Ugt80A1, Ugt80A2). These genes fromSaccharomyces cerevisiae (UGT51 =YLR189C), Pichia pastoris(UGT51B1), Candida albicans(UGT51C1), and Dictyostelium discoideum(ugt52) were expressed in Escherichia coli. In vitro enzyme assays with cell-free extracts of the transgenicE. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors. AnS. cerevisiae null mutant of UGT51 had lost its ability to synthesize sterol glucoside but exhibited normal growth under various culture conditions. Expression of eitherUGT51 or UGT51B1 in this null mutant under the control of a galactose-induced promoter restored sterol glucoside synthesis in vitro. Lipid extracts of these cells contained a novel glycolipid. This lipid was purified and identified as ergosterol-β-d-glucopyranoside by nuclear magnetic resonance spectroscopy. These data prove that the cloned genes encode sterol-β-d-glucosyltransferases and that sterol glucoside synthesis is an inherent feature of eukaryotic microorganisms.
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cloning and functional expression of ugt genes encoding sterol glucosyltransferases from saccharomyces cerevisiae candida albicans pichia pastoris and Dictyostelium discoideum
Journal of Biological Chemistry, 1999Co-Authors: Dirk Warnecke, Ulrich Zähringer, Ralf Erdmann, Annette Fahl, Bernhard Hube, Frank Muller, Thorsten Zank, Ernst HeinzAbstract:Sterol glucosides, typical membrane-bound lipids of many eukaryotes, are biosynthesized by a UDP-glucose:sterol glucosyltransferase (EC 2.4.1.173). We cloned genes from three different yeasts and from Dictyostelium discoideum, the deduced amino acid sequences of which all showed similarities with plant sterol glucosyltransferases (Ugt80A1, Ugt80A2). These genes fromSaccharomyces cerevisiae (UGT51 =YLR189C), Pichia pastoris(UGT51B1), Candida albicans(UGT51C1), and Dictyostelium discoideum(ugt52) were expressed in Escherichia coli. In vitro enzyme assays with cell-free extracts of the transgenicE. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors. AnS. cerevisiae null mutant of UGT51 had lost its ability to synthesize sterol glucoside but exhibited normal growth under various culture conditions. Expression of eitherUGT51 or UGT51B1 in this null mutant under the control of a galactose-induced promoter restored sterol glucoside synthesis in vitro. Lipid extracts of these cells contained a novel glycolipid. This lipid was purified and identified as ergosterol-β-d-glucopyranoside by nuclear magnetic resonance spectroscopy. These data prove that the cloned genes encode sterol-β-d-glucosyltransferases and that sterol glucoside synthesis is an inherent feature of eukaryotic microorganisms.
Joan E. Strassmann - One of the best experts on this subject based on the ideXlab platform.
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low base substitution mutation rate but high rate of slippage mutations in the sequence repeat rich genome of Dictyostelium discoideum
G3: Genes Genomes Genetics, 2020Co-Authors: David C. Queller, Debra A Brock, Sibel Kucukyildirim, Megan G Behringer, Way Sung, Thomas G Doak, Hatice Mergen, Joan E. StrassmannAbstract:We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary, and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. discoideum to evolve an extremely low base-substitution mutation rate.
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Cooperation and conflict in the social amoeba Dictyostelium discoideum.
The International journal of developmental biology, 2019Co-Authors: James M Medina, David C. Queller, P M Shreenidhi, Tyler J Larsen, Joan E. StrassmannAbstract:The social amoeba Dictyostelium discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. discoideum include the sexual cycle as well as the relationship between D. discoideum and its bacterial symbionts. D. discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.
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fruiting bodies of the social amoeba Dictyostelium discoideum increase spore transport by drosophila
BMC Evolutionary Biology, 2014Co-Authors: Jeff Smith, David C. Queller, Joan E. StrassmannAbstract:Background Many microbial phenotypes are the product of cooperative interactions among cells, but their putative fitness benefits are often not well understood. In the cellular slime mold Dictyostelium discoideum, unicellular amoebae aggregate when starved and form multicellular fruiting bodies in which stress-resistant spores are held aloft by dead stalk cells. Fruiting bodies are thought to be adaptations for dispersing spores to new feeding sites, but this has not been directly tested. Here we experimentally test whether fruiting bodies increase the rate at which spores are acquired by passing invertebrates.
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Structured growth and genetic drift raise relatedness in the social amoeba Dictyostelium discoideum
Biology Letters, 2012Co-Authors: NIGEL J BUTTERY, Chandra N. Jack, Boahemaa Adu-oppong, Kate T. Snyder, David C. Queller, Christopher R L Thompson, Joan E. StrassmannAbstract:One condition for the evolution of altruism is genetic relatedness between altruist and beneficiary, often achieved through active kin recognition. Here, we investigate the power of a passive process resulting from genetic drift during population growth in the social amoeba Dictyostelium discoideum. We put labelled and unlabelled cells of the same clone in the centre of a plate, and allowed them to proliferate outward. Zones formed by genetic drift owing to the small population of actively growing cells at the colony edge. We also found that single cells could form zones of high relatedness. Relatedness increased at a significantly higher rate when food was in short supply. This study shows that relatedness can be significantly elevated before the social stage without a small founding population size or recognition mechanism.
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Altruism and social cheating in the social amoeba Dictyostelium discoideum
Nature, 2000Co-Authors: Joan E. Strassmann, Yi Zhu, David C. QuellerAbstract:The social amoeba, Dictyostelium discoideum, is widely used as a simple model organism for multicellular development, but its multicellular fruiting stage is really a society. Most of the time, D. discoideum lives as haploid, free-living, amoeboid cells that divide asexually. When starved, 10(4)-10(5) of these cells aggregate into a slug. The anterior 20% of the slug altruistically differentiates into a non-viable stalk, supporting the remaining cells, most of which become viable spores. If aggregating cells come from multiple clones, there should be selection for clones to exploit other clones by contributing less than their proportional share to the sterile stalk. Here we use microsatellite markers to show that different clones collected from a field population readily mix to form chimaeras. Half of the chimaeric mixtures show a clear cheater and victim. Thus, unlike the clonal and highly cooperative development of most multicellular organisms, the development of D. discoideum is partly competitive, with conflicts of interests among cells. These conflicts complicate the use of D. discoideum as a model for some aspects of development, but they make it highly attractive as a model system for social evolution.
Azam Gholami - One of the best experts on this subject based on the ideXlab platform.
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spontaneous center formation in Dictyostelium discoideum
arXiv: Pattern Formation and Solitons, 2018Co-Authors: Estefania Vidalhenriquez, Azam GholamiAbstract:Dictyostelium discoideum (D.d.) is a widely studied amoeba due to its capabilities of development, survival, and self-organization. During aggregation it produces and relays a chemical signal (cAMP) which shows spirals and target centers. Nevertheless, the natural emergence of these structures is still not well understood. We present a mechanism for creation of centers and target waves of cAMP in D.d. by adding cell inhomogeneity to a well known reaction-diffusion model of cAMP waves and we characterize its properties. We show how stable activity centers appear spontaneously in areas of higher cell density with the oscillation frequency of these centers depending on their density. The cAMP waves have the characteristic dispersion relation of trigger waves and a velocity which increases with cell density. Chemotactically competent cells react to these waves and create aggregation streams even with very simple movement rules. Finally we argue in favor of the existence of bounded phosphodiesterase to maintain the wave properties once small cell clusters appear.
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influence of fast advective flows on pattern formation of Dictyostelium discoideum
PLOS ONE, 2018Co-Authors: Torsten Eckstein, Vladimir S Zykov, Eberhard Bodenschatz, Albert Bae, Estefania Vidalhenriquez, Azam GholamiAbstract:We report experimental and numerical results on pattern formation of self-organizing Dictyostelium discoideum cells in a microfluidic setup under a constant buffer flow. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. At high flow velocities, elongated cAMP waves are formed that cover the whole length of the channel and propagate both parallel and perpendicular to the flow direction. While the wave period and transverse propagation velocity are constant, parallel wave velocity and the wave width increase linearly with the imposed flow. We also observe that the acquired wave shape is highly dependent on the wave generation site and the strength of the imposed flow. We compared the wave shape and velocity with numerical simulations performed using a reaction-diffusion model and found excellent agreement. These results are expected to play an important role in understanding the process of pattern formation and aggregation of D. discoideum that may experience fluid flows in its natural habitat.
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modelling of Dictyostelium discoideum movement in a linear gradient of chemoattractant
Soft Matter, 2017Co-Authors: Zahra Eidi, Farshid Mohammadrafiee, Mohammad Khorrami, Azam GholamiAbstract:Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the statistical features of the chemotactic motion of the social amoeba Dictyostelium discoideum in a linear gradient of cAMP (cyclic adenosine monophosphate). We fit the model to experimental trajectories that are recorded in a microfluidic setup with stationary cAMP gradients and extract the diffusion and drift coefficients in the gradient direction. Our analysis shows that for the majority of gradients, both coefficients decrease over time and become negative as the cells crawl up the gradient. The extracted model parameters also show that besides the expected drift in the direction of the chemoattractant gradient, we observe a nonlinear dependency of the corresponding variance on time, which can be explained by the model. Furthermore, the results of the model show that the non-linear term in the mean squared displacement of the cell trajectories can dominate the linear term on large time scales.
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flow driven two dimensional waves in colonies of Dictyostelium discoideum
New Journal of Physics, 2015Co-Authors: Azam Gholami, Oliver Steinbock, Vladimir S Zykov, Eberhard BodenschatzAbstract:Dictyostelium discoideum (D.d.) is a valuable model organism to study self-organization and pattern formation in biology. Recently we reported flow-driven waves in experiments with uniformly distributed populations of signaling amobae, D.d., and carried out a theoretical study in a one-dimensional model. In this work, we perform two-dimensional numerical simulations using the well-known Martiel–Golbeter model to study the effect of the flow profile and intrinsic noise on the flow-driven waves. We show that, in the presence of flow, a persistence noise due to spontaneous cell firing events can lead to sustained structures that fill the whole length of the system. We also show that external periodic stimuli of cyclic adenosine monophosphate can induce 1:1 and 2:1 entrainments which are in agreement with our experimental observations.
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flow driven instabilities during pattern formation of Dictyostelium discoideum
New Journal of Physics, 2015Co-Authors: Azam Gholami, Oliver Steinbock, Vladimir S Zykov, Eberhard BodenschatzAbstract:The slime mold Dictyostelium discoideum is a well known model system for the study of biological pattern formation. In the natural environment, aggregating populations of starving Dictyostelium discoideum cells may experience fluid flows that can profoundly change the underlying wave generation process. Here we study the effect of advection on the pattern formation in a colony of homogeneously distributed Dictyostelium discoideum cells described by the standard Martiel–Goldbeter model. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. The evolution of small perturbations in cAMP concentrations is studied analytically in the linear regime and by corresponding numerical simulations. We show that flow can significantly influence the dynamics of the system and lead to a flow-driven instability that initiate downstream traveling cAMP waves. We also show that boundary conditions have a significant effect on the observed patterns and can lead to a new kind of instability.
Dirk Warnecke - One of the best experts on this subject based on the ideXlab platform.
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cloning and functional expression of ugt genes encoding sterol glucosyltransferases from saccharomyces cerevisiae candida albicans pichia pastoris and Dictyostelium discoideum
Journal of Biological Chemistry, 1999Co-Authors: Dirk Warnecke, Ulrich Zähringer, Ralf Erdmann, Annette Fahl, Bernhard Hube, Frank Muller, Thorsten Zank, Ernst HeinzAbstract:Next Section Abstract Sterol glucosides, typical membrane-bound lipids of many eukaryotes, are biosynthesized by a UDP-glucose:sterol glucosyltransferase (EC 2.4.1.173). We cloned genes from three different yeasts and from Dictyostelium discoideum, the deduced amino acid sequences of which all showed similarities with plant sterol glucosyltransferases (Ugt80A1, Ugt80A2). These genes fromSaccharomyces cerevisiae (UGT51 =YLR189C), Pichia pastoris(UGT51B1), Candida albicans(UGT51C1), and Dictyostelium discoideum(ugt52) were expressed in Escherichia coli. In vitro enzyme assays with cell-free extracts of the transgenicE. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors. AnS. cerevisiae null mutant of UGT51 had lost its ability to synthesize sterol glucoside but exhibited normal growth under various culture conditions. Expression of eitherUGT51 or UGT51B1 in this null mutant under the control of a galactose-induced promoter restored sterol glucoside synthesis in vitro. Lipid extracts of these cells contained a novel glycolipid. This lipid was purified and identified as ergosterol-β-d-glucopyranoside by nuclear magnetic resonance spectroscopy. These data prove that the cloned genes encode sterol-β-d-glucosyltransferases and that sterol glucoside synthesis is an inherent feature of eukaryotic microorganisms.
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cloning and functional expression of ugt genes encoding sterol glucosyltransferases from saccharomyces cerevisiae candida albicans pichia pastoris and Dictyostelium discoideum
Journal of Biological Chemistry, 1999Co-Authors: Dirk Warnecke, Ulrich Zähringer, Ralf Erdmann, Annette Fahl, Bernhard Hube, Frank Muller, Thorsten Zank, Ernst HeinzAbstract:Sterol glucosides, typical membrane-bound lipids of many eukaryotes, are biosynthesized by a UDP-glucose:sterol glucosyltransferase (EC 2.4.1.173). We cloned genes from three different yeasts and from Dictyostelium discoideum, the deduced amino acid sequences of which all showed similarities with plant sterol glucosyltransferases (Ugt80A1, Ugt80A2). These genes fromSaccharomyces cerevisiae (UGT51 =YLR189C), Pichia pastoris(UGT51B1), Candida albicans(UGT51C1), and Dictyostelium discoideum(ugt52) were expressed in Escherichia coli. In vitro enzyme assays with cell-free extracts of the transgenicE. coli strains showed that the genes encode UDP-glucose:sterol glucosyltransferases which can use different sterols such as cholesterol, sitosterol, and ergosterol as sugar acceptors. AnS. cerevisiae null mutant of UGT51 had lost its ability to synthesize sterol glucoside but exhibited normal growth under various culture conditions. Expression of eitherUGT51 or UGT51B1 in this null mutant under the control of a galactose-induced promoter restored sterol glucoside synthesis in vitro. Lipid extracts of these cells contained a novel glycolipid. This lipid was purified and identified as ergosterol-β-d-glucopyranoside by nuclear magnetic resonance spectroscopy. These data prove that the cloned genes encode sterol-β-d-glucosyltransferases and that sterol glucoside synthesis is an inherent feature of eukaryotic microorganisms.