13. Hepp, M; Palsson, E; Thomsen, SK; Green, DJ. (2021) Predicting the effects of reservoir water level management on the reproductive output of a riparian songbird.PLoS One 16 Predicting the effects of reservoir water level management on the reproductive output of a riparian songbird
Dams and reservoirs alter natural water flow regimes with adverse effects on natural ecosystems. Quantifying and reducing these effects are important as global demands for energy and water, and the number of dams and reservoir, increase. However, costs and logistic constraints typically preclude experimental assessment of reservoir effects on the environment. We developed a stochastic individual-based model (IBM), parameterized using empirical data, to estimate the annual productivity of yellow warblers that breed in riparian habitat within the footprint of the Arrow Lakes Reservoir in British Columbia, Canada. The IBM incorporated information on breeding phenology, nest site selection, brood parasitism, daily nest survival, re-nesting probabilities and post-fledging survival. We used the IBM to estimate the effect of four different water management scenarios on annual productivity. We found that the IBM accurately estimated average nest success (0.39 +/- 0.10 SD), the proportion of females that produced at least one fledgling during a breeding season (0.56 +/- 0.11), and annual fledging success (2.06 +/- 0.43) under current conditions. The IBM estimated that reservoir operations currently reduce the annual productivity of this population by 37%, from an average of 1.62 to 1.06 independent young/female. Delaying when reservoir water levels reach 435m asl (the minimum elevation occupied by yellow warblers) by approximately 2 weeks was predicted to increase annual productivity to 1.44 independent young/female. The standardized effect on annual productivity of reducing the maximum elevation of the reservoir so that yellow warbler habitat is not inundated (Cohen's d = 1.52) or delaying when water is stored (Cohen's d = 0.83) was primarily driven by inundation effects on post-fledging survival. Reservoir operation effects on breeding birds will be species specific, but this IBM can easily be modified to allow the environmental impacts on the entire breeding bird community to be incorporated into water management decisions. DOI PubMed
12. Knutsdottir, H; Zmurchok, C; Bhaskar, D; Palsson, E; Nogare, DD; Chitnis, AB; Edelstein-Keshet, L. (2017) Polarization and migration in the zebrafish posterior lateral line system.PLoS Computational Biology 13 Polarization and migration in the zebrafish posterior lateral line system
Collective cell migration plays an important role in development. Here, we study the posterior lateral line primordium (PLLP) a group of about 100 cells, destined to form sensory structures, that migrates from head to tail in the zebrafish embryo. We model mutually inhibitory FGF-Wnt signalling network in the PLLP and link tissue subdivision (Wnt receptor and FGF receptor activity domains) to receptor-ligand parameters. We then use a 3D cell-based simulation with realistic cell-cell adhesion, interaction forces, and chemotaxis. Our model is able to reproduce experimentally observed motility with leading cells migrating up a gradient of CXCL12a, and trailing (FGF receptor active) cells moving actively by chemotaxis towards FGF ligand secreted by the leading cells. The 3D simulation framework, combined with experiments, allows an investigation of the role of cell division, chemotaxis, adhesion, and other parameters on the shape and speed of the PLLP. The 3D model demonstrates reasonable behaviour of control as well as mutant phenotypes. DOI
11. Knutsdottir, H; Condeelis, JS; Palsson, E. (2016) 3-D individual cell based computational modeling of tumor cell-macrophage paracrine signaling mediated by EGF and CSF-1 gradients.Integrative Biology 8: 104-119 3-D individual cell based computational modeling of tumor cell-macrophage paracrine signaling mediated by EGF and CSF-1 gradients
ICMB, computational modeling, tumor cell, macrophage, paracrine signalling, EGF and CSF-1
High density of macrophages in mammary tumors has been associated with a higher risk of metastasis and thus increased mortality in women. The EGF/CSF-1 paracrine signaling increases the number of invasive tumor cells by both recruiting tumor cells further away and manipulating the macrophages' innate ability to open up a passage into blood vessels thus promoting intravasation and finally metastasis. A 3-D individual-cell-based model is introduced, to better understand the tumor cellmacrophage interactions, and to explore how changing parameters of the paracrine signaling system affects the number of invasive tumor cells. The simulation data and videos of the cell movements correlated well with findings from both in vitro and in vivo experimental results. The model demonstrated how paracrine signaling is necessary to achieve co-migration of tumor cells and macrophages towards a specific signaling source. We showed how the paracrine signaling enhances the number of both invasive tumor cells and macrophages. The simulations revealed that for the in vitro experiments the imposed no-flux boundary condition might be affecting the results, and that changing the setup might lead to different experimental findings. In our simulations, the 3 : 1 tumor cell/macrophage ratio, observed in vivo, was robust for many parameters but sensitive to EGF signal strength and fraction of macrophages in the tumor. The model can be used to identify new agents for targeted therapy and we suggest that a successful strategy to prevent or limit invasion of tumor cells would be to block the tumor cellmacrophage paracrine signaling. This can be achieved by either blocking the EGF or CSF-1 receptors or supressing the EGF or CSF-1 signal. DOI
10. Chubaty, AM; Ma, BO; Stein, RW; Gillespie, DR; Henry, LM; Phelan, C; Palsson, E; Simon, FW; Roitberg, BD. (2014) On the evolution of omnivory in a community context.Ecology and Evolution 4: 251-265 On the evolution of omnivory in a community context
Community structure; density-dependent; diet choice; evolutionary game; frequency-dependent; genotype-environment interaction; omnivory; optimal foraging; phenotype
Omnivory is extremely common in animals, yet theory predicts that when given a choice of resources specialization should be favored over being generalist. The evolution of a feeding phenotype involves complex interactions with many factors other than resource choice alone, including environmental heterogeneity, resource quality, availability, and interactions with other organisms. We applied an evolutionary simulation model to examine how ecological conditions shape evolution of feeding phenotypes (e.g., omnivory), by varying the quality and availability (absolute and relative) of plant and animal (prey) resources. Resulting feeding phenotypes were defined by the relative contribution of plants and prey to diets of individuals. We characterized organisms using seven traits that were allowed to evolve freely in different simulated environments, and we asked which traits are important for different feeding phenotypes to evolve among interacting organisms. Carnivores, herbivores, and omnivores all coexisted without any requirement in the model for a synergistic effect of eating plant and animal prey. Omnivores were most prevalent when ratio of plants and animal prey was low, and to a lesser degree, when habitat productivity was high. A key result of the model is that omnivores evolved through many different combinations of trait values and environmental contexts. Specific combinations of traits tended to form emergent trait complexes, and under certain environmental conditions, are expressed as omnivorous feeding phenotypes. The results indicate that relative availabilities of plants and prey (over the quality of resources) determine an individual's feeding class and that feeding phenotypes are often the product of convergent evolution of emergent trait complexes under specific environmental conditions. Foraging outcomes appear to be consequences of degree and type of phenotypic specialization for plant and animal prey, navigation and exploitation of the habitat, reproduction, and interactions with other individuals in a heterogeneous environment. Omnivory should not be treated as a fixed strategy, but instead a pattern of phenotypic expression, emerging from diverse genetic sources and coevolving across a range of ecological contexts. DOI
9. Knutsdottir, H; Palsson, E; Edelstein-Keshet, L. (2014) Mathematical model of macrophage-facilitated breast cancer cells invasion.Journal of Theoretical Biology 357: 184-199 Mathematical model of macrophage-facilitated breast cancer cells invasion
Paracrine signalling; Linear stability analysis; Chemotaxis equation; Metastasis; Discrete model
Mortality from breast cancer stems from its tendency to invade into surrounding tissues and organs. Experiments have shown that this metastatic process is facilitated by macrophages in a short-ranged chemical signalling loop. Macrophages secrete epidermal growth factor, EGF, and respond to the colony stimulating factor 1, CSF-1. Tumor cells secrete CSF-1 and respond to EGF. In this way, the cells coordinate aggregation and cooperative migration. Here we investigate this process in a model for in vitro interactions using two distinct but related mathematical approaches. In the first, we analyze and simulate a set of partial differential equations to determine conditions for aggregation. In the second, we use a cell-based discrete 3D simulation to follow the fates and motion of individual cells during aggregation. Linear stability analysis of the PDE model reveals that decreasing the chemical secretion, chemotaxis coefficients or density of cells or increasing the chemical degradation in the model could eliminate the spontaneous aggregation of cells. Simulations with the discrete model show that the ratio between tumor cells and macrophages in aggregates increases when the EGF secretion parameter is increased. The results also show how CSF-1/CSF-1R autocrine signalling in tumor cells affects the ratio between the two cell types. Comparing the continuum results with simulations of a discrete cell-based model, we find good qualitative agreement. (C) 2014 Elsevier Ltd. All rights reserved. DOI PubMed
8.Palsson, E. (2009) A CAMP Signaling Model Explains the Benefit of Maintaining Two Forms of Phosphodiesterase in Dictyostelium.Biophysical Journal 97: 2388-2398 A CAMP Signaling Model Explains the Benefit of Maintaining Two Forms of Phosphodiesterase in Dictyostelium
CYCLIC-NUCLEOTIDE PHOSPHODIESTERASE; SPIRAL WAVES; DICYOSTELIUM-DISCOIDEUM; AMP PHOSPHODIESTERASE; PATTERN-FORMATION; CELL-MOVEMENT; CALCIUM WAVES; CHEMOTAXIS; PROPAGATION; SIZE
Starving Dictyostelium cells respond chemotactically to cell-generated waves of cyclic adenosine -3',5'- monophosphate (cAMP) that guide cell aggregation toward a signaling center. In this process, a large number of cells are recruited, resulting in the formation of aggregation territories that are essential for fruiting body formation. The enzyme PdsA phosphodiesterase (PIDE), a crucial component of the signaling system, breaks down the external cAMP and can be either membrane-bound or secreted. The existence of two such forms is unusual in cell biology, and it remains to be determined why they have both been maintained through evolution. Here, using a model of the cAMP signaling system, I show that colonies can successfully organize into aggregates over a wider range of initial cell densities when both forms of PIDE are present in an appropriately tuned ratio than when only a single form is present. The model indicates that membrane-bound PIDE maintains aggregation-territory integrity in colonies with high initial cell density, whereas the secreted form is important for wave propagation at low cell densities. Thus, the ultimate retention of both forms can increase territory size. These findings have implications for other excitable media, including Ca2+ propagation in cardiac cells and propagation of electrical excitation in nerve axons, since these systems have similar features of spatial nonuniform "release" and "degradation" of the relevant signals. DOI
7.Palsson, E. (2008) A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems.Journal of Theoretical Biology 254: 1-13 A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems
Dictyostelium; differential cell adhesion; pattern formation; ellipsoidal cells; deformable cells; prestalk
A three-dimensional mathematical model is used to determine the effects of adhesion and cell signalling on cell movements during the aggregation and slug stages of Dictyostelium discoideum (Dd) and to visualize cell sorting. The building blocks of the model are individual deformable ellipsoidal cells, where movement depends on internal parameter state (cell size and stiffness) and on external cues from the neighboring cells, extracellular matrix, and chemical signals. Cell movement and deformation are calculated from equations of motion using the total force acting on each cell, ensuring that forces are balanced. The simulations show that the sorting patterns of prestalk and prespore cells, emerging during the slug stage, depend critically on the type of cell adhesion and not just on chemotactic differences between cells. This occurs because cell size and stiffness can prevent the otherwise faster cells from passing the slower cells. The patterns are distinctively different when the prestalk cells are more or less adhesive than the prespore cells. These simulations suggest that sorting is not solely due to differential chemotaxis, and that differences in both adhesion strength and type between different cell types play a very significant role, both in Dictyostelium and other systems. (C) 2008 Elsevier Ltd. All rights reserved. DOI
6.Palsson, E. (2007) A 3-D Deformable Ellipsoidal Cell Model with Cell Adhesion and Signaling.In: Mathematics and Biosciences in Interaction Chapter 4 pp 271-299 A 3-D Deformable Ellipsoidal Cell Model with Cell Adhesion and Signaling
In this chapter a three-dimensional model of ellipsoidal cells is presented and used to study how cell-cell signaling, cell adhesion, chemotaxis and differentiation all work together in a coordinated fashion to give rise to the developed organism. The Dictyostelium discoideum is used as a model system, since it is simple, yet has all the basic cell-cell interactions. Another goal of introducing this model is to achieve visualization of cell movements and signal propagation in 3-D space.
4.Palsson, E. (2001) A three-dimensional model of cell movement in multicellular systems.Future Generation Computer Systems 17: 835-852 A three-dimensional model of cell movement in multicellular systems
multicellular systems; Dictyostelium discoideum; chemotactic signals; cell motility
A mathematical model for cell movement in multicellular systems has been developed that allows us to simulate and visualize, in three dimensions, individual cell movements in a number of multicellular systems. These include cell movement during aggregation and slug stage of Dictyostelium discoideum, embryogenesis, limb formation and wound healing. The model is quite adaptable to a number of systems, due to the way it is designed. The building blocks of the model are individual cells, where each cell has certain given properties that are not necessarily the same for all cells. The basic properties are that a cell can deform under force (either stretch or compress), while conserving its volume, it adheres to other cells and it can generate an active motive force. The response of a cell depends on its internal parameter state, and on the information it receives from its external environment, which includes neighbor cells, the extracellular matrix and chemical signals. The net force on a cell is calculated by summing up ail the forces that a cell experiences at its surroundings. Each cell is then moved and deformed according to the equations of motion and deformation. Finally, the net movement of all the cells gives the collective movement of the entire tissue. Here we introduce this model and show examples of its applications and compare the results with experimental data. In the first simulations, we show how different cell types can be sorted out based solely on differences in adhesion. We compare our results to cell sorting experiments done by Steinberg and co-workers [R.A. Foty, C.M. Pfleger, G. Forgacs, M.S. Steinberg, Development 122 (1996) 1611-1620; M.S. Steinberg, Reconstruction of tissues by dissociated cells, Science 141 (1963) 3579] using values for adhesion within the range of the experimental values, acid show that the model reproduces the experiments very well. We also present results from simulations of Dictyostelium movements. We first modeled the aggregation stage, where cells are aggregating chemotactically, towards a signaling center, in response to cAMP waves. In these simulations one can observe stream formation and how the mound arises due to the inward motion of the cells towards the signaling center. Later we studied simulations of 2D slugs, and compared them to observations of 2D slugs done by Bonner [J.T. Bonner, Proc. Natl. Acad. Sci. USA 95 (1998) 9355-9359]. (C) 2001 Elsevier Science B.V. All rights reserved.
3.Palsson, E; Othmer, HG. (2000) A model for individual and collective cell movement in Dictyostelium discoideum.Proceedings of the National Academy of Sciences of the United States of America 97: 10448-10453 A model for individual and collective cell movement in Dictyostelium discoideum
The cellular slime mold Dictyostelium discoideum is a widely used model system for studying a variety of basic processes in development, including cell-cell signaling, signal transduction, pattern formation, cell motility. and the movement of tissue-like aggregates of cells. Many aspects of cell motion are poorly understood, including how individual cell behavior produces the collective motion of cells observed within the mound and slug. Herein, we describe a biologically realistic model for motile D, discoideum cells that can generate active forces, that interact via surface molecules, and that can detect and respond to chemotactic signals. We model the cells as deformable viscoelastic ellipsoids and incorporate signal transduction and cell-cell signaling by using a previously developed model. The shape constraint restricts the admissible deformations but makes the simulation of a large number of interacting cells feasible, Because the model is based on known processes, the parameters can be estimated or measured experimentally. We show that this model can reproduce the observations on the chemotactic behavior of single cells, streaming during aggregation, and the collective motion of an aggregate of cells driven by a small group of pacemakers. The model predicts that the motion of two-dimensional slugs [Bonner. J, T, (1998) Proc. Natl. Acad. Sci. USA 95, 9355-9359] results from the same behaviors that are exhibited by individual cells; it is not necessary to invoke different mechanisms or behaviors. Our computational experiments also suggest previously uncharacterized phenomena that may be experimentally observable.
2.Palsson, E; Lee, KJ; Goldstein, RE; Franke, J; Kessin, RH; Cox, EC. (1997) Selection for spiral waves in the social amoebae Dictyostelium.Proceedings of the National Academy of Sciences of the United States of America 94: 13719-13723 Selection for spiral waves in the social amoebae Dictyostelium
Starving Dictyostelium amoebae emit pulses of the chemoattractant cAMP that are relayed from cell to cell as circular and spiral waves. We have recently modeled spiral wave formation in Dictyostelium. Our model suggests that a secreted protein inhibitor of an extracellular cAMP phosphodiesterase selects for spirals. Herein we test the essential features of this prediction by comparing wave propagation in wild type and inhibitor mutants. We find that mutants rarely form spirals. The territory size of mutant strains is approximately 50 times smaller than wild type, and the mature fruiting bodies are smaller but otherwise normal. These results identify a mechanism for selecting one wave symmetry over another in an excitable system and suggest that the phosphodiesterase inhibitor may be under selection because it helps regulate territory size.
1.Palsson, E; Cox, EC. (1996) Origin and evolution of circular waves and spirals in Dictyostelium discoideum territories.Proceedings of the National Academy of Sciences of the United States of America 93: 1151-1155 Origin and evolution of circular waves and spirals in Dictyostelium discoideum territories
cellular slime molds; phosphodiesterase; morphogenesis; phosphodiesterase inhibitor; self organization
Randomly distributed Dictyostelium discoideum cells form cooperative territories by signaling to each other with cAMP, Cells initiate the process by sending out pulsatile signals, which propagate as waves, With time, circular and spiral patterns form, We show that by adding spatial and temporal noise to the levels of an important regulator of external cAMP levels, the cAMP phosphodiesterase inhibitor, we can explain the natural progression of the system from randomly firing cells to circular waves whose symmetries break to form double- and single- or multi-armed spirals, When phosphodiesterase inhibitor is increased with time, mimicking experimental data, the wavelength of the spirals shortens, and a proportion of them evolve into pairs of connected spirals, We compare these results to recent experiments, finding that the temporal and spatial correspondence between experiment and model is very close.