Biosilicification occurs in many organisms. Sponges and diatoms are major examples of them. In th... more Biosilicification occurs in many organisms. Sponges and diatoms are major examples of them. In this chapter, we introduce a modeling approach that describes several biological mechanisms controlling silicification. Modeling biosilicification is a typical multiscale problem where processes at very different temporal and spatial scales need to be coupled: processes at the molecular level, physiological processes at the subcellular and cellular level, etc. In biosilicification morphology plays a fundamental role, and a spatiotemporal model is required. In the case of sponges, a particle simulation based on diffusion-limited aggregation is presented here. This model can describe fractal properties of silica aggregates in first steps of deposition on an organic template. In the case of diatoms, a reaction-diffusion model is introduced which can describe the concentrations of chemical components and has the possibility to include polymerization chain of reactions.
In this paper the development of a model for simulating radiate accretive growth in 3D is discuss... more In this paper the development of a model for simulating radiate accretive growth in 3D is discussed. This growth process is widely found among members of various classes of marine sessile organisms. The model is developed using an existing 2D model for radiate accretive growth by extending a subset of the rules to 3D. The 2D as well as the 3D model are based on an iterative geometric construction. The final 3D model is suitable for the simulation of the emergence of branching growth forms.
In ancient Lake Baikal (East Siberia), freshwater sponges have diversified to an extraordinary de... more In ancient Lake Baikal (East Siberia), freshwater sponges have diversified to an extraordinary degree. The skeleton of Lubomirskia baicalensis, which attains a size of up to 1 m, is constructed from spicules, which are cemented into longitudinal bundles. Our X-ray analysis revealed that the architecture of the specimens follows a highly ordered radiate accretive growth pattern. The spicules have a central axial canal with an axial filament inside. This organic filament is composed of silicatein, the major enzyme involved in silica formation of the spicules. We found that the specific activity of silicatein in samples from the non-growing (basal) zone is much lower than in those from the growth zone (tips) and that even the composition of this molecule differs in these regions. The present study shows for the first time that the turnover of silicatein, the major element of the axial canal of sponge spicules, changes within a sponge specimen depending on the region in which it is found.
In this chapter the development of a model of a growth in three dimensions is discussed. In the f... more In this chapter the development of a model of a growth in three dimensions is discussed. In the first section it is demonstrated how the modelling system for iterative geometric constructions (see also Sect. 2.6) can be extended to 3D. In Sect. 5.2, a discussion follows on the 3D structure of an organism with radiate accretive growth. In Sects. 5.3 and 5.4 it is discussed how this 3D structure can be represented in a model. The results of these sections, a suitable data representation for a 3D object developing in the radiate accretive growth process, is used in the final Sect. 5.6, in which the development of a model of a radiate growth process in three dimensions is presented. Most of the rules discussed in Sect. 3.6, on the iterative geometric constructions for simulating this growth process, will be extended to 3D. In Sect. 3.6 the biological examples used as a case-study were the sponge Haliclona oculata and the stony coral Montastrea annularis. For reasons which will become clear in the next sections, the sponge Haliclona simulans (see Fig. 3.15) is used as an example in this chapter. The biological significance of the rules will be indicated only briefly in this chapter, since most of them were already discussed in Sect. 3.6. The extension to 3D of the simulation model is an essential one, since many aspects of the growth process (e.g. a larger possibility for the branches to avoid each other, the formation of flattened forms influenced by the flow direction) can only be adequately described with a 3D model. For convenience the symbols used in the sections on the 3D model of radiate accretive growth (Sects. 5.3–5.7 are listed separately in Sect. 5.8).
Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐... more Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐hierarchical, non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography. —Acta Zoologica (Stockholm) 00:1–12.As sessile filter feeders, sponges rely on a highly efficient fluid transport system. Their physiology depends on efficient water exchange, which is performed by the aquiferous system. This prominent poriferan anatomical character represents a dense network of incurrent and excurrent canals on which we lack detailed 3D models. To overcome this, we investigated the complex leucon‐type architecture in the demosponge Tethya wilhelma using corrosion casting, microtomography, and 3D reconstructions. Our integrative qualitative and quantitative approach allowed us to create, for the first time, high‐resolution 3D representations of entire canal systems which were used for detailed geometric and morphometric measurements. Canal diameters lack distinct size classes, and bifurcations are non‐uniformly ramified. A relatively high number of bifurcations show previously unknown and atypical cross‐sectional area ratios. Scaling properties and topological patterns of the canals indicate a more complex overall architecture than previously assumed. As a consequence, it might be more convenient to group canals into functional units rather than hierarchical clusters. Our data qualify the leucon canal system architecture of T. wilhelma as a highly efficient fluid transport system adapted toward minimal flow resistance. Our results and approach are relevant for a better understanding of sponge biology and cultivation techniques.
Biosilicification occurs in many organisms. Sponges and diatoms are major examples of them. In th... more Biosilicification occurs in many organisms. Sponges and diatoms are major examples of them. In this chapter, we introduce a modeling approach that describes several biological mechanisms controlling silicification. Modeling biosilicification is a typical multiscale problem where processes at very different temporal and spatial scales need to be coupled: processes at the molecular level, physiological processes at the subcellular and cellular level, etc. In biosilicification morphology plays a fundamental role, and a spatiotemporal model is required. In the case of sponges, a particle simulation based on diffusion-limited aggregation is presented here. This model can describe fractal properties of silica aggregates in first steps of deposition on an organic template. In the case of diatoms, a reaction-diffusion model is introduced which can describe the concentrations of chemical components and has the possibility to include polymerization chain of reactions.
In this paper the development of a model for simulating radiate accretive growth in 3D is discuss... more In this paper the development of a model for simulating radiate accretive growth in 3D is discussed. This growth process is widely found among members of various classes of marine sessile organisms. The model is developed using an existing 2D model for radiate accretive growth by extending a subset of the rules to 3D. The 2D as well as the 3D model are based on an iterative geometric construction. The final 3D model is suitable for the simulation of the emergence of branching growth forms.
In ancient Lake Baikal (East Siberia), freshwater sponges have diversified to an extraordinary de... more In ancient Lake Baikal (East Siberia), freshwater sponges have diversified to an extraordinary degree. The skeleton of Lubomirskia baicalensis, which attains a size of up to 1 m, is constructed from spicules, which are cemented into longitudinal bundles. Our X-ray analysis revealed that the architecture of the specimens follows a highly ordered radiate accretive growth pattern. The spicules have a central axial canal with an axial filament inside. This organic filament is composed of silicatein, the major enzyme involved in silica formation of the spicules. We found that the specific activity of silicatein in samples from the non-growing (basal) zone is much lower than in those from the growth zone (tips) and that even the composition of this molecule differs in these regions. The present study shows for the first time that the turnover of silicatein, the major element of the axial canal of sponge spicules, changes within a sponge specimen depending on the region in which it is found.
In this chapter the development of a model of a growth in three dimensions is discussed. In the f... more In this chapter the development of a model of a growth in three dimensions is discussed. In the first section it is demonstrated how the modelling system for iterative geometric constructions (see also Sect. 2.6) can be extended to 3D. In Sect. 5.2, a discussion follows on the 3D structure of an organism with radiate accretive growth. In Sects. 5.3 and 5.4 it is discussed how this 3D structure can be represented in a model. The results of these sections, a suitable data representation for a 3D object developing in the radiate accretive growth process, is used in the final Sect. 5.6, in which the development of a model of a radiate growth process in three dimensions is presented. Most of the rules discussed in Sect. 3.6, on the iterative geometric constructions for simulating this growth process, will be extended to 3D. In Sect. 3.6 the biological examples used as a case-study were the sponge Haliclona oculata and the stony coral Montastrea annularis. For reasons which will become clear in the next sections, the sponge Haliclona simulans (see Fig. 3.15) is used as an example in this chapter. The biological significance of the rules will be indicated only briefly in this chapter, since most of them were already discussed in Sect. 3.6. The extension to 3D of the simulation model is an essential one, since many aspects of the growth process (e.g. a larger possibility for the branches to avoid each other, the formation of flattened forms influenced by the flow direction) can only be adequately described with a 3D model. For convenience the symbols used in the sections on the 3D model of radiate accretive growth (Sects. 5.3–5.7 are listed separately in Sect. 5.8).
Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐... more Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐hierarchical, non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography. —Acta Zoologica (Stockholm) 00:1–12.As sessile filter feeders, sponges rely on a highly efficient fluid transport system. Their physiology depends on efficient water exchange, which is performed by the aquiferous system. This prominent poriferan anatomical character represents a dense network of incurrent and excurrent canals on which we lack detailed 3D models. To overcome this, we investigated the complex leucon‐type architecture in the demosponge Tethya wilhelma using corrosion casting, microtomography, and 3D reconstructions. Our integrative qualitative and quantitative approach allowed us to create, for the first time, high‐resolution 3D representations of entire canal systems which were used for detailed geometric and morphometric measurements. Canal diameters lack distinct size classes, and bifurcations are non‐uniformly ramified. A relatively high number of bifurcations show previously unknown and atypical cross‐sectional area ratios. Scaling properties and topological patterns of the canals indicate a more complex overall architecture than previously assumed. As a consequence, it might be more convenient to group canals into functional units rather than hierarchical clusters. Our data qualify the leucon canal system architecture of T. wilhelma as a highly efficient fluid transport system adapted toward minimal flow resistance. Our results and approach are relevant for a better understanding of sponge biology and cultivation techniques.
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