TY - JOUR A1 - Färber, Claudia A1 - Titschack, Jürgen A1 - Schönberg, Christine H. L. A1 - Ehrig, Karsten A1 - Boos, Karin A1 - Baum, Daniel A1 - Illerhaus, Bernd A1 - Asgaard, Ulla A1 - Bromley, Richard G. A1 - Freiwald, André A1 - Wisshak, Max T1 - Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography JF - Biogeosciences N2 - Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 % of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^−2 yr^−1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments. Y1 - 2016 U6 - https://doi.org/10.5194/bg-13-3461-2016 VL - 13 IS - 11 SP - 3461 EP - 3474 CY - http://www.biogeosciences.net/13/3461/2016/ ER - TY - JOUR A1 - Kozlíková, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art Revisited JF - Computer Graphics Forum N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.13072 VL - 36 IS - 8 SP - 178 EP - 204 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Fink, Hiske G. A1 - Baum, Daniel A1 - Wienberg, Claudia A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Mediterranean cold-water corals - an important regional carbonate factory? JF - The Depositional Record Y1 - 2016 U6 - https://doi.org/10.1002/dep2.14 VL - 2 IS - 1 SP - 74 EP - 96 ER - TY - JOUR A1 - Krone, Michael A1 - Kozlíková, Barbora A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Parulek, Julius A1 - Hege, Hans-Christian A1 - Viola, Ivan T1 - Visual Analysis of Biomolecular Cavities: State of the Art JF - Computer Graphics Forum N2 - In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12928 SN - 1467-8659 VL - 35 IS - 3 SP - 527 EP - 551 ER -