Feasibility studies of terrestrial laser scanning in Coastal Geomorphology, Agronomy, and Geoarchaeology

Terrestrial laser scanning (TLS) is a newer, active method of remote sensing for the automatic detection of 3D coordinate points. This method has been developed particularly during the last 20 years, in addition to airborne and mobile laser scanning methods. All these methods use laser light and additional angle measurements for the detection of distances and directions. Thus, several thousands to hundreds of thousands of polar coordinates per second can be measured directly by an automatic deflection of laser beams. For TLS measurements, the coordinates and orientation of the origin of the laser beam can be determined to register different scan positions in a common coordinate system. These measurements are usually conducted by Global Navigation Satellite Systems or total station surveying, but also identical points can be used and data driven methods are possible. Typically, accuracies and point densities of a few centimetres to a few millimetres are achieved depending on the method. The derived 3D point clouds contain millions of points, which can be evaluated in post-processing stages by symbolic or data-driven methods. Besides the creation of digital surface and terrain models, laser scanning is used in many areas for the determination of 3D objects, distances, dimensions, and volumes. In addition, changes can be determined by multi-temporal surveys. The terrestrial laser scanner Riegl LMS Z-420i was used in this work in combination with the Differential Global Positioning System system Topcon Hiper Pro, based on Real Time Kinematic (RTK-DGPS). In addition to the direct position determination of the laser scanner, the position of a self-developed reflector on a ranging pole was measured by the RTK-DGPS system to accurately derive the orientation of each measured point cloud. Moreover, the scanner is equipped with an additional, mounted camera Nikon D200 to capture oriented pictures. These pictures allow colouring the point cloud in true colours and thus allow a better orientation. Furthermore, the pictures can be used for the extraction of detailed 3D information and for texturing the 3D objects. In one of the post-processing steps, the direct georeferencing by RTK-DGPS data was refined using the Multi Station Adjustment, which employs the Iterative Closest Point algorithm. According to the specific objectives, the point clouds were then filtered, clipped, and processed to establish 3D objects for further usage. In this dissertation, the feasibility of the method has been analysed by investigating the applicability of the system, the accuracy, and the post-processing methods by means of case studies from the research areas of coastal geomorphology, agronomy, and geoarchaeology. In general, the measurement system has been proven to be robust and suitable for field surveys in all cases. The surveys themselves, including the selected georeferencing approach, were conducted quickly and reliably. With the refinement of the Multi Station Adjustment a relative accuracy of about 1 cm has been achieved. The absolute accuracy is about 1.5 m, limited by the RTK-DGPS system, which can be enhanced through advanced techniques. Specific post-processing steps have been conducted to solve the specific goals of each research area. The method was applied for coastal geomorphological research in western Greece. This part of the study deals with 3D reconstructed volumes and corresponding masses of boulders, which have been dislocated by high energy events. The boulder masses and other parameters, such as the height and distance to the current sea level, have been used in wave transport equations for the calculation of minimum wave heights and velocities of storm and tsunami scenarios and were compared to each other. A significant increase in accuracy of 30% on average compared with the conventional method of simply measuring the axes was detected. For comparison, annual measurements at seven locations in western Greece were performed over three years (2009-2011) and changes in the sediment budget were successfully detected. The base points of the RTK-DGPS system were marked and used every year. Difficulties arose in areas with high surface roughness and slight changes in the annual position of the laser scanner led to an uneven point density and generated non-existing changes. For this reason, all results were additionally checked by pictures of the mounted camera and a direct point cloud comparison. Similarly, agricultural plants were surveyed by a multi-temporal approach on a field over two years using the stated method. Plant heights and their variability within a field were successfully determined using Crop Surface Models, which represent the top canopy. The spatial variability of plant development was compared with topographic parameters as well as soil properties and significant correlations were found. Furthermore, the method was carried out with four different types of sugar-beet at a higher resolution, which was achieved by increasing the height of the measurement position. The differences between the crop varieties and their growth behaviour under drought stress were represented by the derived plant heights and a relation to biomass and the Leaf Area Index was successfully established. With regard to geoarchaeological investigations in Jordan, Spain, and Egypt, the method was used in order to document respective sites and specific issues, such as proportions and volumes derived from the generated 3D models were solved. However, a full coverage of complexly structured sites, like caves or early settlements is partially prevented by the oversized scanner, slow measurement rates, and the necessary minimum measurement distance. The 3D data can be combined with other data for further research by the common georeference. The selected method has been found suitable to create accurate 3D point clouds and corresponding 3D models that can be used in accordance with the respective research problem. The feasibility of the TLS method for various issues of the case studies was proven, but limitations of the used system have also been detected and are described in the respective chapters. Further methods or other, newer TLS systems may be better suited for specific cases

Genomic Mining for Aspergillus Natural Products

SummaryThe genus Aspergillus is renowned for its ability to produce a myriad of bioactive secondary metabolites. Although the propensity of biosynthetic genes to form contiguous clusters greatly facilitates assignment of putative secondary metabolite genes in the completed Aspergillus genomes, such analysis cannot predict gene expression and, ultimately, product formation. To circumvent this deficiency, we have examined Aspergillus nidulans microarrays for expressed secondary metabolite gene clusters by using the transcriptional regulator LaeA. Deletion or overexpression of laeA clearly identified numerous secondary metabolite clusters. A gene deletion in one of the clusters eliminated the production of the antitumor compound terrequinone A, a metabolite not described, from A. nidulans. In this paper, we highlight that LaeA-based genome mining helps decipher the secondary metabolome of Aspergilli and provides an unparalleled view to assess secondary metabolism gene regulation

Scientific Research Data Management for Soil-Vegetation-Atmosphere Data – The TR32DB

The implementation of a scientific research data management system is an important task within long-term, interdisciplinary research projects. Besides sustainable storage of data, including accurate descriptions with metadata, easy and secure exchange and provision of data is necessary, as well as backup and visualisation. The design of such a system poses challenges and problems that need to be solved.This paper describes the practical experiences gained by the implementation of a scientific research data management system, established in a large, interdisciplinary research project with focus on Soil-Vegetation-Atmosphere Data

Genetic Survey of Psilocybe Natural Products

Psilocybe magic mushrooms are best known for their main natural product, psilocybin, and its dephosphorylated congener, the psychedelic metabolite psilocin. Beyond tryptamines, the secondary metabolome of these fungi is poorly understood. The genomes of five species ( P. azurescens , P. cubensis , P. cyanescens , P. mexicana , and P. serbica ) were browsed to understand more profoundly common and species‐specific metabolic capacities. The genomic analyses revealed a much greater and yet unexplored metabolic diversity than evident from parallel chemical analyses. P. cyanescens and P. mexicana were identified as aeruginascin producers. Lumichrome and verpacamide A were also detected as Psilocybe metabolites. The observations concerning the potential secondary metabolome of this fungal genus support pharmacological and toxicological efforts to find a rational basis for yet elusive phenomena, such as paralytic effects, attributed to consumption of some magic mushrooms

Protection from cytomegalovirus after transplantation is correlated with immediate early 1–specific CD8 T cells

T cells are crucial for the control of cytomegalovirus (CMV) in infected individuals. Although CMV-specific T cells can be quantified by various methods, clear correlates of protection from CMV disease have not been defined. However, responses to the pp65 protein are believed to play an important role. Here, the proportions of interferon γ–producing T cells following ex vivo activation with pools of overlapping peptides representing the pp65 and immediate early (IE)-1 proteins were determined at multiple time points and related to the development of CMV disease in 27 heart and lung transplant recipients. Frequencies of IE-1–specific CD8 T cells above 0.2 and 0.4% at day 0 and 2 wk, respectively, or 0.4% at any time during the first months discriminated patients who did not develop CMV disease from patients at risk, 50–60% of whom developed CMV disease. No similar distinction between risk groups was possible based on pp65-specific CD8 or CD4 T cell responses. Remarkably, CMV disease developed exclusively in patients with a dominant pp65-specific CD8 T cell response. In conclusion, high frequencies of IE-1 but not pp65-specific CD8 T cells correlate with protection from CMV disease. These results have important implications for monitoring T cell responses, adoptive cell therapy, and vaccine design