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Interactions between different formative processes are reflected in the internal structure of rock glaciers. Therefore, the detection of subsurface conditions can help to enhance our understanding of landform development. For an assessment of subsurface conditions, we present an analysis of the spatial variability of active layer thickness, ground ice content and frost table topography for two different rock glaciers in the Eastern Swiss Alps by means of quasi-3-D electrical resistivity imaging (ERI). This approach enables an extensive mapping of subsurface structures and a spatial overlay between site-specific surface and subsurface characteristics. At Nair rock glacier, we discovered a gradual descent of the frost table in a downslope direction and a constant decrease of ice content which follows the observed surface topography. This is attributed to ice formation by refreezing meltwater from an embedded snow bank or from a subsurface ice patch which reshapes the permafrost layer. The heterogeneous ground ice distribution at Uertsch rock glacier indicates that multiple processes on different time domains were involved in the development. Resistivity values which represent frozen conditions vary within a wide range and indicate a successive formation which includes several advances, past glacial overrides and creep processes on the rock glacier surface. In combination with the observed topography, quasi-3-D ERI enables us to delimit areas of extensive and compressive flow in close proximity. Excellent data quality was provided by a good coupling of electrodes to the ground in the pebbly material of the investigated rock glaciers. Results show the value of the quasi-3-D ERI approach but advise the application of complementary geophysical methods for interpreting the results.
The concept of derivative is characterised with reference to four basic mental models. These are described as theoretical constructs based on theoretical considerations. The four basic mental models—local rate of change, tangent slope, local linearity and amplification factor—are not only quantified empirically but are also validated. To this end, a test instrument for measuring students’ characteristics of basic mental models is presented and analysed regarding quality criteria.
Mathematics students (n = 266) were tested with this instrument. The test results show that the four basic mental models of the derivative can be reconstructed among the students with different characteristics. The tangent slope has the highest agreement values across all tasks. The agreement on explanations based on the basic mental model of rate of change is not as strongly established among students as one would expect due to framework settings in the school system by means of curricula and educational standards. The basic mental model of local linearity plays a rather subordinate role. The amplification factor achieves the lowest agreement values. In addition, cluster analysis was conducted to identify different subgroups of the student population. Moreover, the test results can be attributed to characteristics of the task types as well as to the students’ previous experiences from mathematics classes by means of qualitative interpretation. These and other results of students’ basic mental models of the derivative are presented and discussed in detail.
During the past years, the internal transcribed spacer 2 (ITS2) was established as a commonly used molecular phylogenetic marker for the eukaryotes. Its fast evolving sequence is predestinated for the use in low-level phylogenetics. However, the ITS2 also consists of a very conserved secondary structure. This enables the discrimination between more distantly related species. The combination of both in a sequence-structure based analysis increases the resolution of the marker and enables even more robust tree reconstructions on a broader taxonomic range. But, performing such an analysis required the application of different programs and databases making the use of the ITS2 non trivial for the typical biologist. To overcome this hindrance, I have developed the ITS2 Workbench, a completely web-based tool for automated phylogenetic sequence-structure analyses using the ITS2 (http://its2.bioapps.biozentrum.uni-wuerzburg.de). The development started with an optimization of length modelling topologies for Hidden Markov Models (HMMs), which were successfully applied on a secondary structure prediction model of the ITS2 marker. Here, structure is predicted by considering the sequences' composition in combination with the length distribution of different helical regions. Next, I integrated HMMs into the sequence-structure generation process for the delineation of the ITS2 within a given sequence. This re-implemented pipeline could more than double the number of structure predictions and reduce the runtime to a few days. Together with further optimizations of the homology modelling process I can now exhaustively predict secondary structures in several iterations. These modifications currently provide 380,000 annotated sequences including 288,000 structure predictions. To include these structures in the calculation of alignments and phylogenetic trees, I developed the R-package "treeforge". It generates sequence-structure alignments on up to four different coding alphabets. For the first time also structural bonds were considered in alignments, which required the estimation of new scoring matrices. Now, the reconstruction of Maximum Parsimony, Maximum Likelihood as well as Neighbour Joining trees on all four alphabets requires just a few lines of code. The package was used to resolve the controversial chlorophyceaen dataset and could be integrated into future versions of the ITS2 workbench. The platform is based on a modern, feature-rich Web 2.0 user interface equipped with the latest AJAX and Web-service technologies. It performs HMM-based sequence annotation, structure prediction by energy minimization or homology modelling, alignment calculation and tree reconstruction on a flexible data pool that repeats calculations according to data changes. Further, it provides sequence motif detection to control annotation and structure prediction and a sequence-structure based BLAST search, which facilitates the taxon sampling process. All features and the usage of the ITS2 workbench are explained in a video tutorial. However, the workbench bears some limitations regarding the size of datasets. This is caused mainly due to the immense computational power needed for such extensive calculations. To demonstrate the validity of the approach also for large-scale analyses, a fully automated reconstruction of the Chlorophyta (Green Algal) Tree of Life was performed. The successful application of the marker even on large datasets underlines the capabilities of ITS2 sequence-structure analysis and suggests its utilization on further datasets. The ITS2 workbench provides an excellent starting point for such endeavours.
The aim of current work was contribution to the long-term ongoing project on developing human IL-5 agonists/antagonists that intervene with or inhibit IL-5 numerous functions in cell culture and/or in animal disease models. To facilitate design of an IL-5 antagonist variant or low-molecular weight mimetics only capable of binding to the specific receptor alpha chain, but would lack the ability to attract the receptor common β-chain and thus initiate receptor complex activation it is necessary to gain the information on minimal structural and functional epitopes. Such a strategy was successfully adopted in our group on example of Interleukin 4. To precisely localize minimal structural epitope it is essential to have structure of the ligand in its bound form and especially informative would be structure of complex of the ligand and its specific receptor alpha chain. For this purpose large quantities (tens of milligrams), retaining full biological activity IL-5 and extracellular domain of IL-5 specific receptor α-chain were expressed in a bacterial expression system (E.coli). After successful refolding proteins were purified to 95-99% Stable and soluble receptor:ligand complex was prepared. Each established purification and refolding procedures were subjected to optimization targeting maximal yields and purity. Produced receptor:ligand complex was applied to crystallization experiments. Microcrystals were initially obtained with a flexible sparse matrix screening methodology. Crystal quality was subsequently improved by fine-tuning of the crystallization conditions. At this stage crystals of about 800x150x30µm in size can be obtained. They possess desirable visible characteristics of crystals including optical clarity, smooth facecs and sharp edges. Crystals rotate plane polarized light reflecting their well internal organization. Unfortunately relative slimness and sometimes cluster nature of the produced crystals complicates acquisition of high-resolution dataset and resolution of the structure. With some of obtained crystals diffraction to a resolution up to 4Å was observed.