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Parsimonious Histograms
(2010)
The dissertation is concerned with the construction of data driven histograms. Histograms are the most elementary density estimators at all. However, they require the specification of the number and width of the bins. This thesis provides two new construction methods delivering adaptive histograms where the required parameters are determined automatically. Both methods follow the principle of parsimony, i.e. the histograms are solutions of predetermined optimization problems. In both cases, but under different aspects, the number of bins is minimized. The dissertation presents the algorithms that solve the optimization problems and illustrates them by a number of numerical experiments. Important properties of the estimators are shown. Finally, the new developed methods are compared with standard methods by an extensive simulation study. By means of synthetic samples of different size and distribution the histograms are evaluated by special performance criteria. As one main result, the proposed methods yield histograms with considerably fewer bins and with an excellent ability of peak detection.
Deciphering the entire protein complement of a living cell together with the elucidation of dynamic processes on protein level are the main goals of proteomics as it is used today. To achieve this goal, namely the elucidation of dynamic processes of the entire bacterial cell, we have developed strategies and distinct workflows to cover the most proteins in different subcellular localizations in bacteria together with a stable isotopes labeling approach to follow temporal and spatial changes in different proteomic subfractions. In this work, it has been shown that the use of mass spectrometry based in vivo quantitation techniques and the application of subcellular and chromatographic fractionation has lead to a new level of qualitative and quantitative proteomics data. Emphasizing on the studies revealing the dynamics of the bacterial physiology on a time resolved base, both spatial and temporal processes can be monitored to obtain knowledge on physiological processes in a depth that has not been reached before in comparable global studies.
A central point of this thesis is the investigation of surface structure and surface forces, which are created by single layers of linear polyelectrolytes (PE). In detail, the properties of cationic poly(allylamine)hydrochloride (PAH) and poly-l-lysine (PLL) and anionic sodium poly(styrene sulfonate) (PSS) are determined, which have been physisorbed onto oppositely charged silica surfaces in presence of a predefined salt concentration IAds. For these investigations, a new averaging method for colloidal probe (CP) force profiles is developed, which leads to an ultimate force resolution of 1 pN after the data processing, (signal to noise ratio of > 1000). Furthermore, a new kind of tapping mode imaging is presented (so called colloidal probe tapping mode, CPTM), which uses a CP instead of a sharp tip and hence which allows to resolve lateral inhomogeneously distributed surface forces. The basics to understand such-like obtained tapping mode images are developed. For adsorption from salt-free solution (IAds = 0) the dominance of an electrostatic double layer repulsion is observed, which is commonly attributed to the adsorption of the PE chains into a rather flat and compact layer and which is in full agreement with theoretical predictions and enormous experimental data available in literature. However, even a small addition of salt to the deposition solution (i.e. IAds > 1 mM NaCl) introduces a new contribution to the surface force, which is attributed to PE chains that are non-flatly physisorbed. Using scaling considerations, it is shown for all investigated PE that this non-flat conformation can be described by brush-like chain adsorption (cf. Section 3.3.5); other conformations like mushroom or pancake are excluded (cf. Section 5.3). Interestingly, these non-flatly physisorbed chains combine properties of neutral and PE brushes: (i) The force is very well described by the theory of Alexander and de Gennes (AdG, cf. Section 5.4). By fitting the AdG force law to the data, it is possible to determine the (brush) thickness L of the PE layer and the average distance s between brush-like physisorbed chains. Although the chains are charged the electrostatic contribution to the surface forces is too small to be noticeable (cf. Section 5.4.2). (ii) The thickness L of this PE layer is much larger compared to the compact layer (observed for salt-free adsorption) and is also subject to a pronounced swelling and shrinking if the bulk salt concentration I is decreased or increased, respectively. Surprisingly, all measurements indicate that L follows a scaling law known for salted end-grafted PE brushes, i.e. L ~ N (I s^2)^(-1/3) (with N denoting the degree of polymerization). Furthermore, the osmotic brush phase is never observed in the experiments, but chain stretching up to 1 / 3 of the contour length is regularly achieved. CPTM imaging applied to PSS shows that the brush-like physisorbed chains are not homogenously distributed over the surface, but form brush domains which coexist with flatly physisorbed chains (cf. sections 5.5 and 5.6). This clearly shows that PSS generally physisorbs in two distinct phases, which differ in conformation (flat vs. brush) and the surface force caused (electrostatic vs. steric repulsion). The force profile of the two phase system is in good approximation simply the superposition of a steric and an electrostatic repulsion, whereby their respective contribution to the composed force profile is given by their area fraction. The quantitative analysis reveals that L and s of the brush phase are independent on IAds. This is remarkable, as a change in IAds is known to induce a continuous transition between a stretched (low IAds) and coiled chain conformation (high IAds) in the deposition solution (cf. [Fleer1993, Yashiro2002]). Hence, one can conclude that the conformation in solution does not necessarily correspond to the conformation after adsorption. It is also shown that the area fraction A of the brush domains strongly depends on N and IAds. For example, for constant N the scaling relation A ~ sqrt(IAds) is determined, which is very similar to the common observation that the surface coverage %Gamma of adsorbed PE layers increases also with %Gamma ~ sqrt(IAds) [Schmitt1996, Cosgrove1986, Ahrens2001, Yim2000, Gopinadhan2007, Cornelson2010]. This suggest that brush-like physisorbed PE chains are responsible for the increase in %Gamma. In fact, Section 5.6 shows that the mass of the brush phase is approx. 0.5 mg/m² which is comparable to the increase in %Gamma reported in literature for IAds = 1 M NaCl [Cosgrove1986, Schmitt1996, Ahrens2001]. As a change in IAds does not affect L and s, but solely the brush area fraction A, it is argued in Section 5.6 that an increase in IAds can be understood as a phase transition from the (disordered) flat phase towards the (ordered and extended) brush phase. Here, further theoretical considerations would be desirable.
This thesis presents the results of experimental investigations of the vertical and lateral properties of polyelectrolyte multilayer films (PEMs) adsorbed on a solid support. PEMs are a new class of organic thin films based on self-assembly layer-by-layer (LbL) processes of oppositely charged polyelectrolytes (charged polymers). The LbL assembly technique allows precise control of film thickness within a few nanometers and makes PEM systems especially interesting for technical applications. Thin films are prepared by alternating exposure of a hydrophilic substrate to solutions of oppositely charged polyelectrolytes. In this work, synthetic polycation poly (allylamine hydrochloride) (PAH) and polyanion poly (styrene sulfonate) (PSS) have been used. Range and amplitude of the electrostatic force during PEM build-up, has been shielded by use of high salt concentration in the deposition solution. As a foundation of any theory, role of non-elecrostatic (secondary) forces is explored. Four complementary methods have been combined to investigate the properties and composition of PEMs. X-ray reflectivity is sensitive to electron density gradients, and therefore provides information about film thickness, average electron density and interfacial roughness between materials of different electron densities (like PEM and air). Neutrons are the unique probe that is sensitive to the internal order of the multilayers (scattering length density variation) due to selective deuteration of the layers (PSS replaced by PSS_d). Therefore neutron reflectivity at V6 beamline, at the research reactor BER II, Helmholtz Centre for Materials and Energy (former Hahn-Meitner-Institute), was used in this work. Ultraviolet-visible (UV-Vis) light induces the characteristic absorption peak of polyelectrolytes and metallic nanoparticles, therefore with UV-Vis absorption spectroscopy is possible to probe the aggregation of metallic nanoparticles embedded into PEM by measuring their absorption spectra (imaginary part of the refraction index). Atomic force microscopy (AFM) allows to observe lateral structures at nano-level and to obtain surface topology of the films. Application of only small forces (pN) is achieved by use of a intermittent contact (tapping) mode in air. Summarizing the main results, the unambiguous parametrization of the investigated system for neutron reflectivity measurements enables to obtain detailed information about internal interfaces. New approach for polyelectrolyte multilayer architectures consisting of thick protonated and deuterated blocks can be used in order to distinguish different zones of the thin film growth which can be described as precursor and core zones. Thus, almost no bound water is found in precursor layers at 0% relative humidity, which suggests that water is mobile and the precursor layer is not in the glassy state like in the central zone of the PEM. Swelling behaviour of the PEMs (reversibility of the swelling) can be understood in terms of equilibrium reactions. Explored influence of temperature and type of salt used during preparation contributes to a better understanding of the formation of PEMs. The dependence of the film thickness on preparation temperature, concentration and the type of salt can be described by the hydrophobic nature of the effect. Experimental observations demonstrate that it is possible to decrease both the range and the amplitude of the electrostatic force by using an ion concentration of at least 0.1 mol/L in the solution. The role of secondary interactions such as hydrophobic attraction of the chains that can overcome electrostatic repulsion and become the major contributing factor for the layer formation and resulting structures is emphasized.
This work proposes and experimentally evaluates a new method and the first prototypic design of an apparatus for the objective assessment of peripheral dynamic stereovision. Peripheral dynamic stereovision is understood as the ability to perceive, recognize and observe moving objects in the visual periphery without sacrificing foveal fixation, i.e. shifting the line of sight (e.g. moving the eyes or the head) and loosing attention to the scene of interest. The presence of stereopsis on top further enhances the perceptive quality by adding the third dimension with judgment of depth and estimation of relative spatial positions as central clues for orientation, coordinative interaction and navigation in space. Based on findings that moving stereoscopic contours can induce distinctive optokinetic reactions, a panoramic stimulus pattern was rotated round subjects’ heads. Designed after the Frisby Stereotest, solely the binocular parallax resulting from the plate thickness carries stereoscopic information, excluding all other depth clues. A specially fitted goggle frame assured correct binocular alignment of the subjects adding objectivity. In first experiments, voluntary reactions (pushing a buzzer button) and involuntarily triggered ocular responses have been registered. The Performance Level (PL) and Confidence Ratio (CR) were introduced as benchmarks for voluntary reactions. Despite larger spreads, the PL averaged at 60 % while an elevated CR confirmed a low error rate of 16 % and thus high overall credibility. Poor performance of available recording hard- and software, in many cases, rendered the analysis of involuntary ocular reactions less exhaustive. It was however observable that objects that appear in the periphery of the visual field triggered the onset of nystagmoid search and tracking mechanisms. Finally, mean peripheral locations of subjects’ active reactions have been established at 30 degrees. The outcome of this pilot study in principle confirmed basic feasibility, conceptual validity and practical applicability of this novel method. Prospective fields of application with raised demands on peripheral dynamic stereopsis have been identified and critically assessed. The applicative possibilities and exclusive advantages of this test combining the assessment of stereopsis and dynamic visual field testing have not been matched by solutions published so far. Before however commercialization should be aimed at, design-related issues, including the implementation of electrophysiological ocular measurements, need to be addressed first to lead the post-prototype development to higher diagnostic expressiveness and reliability.
To uncover the genetic structure of Populus euphratica forests along the Tarim River in Xinjiang, China, a PCR set of eight microsatellite markers was established. 18 primer pairs originally developed for P. tremuloides and P. trichocarpa were screened for amplification in P. euphratica. The eight most variable loci were selected for further genotyping experiments. Subsequently, two multiplex PCR assays, each containing four loci, were set up and optimized. Three populations containing altogether 436 trees were used to characterize the selected loci. The set was found to be moderately polymorphic (mean expected heterozygosity = 0.57). The resolution was sufficient to discriminate even siblings with high confidence (PID = 1.81x10-5). Cumulative exclusion probabilities were 0.89 (single parent), 0.98 (paternity), and 1.00 (parent pair) and proved the set’s suitability for parentage analysis. Practical and theoretical analysis of consequences of genotyping errors in this semi-clonal plant showed that the vast majority of errors (62.1%) lead to division of identical genotypes. Merging of different genotypes was found to be a very rare case (0.4%). This always leads to an overestimation of genotypes. A similarity threshold of one allele difference between two genotypes to be regarded as being identical lead to an underestimation of clonal richness and genotype number of one per cent compared to an overestimation of more than 20 per cent without such a threshold. Allowing a certain amount of variation is therefore expected to reflect the clonal structure better than an analysis that considers exact matches only. Using a combination of morphological and molecular analyses, a first study demonstrated that root suckers are clearly distinguished from seedlings in their root architecture. Root suckering starts when trees are 10–15 years old and bridges distances of up to 40 m at a time. Root suckers depend on their parent tree for at least five years and are expected to have a higher mortality than generatively grown trees. Molecular analysis of old growth stands revealed a highly variable proportion of clonal growth between different stands. In the study area, the proportion of clonality decreases with distance to the main river bed (R = 0.31 at the site closest to the main river, R = 0.97 at the site farthest away from the river). An analysis of the history of river movements at different sites indicates a dependency of clonal growth on the frequency of ground water replenishment by the yearly floods. Genetic differentiation among the stands in the study area is low (FST = 0.055), and isolation by distance was not detectable (P = 0.058). Also, the river does not function as a vector for directed gene flow in downstream direction (P > 0.11). The forests are therefore considered to be one large panmictic metapopulation with unrestricted gene flow. Clonal growth does not lead to higher final stand densities (P = 0.99) and is obviously not of crucial importance for stand survival. Furthermore, analysis of vitality measures and size differences indicate that root suckers are in disadvantage both in vitality and in survival rate compared to seedlings. In this light, a possible function of clonal growth as a luxury strategy to enhance a genetic individual’s reproduction success under good site conditions can be discussed. The genetic structure of the (meta)population bears direct implications for management and conversation of the Tugai forest in Xinjiang. Due to the low degree of differentiation and the unhindered gene flow even small, fragmented, or isolated populations have conservational value, thereby clearly answering the SLOSS question (a single large or several small protected areas) in the latter sense. More than that, non-clonal stands with the highest amount of genotypic diversity can be easily identified on satellite and aerial images. Selection of such stands for conservation is therefore possible without expensive and time-consuming molecular analyses.
The objectives of the present work are to relate the spatial distribution of benthic macrofauna in the Baltic Sea to patterns in environmental variables describing near-bottom hydrographical conditions and sediment characteristics, analyzing the data for two various spatial extents. The first case study is devoted to an exploratory statistical description of the prevailing ecological structure within the limited area attached to the region of the Mecklenburg Bight. Key environmental descriptors of spatial distribution of macrofaunal communities were disclosed within the area of investigation: water depth, regarded as a proxy for other environmental factors, and total organic content. Distinct benthic assemblages that are discriminated by particular species (Hydrobia ulvae–Scoloplos armiger, Lagis koreni–Mysella bidentata and Capitella capitata–Halicryptus spinulosus) were defined. Each assemblage is related to different spatial subarea and is characterized by a certain variability of environmental factors. This study represented the basis for the predictive modelling of species distribution in the selected investigation area, which constituted the next part of the investigation. Species-specific models predicting the probability of occurrence relative to environmental and sedimentological characteristics were developed for 29 representative macrofaunal species using a logistic regression modelling approach. Subsequently, the technique for a predictive modelling of species distributions in response to abiotic parameters based on single-factor logistic regression models, utilizing Akaike’s information criterion (AIC) and Akaike weights for multimodel inference, was used. Thus, probabilities of occurrence for selected exemplary species (Arctica islandica, Hediste diversicolor, Pygospio elegans, Tubificoides benedii and Scoloplos armiger) were modelled and mapped. Finally, the investigation proceeded on a large spatial scale. The discriminating ability of such factors as salinity, bathymetry, and sediment characteristics (considered only generally due to the lack of more detailed data) to explain the occurrence of typical macrozoobenthic species on the Baltic Sea-wide extend was tested. Full coverage macrofauna distribution maps, though being increasingly demanded, are generally lacking, with information being merely restricted to point observations. In contrast to spatial interpolation, periled by presence of short distance changes in community structure and dependence of the result on density of the samples, predictive habitat suitability modelling allows to objectively produce distribution maps at a level of detail limited only by the availability and resolution of the environmental data. Various literature sources and available databases were analyzed in respect to the information on macrozoobenthos distribution in the Baltic Sea, resulting in the compilation of an extensive list of taxa and an inventory dataset on species distribution for the whole Baltic Sea. The study demonstrates the need to analyze species’ relationships in gradient systems such as the Baltic Sea and provides a basis for a tool to predict natural and anthropogenic forced changes in species distribution.
Kurze Inhaltszusammenfassung in einer weiteren Sprache (Englisch): Muong Lay is one of the important social and economic areas in Northwestern Vietnam. Landslides occur frequently in the area and seriously affect local livelihoods and living conditions. Therefore, the problem of landslide hazard and mitigation for a sustainable development of this area is significant. The spatial analysis of landslide hazard assessment in the mountainous regions in Muong Lay is important to address this development challenge. This study focuses on the application of GIS and RS to landslide hazard assessment, especially for support of GIS modeling to landslide hazard susceptibility for Muong Lay area. By using Remote sensing with LandSat TM image and aerial photos of scale 1:50,000 and using statistical models with GIS-software’s ENVI3.4, ILWIS3.0, PCI9.0 and ARC/GIS9.1, the study tries to evaluate and estimate the landslide in relation with naturally different elements of natural conditions such as geology, geomorphology, geology-engineering, tectonics, hydrology, rainfall, etc… Especial, the study firstly aims to produce the causal factor maps by verifying digital data. These factors then will be applied in a methodology based on statistical methods such as: “bivariate statistical analysis” and “multivariate statistical analysis” approach to calculate the susceptibility level of each class of each factor to landslide. The integration of Geographic Information System (GIS) and Remote Rensing (RS)for landslide hazard zonation and assessment is a valid approach. In these researches various methods for image integration and information extraction have been analysed and evaluated in detail.
Summary Cyanobacteria are a diverse and ancient group of photosynthetic prokaryotic organisms that can inhabit a wide range of environments including extreme conditions such as hot springs, desert soils and the Antarctic. They are abundant producers of natural products well recognized for their bioactivity and utility in drug discovery and biotechnology applications. Novel intracellular and extracellular compounds from various cultured and field cyanobacteria with diverse biological activities and a wide range of chemical classes have considerable potential for development of pharmaceuticals and other biomedical applications. However, cyanobacteria are still viewed as unexplored source of potential drugs. Especially the collections of cyanobacterial strains from South East Asia where biodiversity is high are still largely unexplored. Thus, we investigated twelve soil cyanobacterial strains isolated from soil samples collected from rice, cotton, and coffee fields in Dak Lak province of Vietnam and one marine strain, Lyngbya majuscula collected from Khanh Hoa province of Vietnam for the search for new compounds with antimicrobial and cytotoxic activities. From the 12 soil cyanobacterial strains, 48 extracts prepared with n-hexane, methanol, and water for biomasses and ethyl acetate for growth media were screened for antibacterial activity against Gram-positive bacteria (Bacillus subtilis ATCC 6051 and Staphylococcus aureus ATCC 6538) and Gram-negative bacteria (Escherichia coli ATCC 11229, Pseudomonas aeruginosa ATCC 27853). Of 48 extracts, 47.92% and 45.83% showed activity against Bacillus subtilis and Staphylococcus aureus, respectively, while 22.92% and 6.25% exhibited activity against Escherichia coli and Pseudomonas aeruginosa, respectively. All investigated cyanobacteria (12/12) showed antibacterial activity to at least one of the test organisms applied. Among the active extracts, extracts obtained from 5 cyanobacterial strains, Westiellopsis sp. VN, Calothrix javanica, Scytonema ocellatum, Anabaena sp. and Nostoc sp. showed the highest strength and range of antibacterial activity and therefore were selected for chemical investigation with an emphasis on the isolation and structure elucidation of antimicrobial compounds. Bioassay-guided fractionation of the methanol extract prepared from biomass of Westiellopsis sp. VN by silica gel chromatography, followed by sephadex LH-20 chromatography and reversed-phase HPLC led to isolation and identification of 6 compounds as ambiguine D isonitrile, ambiguine B isonitrile, dechloro-ambiguine B isonitrile, fischerellin A, hydroxy-eicosatetraenoic acid and methoxy-nonadecadienoic acid. Identification of these active compounds was established by direct comparison of our spectroscopic data, including 1H NMR and HR-ESI-MS with those reported in the literature. All these compounds showed biological activity. The identification of fatty acids and other volatile components by GS-MS in the active MeOH fraction obtained from EtOAc extract of growth medium was done before commencing further fractionation processes. Culture optimization of Westiellopsis sp.VN showed that NaNO3 deficiency increased accumulation of antimicrobial compounds. Biosynthesis of antimicrobial compounds increased over cultivation time resulting in increased diameter of inhibition zone of the methanol extract towards the end of the 7-to 8- week growth period, but the most clear inhibition zone of this extract was detected after cultivation time of 8 weeks. Bioassay-guided fractionation of the methanol extract prepared from biomass of either Calothrix javanica by C18 chromatography followed by reversed-phase HPLC or Scytonema ocellatum by C18 chromatography followed by silica gel chromatography and reversed-phase HPLC led to isolation and structure elucidation of new cyclic peptide named daklakapeptin. Structure of daklakapeptin was elucidated by exhaustive 1D (1H) and 2D (COSY, TOCSY, NOESY, HMQC, HMBC) NMR spectroscopy in combination with HR-ESI-MS. Daklakapeptin was found to have totally 12 residues including 6 proteinogenic amino acids (Pro, Tyr, Ile, Leu, Gln, Thr), 4 complexes (X,Y,T,Z) and the methyl derivative of Ile. The exact sequence of daklakapeptin is shown in following figure with X: (CH3)2CHCH2CH2CH(NH-)CH2CO-, Y:(CH3)2CHCH(OH)CH(NH-)CO-, T: HOCH2CH2CH(NH-)CO-, Z: HOCH2CHOHCH(NH-)CO- This new cyclic peptide exhibited antibacterial activity against Staphylococcus aureus with diameter of inhibition zone of 12.5 mm in concentration of 200 mg/disc. Further test for activity to other bacteria and for cytotoxic activity are in progress. Using reversed-phase HPLC to separate compounds in the crude ethyl acetate extract obtained from culture medium of Anabaena sp. led to isolation and structure elucidation of flourensadiol. The structure of flourensadiol was established using an extensive array of 1D (1H, 13C, DEPT-135) and 2D (HMQC, COSY, HMBC) NMR and HR-ESI-MS experiments. Flourensadiol was isolated previously from the common western shrub Flourensia cernua. However, only MS, IR, and proton NMR data but no reports on biological activity were available. In this study, we report the complete NMR data of flourensadiol for the first time. Flourensadiol was found to be very strong antibacterial active against Escherichia coli with diameter of inhibition zone of 20.0 mm in concentration of 200 mg/disc. Further test for activity to other bacteria and cytotoxic activity are in progress. Bioassay-guided fractionation of the methanol extract from biomass of Nostoc sp. by silica gel chromatography followed by C18 chromatography and reversed phase HPLC led to isolation of the active fraction NsF2 which exhibited antibacterial activity against Staphylococcus aureus with diameter of inhibition zone of 10.0 mm in concentration of 500 mg/disc. The low resolution ESI-MS of fraction NsF2 showed signal at m/z 426 [M+H]+. The NMR and MS characterization of compounds in fraction NsF2 is in progress. Bioassay-guided fractionation of the methanol extract prepared from biomass of marine cyanobacterium Lyngbya majuscula collected from Khanh Hoa province of Vietnam by various chromatographic methods (CC, PTLC, HPLC) afforded 3 cytotoxic compounds anhydrodebromoaplysiatoxin, debromoaplysiatoxin, and anhydroaplysiatoxin. Identification of these cytotoxic compounds was established by direct comparison of our spectroscopic data, including (1H, 13C) NMR and HR-ESI-MS with those reported in the literature. In our study, debromoaplysiatoxin and anhydroaplysiatoxin exhibited cytotoxic activity against bladder cancer cell line 5637 with IC50 of 86 ng/ml and 40 ng/ml, respectively but anhydrodebromoaplysiatoxin was not yet tested for cytotoxic activity. The identification of fatty acids by GS-MS technique in the n-hexane extract obtained from biomass of this marine cyanobacterium was undertaken before commencing further fractionation processes. The presented results prove that soil cyanobacteria are a promising source to yield chemical and pharmaceutical interesting compounds.