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A water quality model for shallow river-lake systems and its application in river basin management
(2007)
This work documents the development and application of a new model for simulating mass transport and turnover in rivers and shallow lakes. The simulation tool called 'TRAM' is intended to complement mesoscale eco-hydrological catchment models in studies on river basin management. TRAM aims at describing the water quality of individual water bodies, using problem- and scale-adequate approaches for representing their hydrological and ecological characteristics. The need for such flexible water quality analysis and prediction tools is expected to further increase during the implementation of the European Water Framework Directive (WFD) as well as in the context of climate change research. The developed simulation tool consists of a transport and a reaction module with the latter being highly flexible with respect to the description of turnover processes in the aquatic environment. Therefore, simulation approaches of different complexity can easily be tested and model formulations can be chosen in consideration of the problem at hand, knowledge of process functioning, and data availability. Consequently, TRAM is suitable for both heavily simplified engineering applications as well as scientific ecosystem studies involving a large number of state variables, interactions, and boundary conditions. TRAM can easily be linked to catchment models off-line and it requires the use of external hydrodynamic simulation software. Parametrization of the model and visualization of simulation results are facilitated by the use of geographical information systems as well as specific pre- and post-processors. TRAM has been developed within the research project 'Management Options for the Havel River Basin' funded by the German Ministry of Education and Research. The project focused on the analysis of different options for reducing the nutrient load of surface waters. It was intended to support the implementation of the WFD in the lowland catchment of the Havel River located in North-East Germany. Within the above-mentioned study TRAM was applied with two goals in mind. In a first step, the model was used for identifying the magnitude as well as spatial and temporal patterns of nitrogen retention and sediment phosphorus release in a 100~km stretch of the highly eutrophic Lower Havel River. From the system analysis, strongly simplified conceptual approaches for modeling N-retention and P-remobilization in the studied river-lake system were obtained. In a second step, the impact of reduced external nutrient loading on the nitrogen and phosphorus concentrations of the Havel River was simulated (scenario analysis) taking into account internal retention/release. The boundary conditions for the scenario analysis such as runoff and nutrient emissions from river basins were computed by project partners using the catchment models SWIM and ArcEGMO-Urban. Based on the output of TRAM, the considered options of emission control could finally be evaluated using a site-specific assessment scale which is compatible with the requirements of the WFD. Uncertainties in the model predictions were also examined. According to simulation results, the target of the WFD -- with respect to total phosphorus concentrations in the Lower Havel River -- could be achieved in the medium-term, if the full potential for reducing point and non-point emissions was tapped. Furthermore, model results suggest that internal phosphorus loading will ease off noticeably until 2015 due to a declining pool of sedimentary mobile phosphate. Mass balance calculations revealed that the lakes of the Lower Havel River are an important nitrogen sink. This natural retention effect contributes significantly to the efforts aimed at reducing the river's nitrogen load. If a sustainable improvement of the river system's water quality is to be achieved, enhanced measures to further reduce the immissions of both phosphorus and nitrogen are required.
The need to develop sustainable resource management strategies for semi-arid and arid rangelands is acute as non-adapted grazing strategies lead to irreversible environmental problems such as desertification and associated loss of economic support to society. In such vulnerable ecosystems, successful implementation of sustainable management strategies depends on well-founded under-standing of processes at different scales that underlay the complex system dynamic. There is ample evidence that, in contrast to traditional sectoral approaches, only interdisciplinary research does work for resolving problems in conservation and natural resource management. In this thesis I combined a range of modeling approaches that integrate different disciplines and spatial scales in order to contribute to basic guidelines for sustainable management of semi-arid and arid range-lands. Since water availability and livestock management are seen as most potent determinants for the dynamics of semi-arid and arid ecosystems I focused on (i) the interaction of ecological and hydro-logical processes and (ii) the effect of farming strategies. First, I developed a grid-based and small-scaled model simulating vegetation dynamics and inter-linked hydrological processes. The simulation results suggest that ecohydrological interactions gain importance in rangelands with ascending slope where vegetation cover serves to obstruct run-off and decreases evaporation from the soil. Disturbances like overgrazing influence these positive feedback mechanisms by affecting vegetation cover and composition. In the second part, I present a modeling approach that has the power to transfer and integrate ecological information from the small scale vegetation model to the landscape scale, most relevant for the conservation of biodiversity and sustainable management of natural resources. I combined techniques of stochastic modeling with remotely sensed data and GIS to investigate to which ex-tent spatial interactions, like the movement of surface water by run-off in water limited environments, affect ecosystem functioning at the landscape scale. My simulation experiments show that overgrazing decreases the number of vegetation patches that act as hydrological sinks and run-off increases. The results of both simulation models implicate that different vegetation types should not only be regarded as provider of forage production but also as regulator of ecosystem functioning. Vegetation patches with good cover of perennial vegetation are capable to catch and conserve surface run-off from degraded surrounding areas. Therefore, downstream out of the simulated system is prevented and efficient use of water resources is guaranteed at all times. This consequence also applies to commercial rotational grazing strategies for semi-arid and arid rangelands with ascending slope where non-degraded paddocks act as hydrological sinks. Finally, by the help of an integrated ecological-economic modeling approach, I analyzed the relevance of farmers’ ecological knowledge for longterm functioning of semi-arid and arid grazing systems under current and future climatic conditions. The modeling approach consists of an ecological and an economic module and combines relevant processes on either level. Again, vegetation dynamics and forage productivity is derived by the small-scaled vegetation model. I showed that sustainable management of semi-arid and arid rangelands relies strongly on the farmers’ knowledge on how the ecosystem works. Furthermore, my simulation results indicate that the projected lower annual rainfall due to climate change in combination with non-adapted grazing strategies adds an additional layer of risk to these ecosystems that are already prone to land degradation. All simulation models focus on the most essential factors and ignore specific details. Therefore, even though all simulation models are parameterized for a specific dwarf shrub savanna in arid southern Namibia, the conclusions drawn are applicable for semi-arid and arid rangelands in general.
Analysis and modelling of nutrient transport and transformation processes on the catchment scale
(2007)
Analysis and modelling of nutrient transport and transformation processes on the catchment scale
(2007)
Sulphur, a macronutrient essential for plant growth, is among the most versatile elements in living organisms. Unfortunately, little is known about regulation of sulphate uptake and assimilation by plants. Identification of sulphate signalling processes will allow to control sulphate acquisition and assimilation and may prove useful in the future to improve sulphur-use efficiency in agriculture. Many of genes involved in sulphate metabolism are regulated on transcriptional level by products of other genes called transcription factors (TF). Several published experiments revealed TF genes that respond to sulphate deprivation, but none of these have been so far been characterized functionally. Thus, we aimed at identifying and characterising transcription factors that control sulphate metabolism in the model plant Arabidopsis thaliana. To achieve that goal we postulated that factors regulating Arabidopsis responses to inorganic sulphate deficiency change their transcriptional levels under sulphur-limited conditions. By comparing TF transcript profiles from plants grown on different sulphate regimes, we identified TF genes that may specifically induce or repress changes in expression of genes that allow plants to adapt to changes in sulphate availability. Candidate genes obtained from this screening were tested by reverse genetics approaches. Transgenic plants constitutively overproducing selected TF genes and mutant plants, lacking functional selected TF genes (knock out), were used. By comparing metabolite and transcript profiles from transgenic and wild type plants we aimed at confirming the role of selected AP2 TF candidate genes in plant adaptation to sulphur unavailability. After preliminary characterisation of WRKY24 and MYB93 TF genes, we postulate that these factors are involved in a complex multifactorial regulatory network, in which WRKY24 and MYB93 would act as superior factors regulating other transcription factors directly involved in the regulation of S-metabolism genes. Results obtained for plants overproducing TOE1 and TOE2 TF genes suggests that these factors may be involved in a mechanism, which is promoting synthesis of an essential amino acid, methionine, over synthesis of another amino acid, cysteine. Thus, TOE1 and TOE2 genes might be a part of transcriptional regulation of methionine synthesis. Approaches creating genetically manipulated plants may produce plant phenotypes of immediate biotechnological interest, such as plants with increased sulphate or sulphate-containing amino acid content, or better adapted to the sulphate unavailability.
The overall program "arborescent numbers" is to similarly perform the constructions from the natural numbers (N) to the positive fractional numbers (Q+) to positive real numbers (R+) beginning with (specific) binary trees instead of natural numbers. N can be regarded as the associative binary trees. The binary trees B and the left-commutative binary trees P allow the hassle-free definition of arbitrary high arithmetic operations (hyper ... hyperpowers). To construct the division trees the algebraic structure "coppice" is introduced which is a group with an addition over which the multiplication is right-distributive. Q+ is the initial associative coppice. The present work accomplishes one step in the program "arborescent numbers". That is the construction of the arborescent equivalent(s) of the positive fractional numbers. These equivalents are the "division binary trees" and the "fractional trees". A representation with decidable word problem for each of them is given. The set of functions f:R1->R1 generated from identity by taking powers is isomorphic to P and can be embedded into a coppice by taking inverses.
Atmospheric circulation and the surface mass balance in a regional climate model of Antarctica
(2007)
Understanding the Earth's climate system and particularly climate variability presents one of the most difficult and urgent challenges in science. The Antarctic plays a crucial role in the global climate system, since it is the principal region of radiative energy deficit and atmospheric cooling. An assessment of regional climate model HIRHAM is presented. The simulations are generated with the HIRHAM model, which is modified for Antarctic applications. With a horizontal resolution of 55km, the model has been run for the period 1958-1998 creating long-term simulations from initial and boundary conditions provided by the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA40 re-analysis. The model output is compared with observations from observation stations, upper air data, global atmospheric analyses and satellite data. In comparison with the observations, the evaluation shows that the simulations with the HIRHAM model capture both the large and regional scale circulation features with generally small bias in the modeled variables. On the annual time scale the largest errors in the model simulations are the overestimation total cloud cover and the colder near-surface temperature over the interior of the Antarctic plateau. The low-level temperature inversion as well as low-level wind jet is well captured by the model. The decadal scale processes were studied based on trend calculations. The long-term run was divided into two 20 years parts. The 2m temperature, 500 hPa temperature, MSLP, precipitation and net mass balance trends were calculated for both periods and over 1958 - 1998. During the last two decades the strong surface cooling was observed over the Eastern Antarctica, this result is in good agreement with the result of Chapman and Walsh (2005) who calculated the temperature trend based on the observational data. The MSLP trend reveals a big disparity between the first and second parts of the 40 year run. The overall trend shows the strengthening of the circumpolar vortex and continental anticyclone. The net mass balance as well as precipitation show a positive trend over the Antarctic Peninsula region, along Wilkes Land and in Dronning Maud Land. The Antarctic ice sheet grows over the Eastern part of Antarctica with small exceptions in Dronning Maud Land and Wilkes Land and sinks in the Antarctic Peninsula; this result is in good agreement with the satellite-measured altitude presented in Davis (2005) . To better understand the horizontal structure of MSLP, temperature and net mass balance trends the influence of the Southern Annual Mode (SAM) on the Antarctic climate was investigated. The main meteorological parameters during the positive and negative Antarctic Oscillation (AAO) phases were compared to each other. A positive/negative AAO index means strengthening/weakening of the circumpolar vortex, poleward/northward storm tracks and prevailing/weakening westerly winds. For detailed investigation of global teleconnection, two positive and one negative periods of AAO phase were chosen. The differences in MSLP and 2m temperature between positive and negative AAO years during the winter months partly explain the surface cooling during the last decades.
Characterisation of silica in Equisetum hyemale and its transformation into biomorphous ceramics
(2007)
Equisetum spp. (horsetail / “Schachtelhalm”) is the only surviving genus of the primitive Sphenopsids vascular plants which reached their zenith during the Carboniferous era. It is an herbaceous plant and is distinguished by jointed stems with fused whorl of nodal leaves. The plant has been used for scouring kitchen utensils and polishing wood during the past time due to its high silica encrustations in the epidermis. Equisetum hyemale (scouring rush) can accumulate silica up to 16% dry weight in its tissue, which makes this plant an interesting candidate as a renewable resource of silica for the synthesis of biomorphous ceramics. The thesis comprises a comprehensive experimental study of silica accumulations in E.hyemale using different characterisation techniques at all hierarchical levels. The obtained results shed light on the local distribution, chemical form, crystallinity, and nanostructure of biogenic silica in E.hyemale which were quite unclear until now. Furthermore, isolation of biogenic silica from E.hyemale to obtain high grade mesoporous silica with high purity is investigated. Finally, syntheses of silicon carbide (b-SiC) by a direct thermoconversion process of E.hyemale is attempted, which is a promising material for high performance ceramics. It is found that silica is deposited continuously on the entire epidermal layer with the highest concentration on the knobs. The highest silicon content is at the knob tips (≈ 33%), followed by epidermal flank (≈ 17%), and inner lower knob (≈ 6%), whereas there is almost no silicon found in the interior parts. Raman spectroscopy reveals the presence of at least two silica modifications in E.hyemale. The first type is pure hydrated amorphous silica restricted to the knob tips. The second type is accumulated on the entire continuous outer layer adjacent to the epidermis cell walls. It is lacking silanol groups and is intimately associated with polysaccharides (cellulose, hemicellulose, pectin) and inorganic compounds. Silica deposited in E.hyemale is found to be mostly amorphous with almost negligible amounts of crystalline silica in the form of a-quartz (< 7%). The silica primary particles have a plate-like shape with a thickness of about 2 nm. Pure mesoporous amorphous silica with an open surface area up to 400 m2/g can be obtained from E.hyemale after leaching the plant with HCl to remove the inorganic impurities followed by a calcination treatment. The optimum calcination temperature appears to be around 500°C. Calcination of untreated E.hyemale causes a collapse of the biogenic silica structure which is mainly attributed to the detrimental action of alkali ions present in the native plant. Finally, pure b-SiC with a surface area of about 12 m2/g is obtained upon direct pyrolysis of HCl-treated E.hyemale samples in argon atmosphere. The original structure of native E.hyemale is substantially retained in the biomorphous b-SiC. The results of this thesis lead to a better understanding of the silicification process and allow to draw conclusions about the role of silica in E.hyemale. In particular, a templating role of the plant biopolymers for the synthesis of the nanostructured silica within the plant body can be deduced. Moreover, the high grade ultrafine amorphous silica isolated from E.hyemale promises applications as adsorbent and catalyst support and as silica source for the fabrication of silica-based composites. The synthesis of biomorphous b-SiC from sustainable and low-cost E.hyemale is still in its initial stage. The present thesis demonstrates the principal possibility of carbothermal synthesis of SiC from E.hyemale with the prospect of potential applications, for instance as refractory materials, catalyst supports, or high performance advanced ceramics.
Our Solar system contains a large amount of dust, containing valuable information about our close cosmic environment. If created in a planet's system, the particles stay predominantly in its vicinity and can form extended dust envelopes, tori or rings around them. A fascinating example of these complexes are Saturnian rings containing a wide range of particles sizes from house-size objects in the main rings up to micron-sized grains constituting the E ring. Other example are ring systems in general, containing a large fraction of dust or also the putative dust-tori surrounding the planet Mars. The dynamical life'' of such circumplanetary dust populations is the main subject of our study. In this thesis a general model of creation, dynamics and death'' of circumplanetary dust is developed. Endogenic and exogenic processes creating dust at atmosphereless bodies are presented. Then, we describe the main forces influencing the particle dynamics and study dynamical responses induced by stochastic fluctuations. In order to estimate the properties of steady-state population of considered dust complex, the grain mean lifetime as a result of a balance of dust creation, life'' and loss mechanisms is determined. The latter strongly depends on the surrounding environment, the particle properties and its dynamical history. The presented model can be readily applied to study any circumplanetary dust complex. As an example we study dynamics of two dust populations in the Solar system. First we explore the dynamics of particles, ejected from Martian moon Deimos by impacts of micrometeoroids, which should form a putative tori along the orbit of the moon. The long-term influence of indirect component of radiation pressure, the Poynting-Robertson drag gives rise in significant change of torus geometry. Furthermore, the action of radiation pressure on rotating non-spherical dust particles results in stochastic dispersion of initially confined ensemble of particles, which causes decrease of particle number densities and corresponding optical depth of the torus. Second, we investigate the dust dynamics in the vicinity of Saturnian moon Enceladus. During three flybys of the Cassini spacecraft with Enceladus, the on-board dust detector registered a micron-sized dust population around the moon. Surprisingly, the peak of the measured impact rate occurred 1 minute before the closest approach of the spacecraft to the moon. This asymmetry of the measured rate can be associated with locally enhanced dust production near Enceladus south pole. Other Cassini instruments also detected evidence of geophysical activity in the south polar region of the moon: high surface temperature and extended plumes of gas and dust leaving the surface. Comparison of our results with this in situ measurements reveals that the south polar ejecta may provide the dominant source of particles sustaining the Saturn's E ring.
There is already strong evidence that temperate lakes have been highly vulnerable to human induced climate warming during the last century. Hitherto climate impact studies have mainly focussed on the impacts of the recent long-term warming in winter and spring and little is known on the influence of climate warming on temperate lakes in summer. In the present thesis, I studied some aspects, which may have been strongly involved in determining the response of a lake to climate warming in summer. Thereby I have focussed on climate induced impacts on the thermal characteristics and the phenology and abundance of summer plankton in a shallow polymictic lake (Müggelsee, Germany). First, the influence of climate warming on the phenology and abundance of the lake plankton was investigated across seasons. Fast-growing spring phytoplankton and zooplankton (Daphnia) advanced largely synchronously, whereas long-term changes in the phenology of slow-growing summer zooplankton were clearly species-specific and not synchronised. The phenology and/or abundance of several summer copepod species changed according to their individual thermal requirements at decisive developmental stages such as emergence from diapause in spring. The study emphasises that not only the degree of warming, but also its timing within the annual cycle is of great ecological importance. To analyse the impact of climate change on the thermal characteristics of the lake, I examined the long-term development of the daily epilimnetic temperature extrema during summer. The study demonstrated for the first time for lakes that the daily epilimnetic minima (during nighttime) have increased more rapidly than the daily epilimnetic maxima (during daytime), resulting in a distinct decrease in the daily epilimnetic temperature range. This day-night asymmetry in epilimnetic temperature was likely caused by an increased nighttime emission of long-wave radiation from the atmosphere. This underlines that not only increases in air temperature, but also changes in other meteorological variables such as wind speed, relative humidity and cloud cover may play an important role in determining the lake temperature with respect to further climate change. Furthermore, a short-term analysis on the mixing regime of the polymictic lake was conducted to examine the frequency and duration of stratification events and their impacts on dissolved oxygen, dissolved nutrients and summer phytoplankton. Even during the longest stratification events (heatwaves in 2003 and 2006) the thermal characteristics of the lake differed from those typically found in shallow dimictic lakes, which exhibit a continuous stratification during summer. Particularly, hypolimnetic temperatures were higher, favouring the depletion of oxygen and the accumulation of dissolved nutrient in the hypolimnion. Thermal stratification will be very likely amplified in the future, thus, I conclude that polymictic lakes will be very vulnerable to alterations in the thermal regime with respect to projections of further climate change during summer. Finally, a long-term case study on the long and short-term changes in the development of the planktonic larvae of the freshwater mussel Dreissena polymorpha was performed to analyse the impacts of simultaneous changes in the thermal and in the trophic regime of the lake. Both the climate warming and the decrease in external nutrient load were important in determining the abundance of the pelagic larvae by affecting different features of the life-history of this species throughout the warm season. The long-term increase in the abundance and length of larvae was related to the decrease in external nutrient loading and the change in phytoplankton composition. However, the recent heatwaves in 2003 and 2006 have offset this positive effect on larval abundance, due to unfavourable low oxygen concentrations that had resulted from extremely long stratification events, mimicking the effects of nutrient enrichment. Climate warming may thus induce counteracting effects in productive shallow lakes that underwent lake restoration through a decrease in external nutrient loading. I conclude that not only the nature of climate change and thus the timing of climate warming throughout the seasons and the occurrence of climatic extremes as heatwaves, but also site-specific lake conditions as the thermal mixing regime and the trophic state are crucial factors governing the impacts of climate warming on internal lake processes during summer. Consequently, further climate impact research on lake functioning should focus on how the different lake types respond to the complex environmental forcing in summer, to allow for a comprehensive understanding of human induced environmental changes in lakes.
Being living systems unable to adjust their location to changing environmental conditions, plants display homeostatic networks that have evolved to maintain transition metal levels in a very narrow concentration range in order to avoid either deficiency or toxicity. Hence, plants possess a broad repertoire of mechanisms for the cellular uptake, compartmentation and efflux, as well as for the chelation of transition metal ions. A small number of plants are hypertolerant to one or a few specific transition metals. Some metal tolerant plants are also able to hyperaccumulate metal ions. The Brassicaceae family member Arabidopis halleri ssp. halleri (L.) O´KANE and AL´SHEHBAZ is a hyperaccumulator of zinc (Zn), and it is closely related to the non-hypertolerant and non-hyperaccumulating model plant Arabidopsis thaliana (L.) HEYNHOLD. The close relationship renders A. halleri a promising emerging model plant for the comparative investigation of the molecular mechanisms behind hypertolerance and hyperaccumulation. Among several potential candidate genes that are probably involved in mediating the zinc-hypertolerant and zinc-hyperaccumulating trait is AhHMA3. The AhHMA3 gene is highly similar to AtHMA3 (AGI number: At4g30120) in A. thaliana, and its encoded protein belongs to the P-type IB ATPase family of integral membrane transporter proteins that transport transition metals. In contrast to the low AtHMA3 transcript levels in A. thaliana, the gene was found to be constitutively highly expressed across different Zn treatments in A. halleri, especially in shoots. In this study, the cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O´KANE and AL´SHEHBAZ and Arabidopsis thaliana (L.) HEYNHOLD is described. Heterologously expressed AhHMA3 mediated enhanced tolerance to Zn and to a much lesser degree to cadmium (Cd) but not to cobalt (Co) in metal-sensitive mutant strains of budding yeast. It is demonstrated that the genome of A. halleri contains at least four copies of AhHMA3, AhHMA3-1 to AhHMA3-4. A copy-specific real-time RT-PCR indicated that an AhHMA3-1 related gene copy is the source of the constitutively high transcript level in A. halleri and not a gene copy similar to AhHMA3-2 or AhHMA3-4. In accordance with the enhanced AtHMA3mRNA transcript level in A. thaliana roots, an AtHMA3 promoter-GUS gene construct mediated GUS activity predominantly in the vascular tissues of roots and not in shoots. However, the observed AhHMA3-1 and AhHMA3-2 promoter-mediated GUS activity in A. thaliana or A. halleri plants did not reflect the constitutively high expression of AhHMA3 in shoots of A. halleri. It is suggested that other factors e. g. characteristic sequence inserts within the first intron of AhHMA3-1 might enable a constitutively high expression. Moreover, the unknown promoter of the AhHMA3-3 gene copy could be the source of the constitutively high AhHMA3 transcript levels in A. halleri. In that case, the AhHMA3-3 sequence is predicted to be highly homologous to AhHMA3-1. The lack of solid localisation data for the AhHMA3 protein prevents a clear functional assignment. The provided data suggest several possible functions of the AhHMA3 protein: Like AtHMA2 and AtHMA4 it might be localised to the plasma membrane and could contribute to the efficient translocation of Zn from root to shoot and/or to the cell-to-cell distribution of Zn in the shoot. If localised to the vacuolar membrane, then a role in maintaining a low cytoplasmic zinc concentration by vacuolar zinc sequestration is possible. In addition, AhHMA3 might be involved in the delivery of zinc ions to trichomes and mesophyll leaf cells that are major zinc storage sites in A. halleri.
In the present dissertation paper we study problems related to synchronization phenomena in the presence of noise which unavoidably appears in real systems. One part of the work is aimed at investigation of utilizing delayed feedback to control properties of diverse chaotic dynamic and stochastic systems, with emphasis on the ones determining predisposition to synchronization. Other part deals with a constructive role of noise, i.e. its ability to synchronize identical self-sustained oscillators. First, we demonstrate that the coherence of a noisy or chaotic self-sustained oscillator can be efficiently controlled by the delayed feedback. We develop the analytical theory of this effect, considering noisy systems in the Gaussian approximation. Possible applications of the effect for the synchronization control are also discussed. Second, we consider synchrony of limit cycle systems (in other words, self-sustained oscillators) driven by identical noise. For weak noise and smooth systems we proof the purely synchronizing effect of noise. For slightly different oscillators and/or slightly nonidentical driving, synchrony becomes imperfect, and this subject is also studied. Then, with numerics we show moderate noise to be able to lead to desynchronization of some systems under certain circumstances. For neurons the last effect means “antireliability” (the “reliability” property of neurons is treated to be important from the viewpoint of information transmission functions), and we extend our investigation to neural oscillators which are not always limit cycle ones. Third, we develop a weakly nonlinear theory of the Kuramoto transition (a transition to collective synchrony) in an ensemble of globally coupled oscillators in presence of additional time-delayed coupling terms. We show that a linear delayed feedback not only controls the transition point, but effectively changes the nonlinear terms near the transition. A purely nonlinear delayed coupling does not affect the transition point, but can reduce or enhance the amplitude of collective oscillations.
Conceptual Capacities
(2007)
The biological function and the technological applications of semiflexible polymers, such as DNA, actin filaments and carbon nanotubes, strongly depend on their rigidity. Semiflexible polymers are characterized by their persistence length, the definition of which is the subject of the first part of this thesis. Attractive interactions, that arise e.g.~in the adsorption, the condensation and the bundling of filaments, can change the conformation of a semiflexible polymer. The conformation depends on the relative magnitude of the material parameters and can be influenced by them in a systematic manner. In particular, the morphologies of semiflexible polymer rings, such as circular nanotubes or DNA, which are adsorbed onto substrates with three types of structures, are studied: (i) A topographical channel, (ii) a chemically modified stripe and (iii) a periodic pattern of topographical steps. The results are compared with the condensation of rings by attractive interactions. Furthermore, the bundling of two individual actin filaments, whose ends are anchored, is analyzed. This system geometry is shown to provide a systematic and quantitative method to extract the magnitude of the attraction between the filaments from experimentally observable conformations of the filaments.
The cytoskeletal motor protein kinesin-1 (conventional kinesin) is the fast carrier for intracellular cargo transport along microtubules. So far most studies aimed at investigating the transport properties of individual motor molecules. However, the transport in cells usually involves the collective work of more than one motor. In the present work, we have studied the movement of beads as artificial loads/organelles pulled by several kinesin-1 motors in vitro. For a wide range of motor coverage of the beads and different bead (cargo) sizes the transport parameters walking distance or run length, velocity and force generation are measured. The results indicate that the transport parameters are influenced by the number of motors carrying the bead. While the transport velocity slightly decreases, an increase in the run length was measured and higher forces are determined, when more motors are involved. The effective number of motors pulling a bead is estimated by measuring the change in the hydrodynamic diameter of kinesin-coated beads using dynamic light scattering. The geometrical constraints imposed by the transport system have been taken into account. Thus, results for beads of different size and motor-surface coverage could be compared. In addition, run length-distributions obtained for the smallest bead size were matched to theoretically calculated distributions. The latter yielded an average number of pulling motors, which is in agreement with the effective motor numbers determined experimentally.
This thesis describes two main projects; the first one is the optimization of a hierarchical search strategy to search for unknown pulsars. This project is divided into two parts; the first part (and the main part) is the semi-coherent hierarchical optimization strategy. The second part is a coherent hierarchical optimization strategy which can be used in a project like Einstein@Home. In both strategies we have found that the 3-stages search is the optimum strategy to search for unknown pulsars. For the second project we have developed a computer software for a coherent Multi-IFO (Interferometer Observatory) search. To validate our software, we have worked on simulated data as well as hardware injected signals of pulsars in the fourth LIGO science run (S4). While with the current sensitivity of our detectors we do not expect to detect any true Gravitational Wave signals in our data, we can still set upper limits on the strength of the gravitational waves signals. These upper limits, in fact, tell us how weak a signal strength we would detect. We have also used our software to set upper limits on the signal strength of known isolated pulsars using LIGO fifth science run (S5) data.
It is desirable to reduce the potential threats that result from the variability of nature, such as droughts or heat waves that lead to food shortage, or the other extreme, floods that lead to severe damage. To prevent such catastrophic events, it is necessary to understand, and to be capable of characterising, nature's variability. Typically one aims to describe the underlying dynamics of geophysical records with differential equations. There are, however, situations where this does not support the objectives, or is not feasible, e.g., when little is known about the system, or it is too complex for the model parameters to be identified. In such situations it is beneficial to regard certain influences as random, and describe them with stochastic processes. In this thesis I focus on such a description with linear stochastic processes of the FARIMA type and concentrate on the detection of long-range dependence. Long-range dependent processes show an algebraic (i.e. slow) decay of the autocorrelation function. Detection of the latter is important with respect to, e.g. trend tests and uncertainty analysis. Aiming to provide a reliable and powerful strategy for the detection of long-range dependence, I suggest a way of addressing the problem which is somewhat different from standard approaches. Commonly used methods are based either on investigating the asymptotic behaviour (e.g., log-periodogram regression), or on finding a suitable potentially long-range dependent model (e.g., FARIMA[p,d,q]) and test the fractional difference parameter d for compatibility with zero. Here, I suggest to rephrase the problem as a model selection task, i.e.comparing the most suitable long-range dependent and the most suitable short-range dependent model. Approaching the task this way requires a) a suitable class of long-range and short-range dependent models along with suitable means for parameter estimation and b) a reliable model selection strategy, capable of discriminating also non-nested models. With the flexible FARIMA model class together with the Whittle estimator the first requirement is fulfilled. Standard model selection strategies, e.g., the likelihood-ratio test, is for a comparison of non-nested models frequently not powerful enough. Thus, I suggest to extend this strategy with a simulation based model selection approach suitable for such a direct comparison. The approach follows the procedure of a statistical test, with the likelihood-ratio as the test statistic. Its distribution is obtained via simulations using the two models under consideration. For two simple models and different parameter values, I investigate the reliability of p-value and power estimates obtained from the simulated distributions. The result turned out to be dependent on the model parameters. However, in many cases the estimates allow an adequate model selection to be established. An important feature of this approach is that it immediately reveals the ability or inability to discriminate between the two models under consideration. Two applications, a trend detection problem in temperature records and an uncertainty analysis for flood return level estimation, accentuate the importance of having reliable methods at hand for the detection of long-range dependence. In the case of trend detection, falsely concluding long-range dependence implies an underestimation of a trend and possibly leads to a delay of measures needed to take in order to counteract the trend. Ignoring long-range dependence, although present, leads to an underestimation of confidence intervals and thus to an unjustified belief in safety, as it is the case for the return level uncertainty analysis. A reliable detection of long-range dependence is thus highly relevant in practical applications. Examples related to extreme value analysis are not limited to hydrological applications. The increased uncertainty of return level estimates is a potentially problem for all records from autocorrelated processes, an interesting examples in this respect is the assessment of the maximum strength of wind gusts, which is important for designing wind turbines. The detection of long-range dependence is also a relevant problem in the exploration of financial market volatility. With rephrasing the detection problem as a model selection task and suggesting refined methods for model comparison, this thesis contributes to the discussion on and development of methods for the detection of long-range dependence.
Development and application of novel genetic transformation technologies in maize (Zea mays L.)
(2007)
Plant genetic engineering approaches are of pivotal importance to both basic and applied research. However, rapid commercialization of genetically engineered crops, especially maize, raises several ecological and environmental concerns largely related to transgene flow via pollination. In most crops, the plastid genome is inherited uniparentally in a maternal manner. Consequently, a trait introduced into the plastid genome would not be transferred to the sexually compatible relatives of the crops via pollination. Thus, beside its several other advantages, plastid transformation provides transgene containment, and therefore, is an environmentally friendly approach for genetic engineering of crop plants. Reliable in vitro regeneration systems allowing repeated rounds of regeneration are of utmost importance to development of plastid transformation technologies in higher plants. While being the world’s major food crops, cereals are among the most difficult-to-handle plants in tissue culture which severely limits genetic engineering approaches. In maize, immature zygotic embryos provide the predominantly used material for establishing regeneration-competent cell or callus cultures for genetic transformation experiments. The procedures involved are demanding, laborious and time consuming and depend on greenhouse facilities. In one part of this work, a novel tissue culture and plant regeneration system was developed that uses maize leaf tissue and thus is independent of zygotic embryos and greenhouse facilities. Also, protocols were established for (i) the efficient induction of regeneration-competent callus from maize leaves in the dark, (ii) inducing highly regenerable callus in the light, and (iii) the use of leaf-derived callus for the generation of stably transformed maize plants. Furthermore, several selection methods were tested for developing a plastid transformation system in maize. However, stable plastid transformed maize plants could not be yet recovered. Possible explanations as well as suggestions for future attempts towards developing plastid transformation in maize are discussed. Nevertheless, these results represent a first essential step towards developing chloroplast transformation technology for maize, a method that requires multiple rounds of plant regeneration and selection to obtain genetically stable transgenic plants. In order to apply the newly developed transformation system towards metabolic engineering of carotenoid biosynthesis, the daffodil phytoene synthase (PSY) gene was integrated into the maize genome. The results illustrate that expression of a recombinant PSY significantly increases carotenoid levels in leaves. The beta-carotene (pro-vitamin A) amounts in leaves of transgenic plants were increased by ~21% in comparison to the wild-type. These results represent evidence for maize to have significant potential to accumulate higher amounts of carotenoids, especially beta-carotene, through transgenic expression of phytoene synthases. Finally, progresses were made towards developing transformation technologies in Peperomia (Piperaceae) by establishing an efficient leaf-based regeneration system. Also, factors determining plastid size and number in Peperomia, whose species display great interspecific variation in chloroplast size and number per cell, were investigated. The results suggest that organelle size and number are regulated in a tissue-specific manner rather than in dependency on the plastid type. Investigating plastid morphology in Peperomia species with giant chloroplasts, plasmatic connections between chloroplasts (stromules) were observed under the light microscope and in the absence of tissue fixation or GFP overexpression demonstrating the relevance of these structures in vivo. Furthermore, bacteria-like microorganisms were discovered within Peperomia cells, suggesting that this genus provides an interesting model not only for studying plastid biology but also for investigating plant-microbe interactions.
Nature has always served as a model for mimicking and inspiration to humans in their efforts to improve their life. Researchers have been inspired by nature to produce biomimetic materials with molecular recognition properties by design rather than evolution. Molecular imprinting is one way to prepare such materials. Such smart materials with new functionalities are at the forefront of the development of a relevant number of ongoing and perspective applications ranging from consumer to space industry. Molecularly imprinted polymers were developed by mimicking the natural enzymes or antibodies that serve as host for binding target molecules. These imprints were used as a recognition element to substitute natural biomolecules in biosensors. The concept behind molecular imprinting is to mold a material (with the desired chemical properties) around individual molecules. Upon removal of the molecular templates, one is left with regions in the molded material that fit the shape of the template molecules. Thus, molecular imprinting results in materials that can selectively bind to molecules of interest. Imprinted materials resulted in applications ranging from chemical separation to bioanalytics. In this work attempts were made particularly in the development of molecularly imprinted polymer based thermometric sensors. The main effort was focused towards the development of an covalently imprinted polymer that would be able to selectively bind fructosyl valine (Fru-Val), the N-terminal constituent of hemoglobin A1c ß-chains. Taking into account the known advantages of imprinted polymers, e.g. robustness, thermal and chemical stability, imprinted materials were successfully used as a recognition element in the sensor. One of the serious problems associated with the development of MIP sensors and which lies in the absence of a generic procedure for the transformation of the polymer-template binding event into a detectable signal has been addressed by developing the "thermometric" approach. In general the developed approach gives a new insight on MIP/Analyte interactions.
The styles of deformation of the fore-arc wedges along the Chilean convergent margin are observed to vary significantly, despite similar plate kinematic conditions. Here, I focus on the analysis of fore-arc deformation on two regions along the Chilean convergent margin at 20°-24°S and 37°-42°S. Although both regions are subjected to the oblique subduction of the oceanic Nazca plate and backstopped by the Andes mountain chain; they display different patterns of deformation. The northern Chilean study area (20° - 24°S) is characterized by an exceptionally thick crust of about 60 km beneath the Altiplano – Puna plateau, lack of an accretionary wedge in the fore-arc due to hyperarid climate, and consequently a sediment starved trench. Two major margin parallel strike slip faults are observed in this area, the Atacama Fault Zone (AFZ) and the Precordilleran Fault System (PFS). Both strike-slip faults do not exhibit significant recent displacement. The southern study area (37° - 42°S), compared to the northern study area, is characterized by lower topography, high precipitation rates (~2000 mm/yr), and a younger subducted oceanic plate. An active strike-slip fault, the Liquiñe-Ofqui-Fault-Zone (LOFZ), shows ~1 cm/yr recent dextral movement and shapes the surface of this area. Thus, the southern Chilean study area exhibits localized strike-slip motion. Within this area the largest earthquake ever recorded, the 1960 Valdivia earthquake, occurred with a moment magnitude of MW=9.5. I have constructed 2D thermal models and 3D mechanical models for both Chilean study areas to study processes related to active subduction. The applied numerical method is the finite element technique by means of the commercial software package ABAQUS. The thermal models are focused on the thermal conditions along the plate interface. The thermal structure along the plate interface reveals the limits of coupling but also the type of transition from coupled to uncoupled and vice versa. The model results show that shear heating at the plate interface is an important mechanism that should be taken into account. The models also show that the thermal condition at the downdip limit of the coupling zone leads to a sharp decrease of friction along the interface. Due to the different geometries of the two Chilean study areas, such as the slab dip and the thickness of the continental crust, the downdip limit of the southern study area is slightly shallower than that of the northern study area. The results of the 2D thermal models are used to constrain the spatial extent of the coupling zone in the 3D mechanical models. 3D numerical simulations are used to investigate how geometry, rheology and mechanical parameters influence strain partitioning and styles of deformation in the Chilean fore-arc. The general outline of the models is based on the fore-arc geometry and boundary conditions as derived from geophysical and geological field data. I examined the influence of different rheological approaches and varying physical properties of the fore-arc to identify and constrain the parameters controlling the difference in surface deformation between the northern and southern study area. The results of numerical studies demonstrate that a small slab dip, a high coefficient of basal friction, a high obliquity of convergence, and a high Young’s modulus favour localisation of deformation in the fore-arc wedge. This parameter study helped me to constrain preferred models for the two Chilean study areas that fit to first order observations. These preferred models explain the difference in styles of deformation as controlled by the angle of obliquity, the dip of subducting slab, and the strength of wedge material. The difference in styles can be even larger if I apply stronger coupling between plates within the southern area; however, several independent observations indicate opposite tendency showing southward decrease of intensity of coupling. The weaker wedge material of the preferred model for the northern study area is associated with advanced development of the adjacent orogen, the Central Andes. Analysis of world-wide examples of oblique subduction zones supports the conclusion that more mature subduction zones demonstrate less pronounced localization of strike-slip motion.
Exploring elections features from a geographical perspective is the focus of this study. Its primary objective is to develop a scientific approach based on geoinformation technology (GIT) that promotes deeper understanding how geographical settings affect the spatial and temporal variations of voting behaviour and election outcomes. For this purpose, the five parliamentary elections (1991-2005) following the political turnaround in 1990 in the South East European reform country Albania have been selected as a case study. Elections, like other social phenomena that do not develop uniformly over a territory, inherit a spatial dimension. Despite of fact that elections have been researched by various scientific disciplines ranging from political science to geography, studies that incorporate their spatial dimension are still limited in number and approaches. Consequently, the methodologies needed to generate an integrated knowledge on many facets that constitute election features are lacking. This study addresses characteristics and interactions of the essential elements involved in an election process. Thus, the baseline of the approach presented here is the exploration of relations between three entities: electorate (political and sociodemographic features), election process (electoral system and code) and place (environment where voters reside). To express this interaction the concept of electoral pattern is introduced. Electoral patterns are defined by the study as the final view of election results, chiefly in tabular and/or map form, generated by the complex interaction of social, economic, juridical, and spatial features of the electorate, which has occurred at a specific time and in a particular geographical location. GIT methods of geoanalysis and geovisualization are used to investigate the characteristics of electoral patterns in their spatial and temporal distribution. Aggregate-level data modelled in map form were used to analyse and visualize the spatial distribution of election patterns components and relations. The spatial dimension of the study is addressed in the following three main relations: One, the relation between place and electorate and its expression through the social, demographic and economic features of the electorate resulting in the profile of the electorate’s context; second, the electorate-election interaction which forms the baseline to explore the perspective of local contextual effects in voting behaviour and election results; third, the relation between geographical location and election outcomes reflecting the implication of determining constituency boundaries on election results. To address the above relations, three types of variables: geo, independent and dependent, have been elaborated and two models have been created. The Data Model, developed in a GIS environment, facilitates structuring of election data in order to perform spatial analysis. The peculiarity of electoral patterns – a multidimensional array that contains information on three variables, stored in data layers of dissimilar spatial units of reference and scales of value measurement – prohibit spatial analysis based on the original source data. To perform a joint spatial analysis it is therefore mandatory to restructure the spatial units of reference while preserving their semantic content. In this operation, all relevant electoral as well as socio-demographic data referenced to different administrative spatial entities are re-referenced to uniform grid cells as virtual spatial units of reference. Depending on the scale of data acquisition and map presentation, a cell width of 0.5 km has been determined. The resulting fine grid forms the basis of subsequent data analyses and correlations. Conversion of the original vector data layers into target raster layers allows for unification of spatial units, at the same time retaining the existing level of detail of the data (variables, uniform distribution over space). This in turn facilitates the integration of the variables studied and the performance of GIS-based spatial analysis. In addition, conversion to raster format makes it possible to assign new values to the original data, which are based on a common scale eliminating existing differences in scale of measurement. Raster format operations of the type described are well-established data analysis techniques in GIT, yet they have rarely been employed to process and analyse electoral data. The Geovisualization Model, developed in a cartographic environment, complements the Data Model. As an analog graphic model it facilitates efficient communication and exploration of geographical information through cartographic visualization. Based on this model, 52 choropleth maps have been generated. They represent the outcome of the GIS-based electoral data analysis. The analog map form allows for in-depth visual analysis and interpretation of the distribution and correlation of the electoral data studied. For researchers, decision makers and a wider public the maps provide easy-to-access information on and promote easy-to-understand insight into the spatial dimension, regional variation and resulting structures of the electoral patterns defined.
Our dynamic Sun manifests its activity by different phenomena: from the 11-year cyclic sunspot pattern to the unpredictable and violent explosions in the case of solar flares. During flares, a huge amount of the stored magnetic energy is suddenly released and a substantial part of this energy is carried by the energetic electrons, considered to be the source of the nonthermal radio and X-ray radiation. One of the most important and still open question in solar physics is how the electrons are accelerated up to high energies within (the observed in the radio emission) short time scales. Because the acceleration site is extremely small in spatial extent as well (compared to the solar radius), the electron acceleration is regarded as a local process. The search for localized wave structures in the solar corona that are able to accelerate electrons together with the theoretical and numerical description of the conditions and requirements for this process, is the aim of the dissertation. Two models of electron acceleration in the solar corona are proposed in the dissertation: I. Electron acceleration due to the solar jet interaction with the background coronal plasma (the jet--plasma interaction) A jet is formed when the newly reconnected and highly curved magnetic field lines are relaxed by shooting plasma away from the reconnection site. Such jets, as observed in soft X-rays with the Yohkoh satellite, are spatially and temporally associated with beams of nonthermal electrons (in terms of the so-called type III metric radio bursts) propagating through the corona. A model that attempts to give an explanation for such observational facts is developed here. Initially, the interaction of such jets with the background plasma leads to an (ion-acoustic) instability associated with growing of electrostatic fluctuations in time for certain range of the jet initial velocity. During this process, any test electron that happen to feel this electrostatic wave field is drawn to co-move with the wave, gaining energy from it. When the jet speed has a value greater or lower than the one, required by the instability range, such wave excitation cannot be sustained and the process of electron energization (acceleration and/or heating) ceases. Hence, the electrons can propagate further in the corona and be detected as type III radio burst, for example. II. Electron acceleration due to attached whistler waves in the upstream region of coronal shocks (the electron--whistler--shock interaction) Coronal shocks are also able to accelerate electrons, as observed by the so-called type II metric radio bursts (the radio signature of a shock wave in the corona). From in-situ observations in space, e.g., at shocks related to co-rotating interaction regions, it is known that nonthermal electrons are produced preferably at shocks with attached whistler wave packets in their upstream regions. Motivated by these observations and assuming that the physical processes at shocks are the same in the corona as in the interplanetary medium, a new model of electron acceleration at coronal shocks is presented in the dissertation, where the electrons are accelerated by their interaction with such whistlers. The protons inflowing toward the shock are reflected there by nearly conserving their magnetic moment, so that they get a substantial velocity gain in the case of a quasi-perpendicular shock geometry, i.e, the angle between the shock normal and the upstream magnetic field is in the range 50--80 degrees. The so-accelerated protons are able to excite whistler waves in a certain frequency range in the upstream region. When these whistlers (comprising the localized wave structure in this case) are formed, only the incoming electrons are now able to interact resonantly with them. But only a part of these electrons fulfill the the electron--whistler wave resonance condition. Due to such resonant interaction (i.e., of these electrons with the whistlers), the electrons are accelerated in the electric and magnetic wave field within just several whistler periods. While gaining energy from the whistler wave field, the electrons reach the shock front and, subsequently, a major part of them are reflected back into the upstream region, since the shock accompanied with a jump of the magnetic field acts as a magnetic mirror. Co-moving with the whistlers now, the reflected electrons are out of resonance and hence can propagate undisturbed into the far upstream region, where they are detected in terms of type II metric radio bursts. In summary, the kinetic energy of protons is transfered into electrons by the action of localized wave structures in both cases, i.e., at jets outflowing from the magnetic reconnection site and at shock waves in the corona.
In this work, some new results to exploit the recurrence properties of quasiperiodic dynamical systems are presented by means of a two dimensional visualization technique, Recurrence Plots(RPs). Quasiperiodicity is the simplest form of dynamics exhibiting nontrivial recurrences, which are common in many nonlinear systems. The concept of recurrence was introduced to study the restricted three body problem and it is very useful for the characterization of nonlinear systems. I have analyzed in detail the recurrence patterns of systems with quasiperiodic dynamics both analytically and numerically. Based on a theoretical analysis, I have proposed a new procedure to distinguish quasiperiodic dynamics from chaos. This algorithm is particular useful in the analysis of short time series. Furthermore, this approach demonstrates to be efficient in recognizing regular and chaotic trajectories of dynamical systems with mixed phase space. Regarding the application to real situations, I have shown the capability and validity of this method by analyzing time series from fluid experiments.
The solar tachocline is a thin transition layer between the solar radiative zone rotating uniformly and the solar convection zone, which has a mainly latitudinal differential rotation profile. This layer has a thickness of less than $0.05R_{\sun}$ and is subject to extreme radial as well as latitudinal shears. Helioseismological estimates put this layer at roughly $0.7R_{\sun}$. The tachocline mostly resides in the sub-adiabatic, non-turbulent radiative interior, except for a small overlap with the convection zone on the top. Many proposed dynamo mechanisms involve strong toroidal magnetic fields in this transition region. The exact mechanisms behind the formation of such a thin layer is still disputed. A very plausible mechanism is the one involving a weak, relic poloidal magnetic field trapped inside the radiative zone, which is responsible for expelling differential rotation outwards. This was first proposed by \citet{RK97}. The present work develops this idea with numerical simulations including additional effects like meridional circulation. It is shown that a relic field of 1~Gauss or smaller would be sufficient to explain the observed thickness of the tachocline. The stability of the solar tachocline is addressed as the next part of the problem. It is shown that the tachocline is stable up to a differential rotation of 52\% in the absence of magnetic fields. This is a new finding as compared to the earlier two dimensional models which estimated the solar differential rotation (about 28\%) to be marginally stable or even unstable. The changed stability limit is attributed to the changed stability criterion of the 3-dimensional model which also involves radial gradients of the angular velocity. In the presence of toroidal magnetic field belts, the lowest non-axisymmetric mode is shown to be the most unstable one for the radiative part of the tachocline. It is estimated that the tachocline would become unstable for toroidal fields exceeding about 100~Gauss. With both formation and stability questions satisfactorily addressed, this work presents the most comprehensive analysis of the physical processes in the solar tachocline to date.
Functional analysis of selected DOF transcription factors in the model plant Arabidopsis thaliana
(2007)
Transcription factors (TFs) are global regulators of gene expression playing essential roles in almost all biological processes, and are therefore of great scientific and biotechnological interest. This project focused on functional characterisation of three DNA-binding-with-one-zinc-finger (DOF) TFs from the genetic model plant Arabidopsis thaliana, namely OBP1, OBP2 and AtDOF4;2. These genes were selected due to severe growth phenotypes conferred upon their constitutive over-expression. To identify biological processes regulated by OBP1, OBP2 and AtDOF4;2 in detail molecular and physiological characterization of transgenic plants with modified levels of OBP1, OBP2 and AtDOF4;2 expression (constitutive and inducible over-expression, RNAi) was performed using both targeted and profiling technologies. Additionally expression patterns of studied TFs and their target genes were analyzed using promoter-GUS lines and publicly available microarray data. Finally selected target genes were confirmed by chromatin immuno-precipitation and electrophoretic-mobility shift assays. This combinatorial approach revealed distinct biological functions of OBP1, OBP2 and AtDOF4;2. Specifically OBP2 controls indole glucosinolate / auxin homeostasis by directly regulating the enzyme at the branch of these pathways; CYP83B1 (Skirycz et al., 2006). Glucosinolates are secondary compounds important for defence against herbivores and pathogens in the plants order Caparales (e.g. Arabidopsis, canola and broccoli) whilst auxin is an essential plant hormone. Hence OBP2 is important for both response to biotic stress and plant growth. Similarly to OBP2 also AtDOF4;2 is involved in the regulation of plant secondary metabolism and affects production of various phenylpropanoid compounds in a tissue and environmental specific manner. It was found that under certain stress conditions AtDOF4;2 negatively regulates flavonoid biosynthetic genes whilst in certain tissues it activates hydroxycinnamic acid production. It was hypothesized that this dual function is most likely related to specific interactions with other proteins; perhaps other TFs (Skirycz et al., 2007). Finally OBP1 regulates both cell proliferation and cell expansion. It was shown that OBP1 controls cell cycle activity by directly targeting the expression of core cell cycle genes (CYCD3;3 and KRP7), other TFs and components of the replication machinery. Evidence for OBP1 mediated activation of cell cycle during embryogenesis and germination will be presented. Additionally and independently on its effects on cell proliferation OBP1 negatively affects cell expansion via reduced expression of cell wall loosening enzymes. Summing up this work provides an important input into our knowledge on DOF TFs function. Future work will concentrate on establishing exact regulatory networks of OBP1, OBP2 and AtDOF4;2 and their possible biotechnological applications.
Each organ of a multicellular organism is unique at the level of its tissues and cells. Furthermore, responses to environmental stimuli or developmental signals occur differentially at the single cell or tissue level. This underlines the necessity of precise investigation of the “building block of life” -the individual cell. Although recently large amount of data concerning different aspects of single cell performance was accumulated, our knowledge about development and differentiation of individual cell within specialized tissue are still far from being complete. To get more insight into processes that occur in certain individual cell during its development and differentiation changes in gene expression during life cycle of A. thaliana leaf hair cell (trichome) were explored in this work. After onset of trichome development this cell changes its cell cycle: it starts endoreduplication (a modified cell cycle in which DNA replication continues in the absence of mitosis and cytokinesis). This makes trichomes a suitable model for studying cell cycle regulation, regulation of cell development and differentiation. Cells of interest were sampled by puncturing them with glass microcapillaries. Each sample contained as few as ten single cells. At first time trichomes in initial stage of trichome development were investigated. To allow their sampling they were specifically labelled by green fluorescent protein (GFP). In total three cell types were explored: pavement cells, trichome initials and mature trichomes. Comparison of gene expression profiles of these cells allowed identification of the genes differentially expressed in subsequent stages of trichome development. Bioinformatic analysis of genes preferentially expressed in trichome initials showed their involvement in hormonal, metal, sulphur response and cell-cycle regulation. Expression pattern of three selected candidate genes, involved in hormonal response and early developmental processes was confirmed by independent method. Effects of mutations in these genes on both trichome and plant development as well as on plant metabolism were analysed. As an outcome of this work novel components in the sophisticated machinery of trichome development and cell cycle progression were identified. These factors could integrate hormone stimuli and network interactions between characterized and as yet unknown members of this machinery. I expect findings presented in this work to enhance and complement our current knowledge about cell cycle progression and trichome development, as well as about performance of the individual cell in general.
Magnetorotational instability (MRI) is one of the most important and most common instabilities in astrophysics. Today it is widely accepted that it serves as a major source of turbulent viscosity in accretion disks, the most energy efficient objects in the universe. The importance of the MRI for astrophysics has been realized only in recent fifteen years. However, originally it was discovered much earlier, in 1959, in a very different context. Theoretical flow of a conducting liquid confined between differentially rotating cylinders in the presence of an external magnetic field was analyzed. The central conclusion is that the additional magnetic field parallel to the axis of rotation can destabilize otherwise stable flow. Theory of non-magnetized fluid motion between rotating cylinders has much longer history, though. It has been studied already in 1888 and today such setup is usually referred as a Taylor-Couette flow. To prove experimentally the existence of MRI in a magnetized Taylor-Couette flow is a demanding task and different MHD groups around the world try to achieve it. The main problem lies in the fact that laboratory liquid metals which are used in such experiments are characterized by small magnetic Prandtl number. Consequently rotation rates of the cylinders must be extremely large and vast amount of technical problems emerge. One of the most important difficulties is an influence of plates enclosing the cylinders in any experiment. For fast rotation the plates tend to dominate the whole flow and the MRI can not be observed. In this thesis we discuss a special helical configuration of the applied magnetic field which allows the critical rotation rates to be much smaller. If only the axial magnetic field is present, the cylinders must rotate with angular velocities corresponding to Reynolds numbers of order Re ≈ 10^6. With the helical field this number is dramatically reduced to Re ≈ 10^3. The azimuthal component of the magnetic field can be easily generated by letting an electric current through the axis of rotation, In a Taylor-Couette flow the (primary) instability manifests itself as Taylor vortices. The specific geometry of the helical magnetic field leads to a traveling wave solution and the vortices are drifting in a direction determined by rotation and the magnetic field. In an idealized study for infinitely long cylinders this is not a problem. However, if the cylinders have finite length and are bounded vertically by the plates the situation is different. In this dissertation it is shown, with use of numerical methods, that the traveling wave solution also exists for MHD Taylor-Couette flow at finite aspect ratio H/D, H being height of the cylinders, D width of the gap between them. The nonlinear simulations provide amplitudes of fluid velocity which are helpful in designing an experiment. Although the plates disturb the flow, parameters like the drift velocity indicate that the helical MRI operates in this case. The idea of the helical MRI was implemented in a very recent experiment PROMISE. The results provided, for the first time, an evidence that the (helical) MRI indeed exists. Nevertheless, the influence of the vertical endplates was evident and the experiment can be, in principle, improved. Exemplary methods of reduction of the end-effect are here proposed. Near the vertical boundaries develops an Ekman-Hartmann layer. Study of this layer for the MHD Taylor-Couette system as well as its impact on the global flow properties is presented. It is shown that the plates, especially if they are conducting, can disturb the flow far more then previously thought also for relatively slow rotation rates.
Hierarchical meso- and macropore architectures by liquid crystalline and polymer colloid templating
(2007)
The objective of this thesis is to improve the knowledge of control mechanisms of hydrological induced mass movements. To this end, detailed hydrological process studies and physically-based hydrological modelling were applied. The study site is a hillslope in the Dornbirn Ache valley near Bregenz, Austria. This so called Heumös slope features a deep-seated translational shear zone and surface near creep movements of up to 10 cm a year. The Cretaceous marlstones of the Austrian Helveticum have a high susceptibility for weathering and might form clay-rich cohesive sediments. In addition, glacial and post-glacial processes formed an unstable hillslope. High yearly precipitation depths of about 2100 mm and rainstorms with both high intensities and precipitation depths govern surface and subsurface hydrological processes. Pressure propagation induced in hydrological active areas influences laterally the groundwater reactions of the moving mass. A complex three-dimensional subsurface pressure system is the cause for fast groundwater reactions despite low hydraulic conductivities. To understand hillslope scale variability, hydrotopes representing specific dominating processes were mapped using vegetation association distribution and soil core analysis. Detailed small-scale soil investigations followed to refine the understanding of these hydrotopes. A perceptional model was developed from the hydrotope distribution and was corroborated by these detailed investigations. The moving hillslope is dominated by surface-runoff generation. Infiltration and deep percolation of water is inhibited through clay-rich gleysols; the yearly average soil moisture is close to saturation. Steep slopes adjacent to the moving hillslope are far more active concerning infiltration, preferential flow and groundwater fluctuations. Spring discharge observations at the toe of the steep slopes are in close relation to groundwater table observations on the moving hillslope body. Evidence of pressure propagation from the steep slopes towards the hillslope body is gathered by comparison of dominating structures and processes. The application of the physically-based hydrological model CATFLOW substantiates the idea of pressure propagation as a key process for groundwater reactions and as a possible trigger for movement in the hillslope.
Numerous recent publications on the psychological meaning of “if” have proposed a probabilistic interpretation of conditional sentences. According to the proponents of probabilistic approaches, sentences like “If the weather is nice, I will be at the beach tomorrow” (or “If p, then q” in the abstract version) express a high probability of the consequent (being at the beach), given the antecedent (nice weather). When people evaluate conditional sentences, they assumingly do so by deriving the conditional probability P(q|p) using a procedure called the Ramsey test. This is a contradicting view to the hitherto dominant Mental Model Theory (MMT, Johnson-Laird, 1983), that proposes conditional sentences refer to possibilities in the world that are represented in form of mental models. Whereas probabilistic approaches gained a lot of momentum in explaining the interpretation of conditionals, there is still no conclusive probabilistic account of conditional reasoning. This thesis investigates the potential of a comprehensive probabilistic account on conditionals that covers the interpretation of conditionals as well as conclusion drawn from these conditionals when used as a premise in an inference task. The first empirical chapter of this thesis, Chapter 2, implements a further investigation of the interpretation of conditionals. A plain version of the Ramsey test as proposed by Evans and Over (2004) was tested against a similarity sensitive version of the Ramsey test (Oberauer, 2006) in two experiments using variants of the probabilistic truth table task (Experiments 2.1 and 2.2). When it comes to decide whether an instance is relevant for the evaluation of a conditional, similarity seems to play a minor role. Once the decision about relevance is made, believability judgments of the conditional seem to be unaffected by the similarity manipulation and judgments are based on frequency of instances, in the way predicted by the plain Ramsey test. In Chapter 3 contradicting predictions of the probabilistic approaches on conditional reasoning of Verschueren et al (2005), Evans and Over (2004) and Oaksford & Chater (2001) are tested against each other. Results from the probabilistic truth table task modified for inference tasks supports the account of Oaksford and Chater (Experiment 3.1). A learning version of the task and a design with every day conditionals yielded results unpredicted by any of the theories (Experiments 3.2-3.4). Based on these results, a new probabilistic 2-stage model of conditional reasoning is proposed. To preclude claims that the use of the probabilistic truth table task (or variants thereof) favors judgments reflecting conditional probabilities, Chapter 4 combines methodologies used by proponents of the MMT with the probabilistic truth table task. In three Experiments (4.1 -4.3) it could be shown for believability judgments of the conditional and inferences drawn from it, that causal information about counterexamples only prevails, when no frequencies of exceptional cases are present. Experiment 4.4 extends these findings to every day conditionals. A probabilistic estimation process based on frequency information is used to explain results on all tasks. The findings confirm with a probabilistic approach on conditionals and moreover constitute an explanatory challenge for the MMT. In conclusion of all the evidence gathered in this dissertation it seems justified to draw the picture of a comprehensive probabilistic view on conditionals quite optimistically. Probability estimates not only explain the believability people assign to a conditional sentence, they also explain to what extend people are willing to draw conclusions from those sentences.
Microsaccades are an important component of the small eye movements that constitute fixation, the basis of visual perception. The specific function of microsaccades has been a long-standing research problem. Only recently, conclusive evidence emerged, showing that microsaccades aid both visual perception and oculomotor control. The main goal of this thesis was to improve our understanding of the implementation of microsaccade generation within the circuitry of saccade control, an unsolved issue in oculomotor research. We make a case for a model according to which microsaccades and saccades result from mutually dependent motor plans, competing for expression. The model consists of an activation field, coding for fixation at its center and for saccades at peripheral locations; saccade amplitude increases with eccentricity. Activity during fixation spreads to slightly peripheral locations in the field and, thus, may result in the generation of microsaccades. Inhibition of remote and excitation of neighbouring locations govern the dynamics of the field, resulting in a strong competition between fixation and saccade generation. We propose that this common-field model of microsaccade and saccade generation finds a neurophysiological counterpart in the motor map of the superior colliculus (SC), a key brainstem structure involved in the generation of saccades. In a series of five behavioral experiments, we tested implications of the model. Predictions were derived concerning (1) the behavior of microsaccades in a given task (microsaccade rate, amplitude, and direction), (2) the interactions of microsaccades and subsequent saccades, and (3) the relationship between microsaccadic behavior and neurophysiological processes at the level of the SC. The results yielded strong support for the model at all three levels of analysis, suggesting that microsaccade statistics are indicative of the state of the fixation-related part of the SC motor map.