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In this dissertation, an electric field-assisted method was developed and applied to achieve immobilization and alignment of biomolecules on metal electrodes in a simple one-step experiment. Neither modifications of the biomolecule nor of the electrodes were needed. The two major electrokinetic effects that lead to molecule motion in the chosen electrode configurations used were identified as dielectrophoresis and AC electroosmotic flow. To minimize AC electroosmotic flow, a new 3D electrode configuration was designed. Thus, the influence of experimental parameters on the dielectrophoretic force and the associated molecule movement could be studied. Permanent immobilization of proteins was examined and quantified absolutely using an atomic force microscope. By measuring the volumes of the immobilized protein deposits, a maximal number of proteins contained therein was calculated. This was possible since the proteins adhered to the tungsten electrodes even after switching off the electric field. The permanent immobilization of functional proteins on surfaces or electrodes is one crucial prerequisite for the fabrication of biosensors.
Furthermore, the biofunctionality of the proteins must be retained after immobilization. Due to the chemical or physical modifications on the proteins caused by immobilization, their biofunctionality is sometimes hampered. The activity of dielectrophoretically immobilized proteins, however, was proven here for an enzyme for the first time. The enzyme horseradish peroxidase was used exemplarily, and its activity was demonstrated with the oxidation of dihydrorhodamine 123, a non-fluorescent precursor of the fluorescence dye rhodamine 123.
Molecular alignment and immobilization - reversible and permanent - was achieved under the influence of inhomogeneous AC electric fields. For orientational investigations, a fluorescence microscope setup, a reliable experimental procedure and an evaluation protocol were developed and validated using self-made control samples of aligned acridine orange molecules in a liquid crystal.
Lambda-DNA strands were stretched and aligned temporarily between adjacent interdigitated electrodes, and the orientation of PicoGreen molecules, which intercalate into the DNA strands, was determined. Similarly, the aligned immobilization of enhanced Green Fluorescent Protein was demonstrated exploiting the protein's fluorescence and structural properties. For this protein, the angle of the chromophore with respect to the protein's geometrical axis was determined in good agreement with X-ray crystallographic data. Permanent immobilization with simultaneous alignment of the proteins was achieved along the edges, tips and on the surface of interdigitated electrodes. This was the first demonstration of aligned immobilization of proteins by electric fields.
Thus, the presented electric field-assisted immobilization method is promising with regard to enhanced antibody binding capacities and enzymatic activities, which is a requirement for industrial biosensor production, as well as for general interaction studies of proteins.
Molekulare Charakterisierung von CP75, einem neuen centrosomalen Protein in Dictyostelium discoideum
(2016)
Das Centrosom ist ein Zellkern-assoziiertes Organell, das nicht von einer Membran umschlossen ist. Es spielt eine wichtige Rolle in vielen Mikrotubuli- abhängigen Prozessen wie Organellenpositionierung, Zellpolarität oder die Organisation der mitotischen Spindel. Das Centrosom von Dictyostelium besteht aus einer dreischichtigen Core-Struktur umgeben von einer Corona, die Mikrotubuli-nukleierende Komplexe enthält. Die Verdoppelung des Centrosoms in Dictyostelium findet zu Beginn der Mitose statt. In der Prophase vergrößert sich die geschichtete Core-Struktur und die Corona löst sich auf. Anschließend trennen sich die beiden äußeren Lagen der Core-Struktur und bilden in der Metaphase die beiden Spindelpole, die in der Telophase zu zwei vollständigen Centrosomen heranreifen. Das durch eine Proteom-Analyse identifizierte Protein CP75 lokalisiert am Centrosom abhängig von den Mitosephasen. Es dissoziiert von der Core-Struktur in der Prometaphase und erscheint an den Spindelpolen in der Telophase wieder. Dieses Verhalten korreliert mit dem Verhalten der mittleren Lage der Core-Struktur in der Mitose, was darauf hinweist, dass CP75 eine Komponente dieser Schicht sein könnte. Die FRAP-Experimente am Interphase- Centrosom zeigen, dass GFP-CP75 dort nicht mobil ist. Das deutet darauf hin, dass das Protein wichtige Funktionen im Strukturerhalt der centrosomalen Core- Struktur übernehmen könnte. Sowohl die C- als auch die N-terminale Domäne von CP75 enthalten centrosomale Targeting-Domäne. Als GFP-Fusionsproteine (GFP-CP75-N und -C) lokalisieren die beiden Fragmente am Centrosom in der Interphase. Während GFP-CP75-C in der Mitose am Centrosom verbleibt, verschwindet GFP-CP75-N in der Metaphase und kehrt erst in der späten Telophase zurück. GFP-CP75-C und GFP-CP75O/E kolokalisieren mit F-Aktin am Zellcortex, zeigen aber keine Interaktion mit Aktin mit der BioID-Methode. Die N-terminale Domäne von CP75 enthält eine potentielle Plk1- Phosphorylierungssequenz. Die Überexpression der nichtphosphorylierbaren Punktmutante (GFP-CP75-Plk-S143A) ruft verschiedene Phänotypen wie verlängerte oder überzählige Centrosomen, vergrößerte Zellkerne und Anreicherung von detyrosinierten Mikrotubuli hervor. Die ähnlichen Phänotypen konnten auch bei GFP-CP75-N und CP75-RNAi beobachtet werden. Der
Phänotyp der detyrosinierten Mikrotubuli bringt erstmals den Beweis dafür, dass I
in Dictyostelium posttranslationale Modifikation an Tubulinen stattfindet. Außerdem zeigten CP75-RNAi-Zellen Defekte in der Organisation der mitotischen Spindel. Mittels BioID-Methode konnten drei potentielle Interaktionspartner von CP75 identifiziert werden. Diese drei Proteine CP39, CP91 und Cep192 sind ebenfalls Bestandteile des Centrosoms.
Savannas cover a broad geographical range across continents and are a biome best described by a mix of herbaceous and woody plants. The former create a more or less continuous layer while the latter should be sparse enough to leave an open canopy. What has long intrigued ecologists is how these two competing plant life forms of vegetation coexist.
Initially attributed to resource competition, coexistence was considered the stable outcome of a root niche differentiation between trees and grasses. The importance of environmental factors became evident later, when data from moister environments demonstrated that tree cover was often lower than what the rainfall conditions would allow for. Our current understanding relies on the interaction of competition and disturbances in space and time. Hence, the influence of grazing and fire and the corresponding feedbacks they generate have been keenly investigated. Grazing removes grass cover, initiating a self-reinforcing process propagating tree cover expansion. This is known as the encroachment phenomenon. Fire, on the other hand, imposes a bottleneck on the tree population by halting the recruitment of young trees into adulthood. Since grasses fuel fires, a feedback linking grazing, grass cover, fire, and tree cover is created. In African savannas, which are the focus of this dissertation, these feedbacks play a major role in the dynamics.
The importance of these feedbacks came into sharp focus when the notion of alternative states began to be applied to savannas. Alternative states in ecology arise when different states of an ecosystem can occur under the same conditions. According to this an open savanna and a tree-dominated savanna can be classified as alternative states, since they can both occur under the same climatic conditions. The aforementioned feedbacks are critical in the creation of alternative states. The grass-fire feedback can preserve an open canopy as long as fire intensity and frequency remain above a certain threshold. Conversely, crossing a grazing threshold can force an open savanna to shift to a tree-dominated state. Critically, transitions between such alternative states can produce hysteresis, where a return to pre-transition conditions will not suffice to restore the ecosystem to its original state.
In the chapters that follow, I will cover aspects relating to the coexistence mechanisms and the role of feedbacks in tree-grass interactions. Coming back to the coexistence question, due to the overwhelming focus on competition and disturbance another important ecological process was neglected: facilitation. Therefore, in the first study within this dissertation I examine how facilitation can expand the tree-grass coexistence range into drier conditions. For the second study I focus on another aspect of savanna dynamics which remains underrepresented in the literature: the impacts of inter-annual rainfall variability upon savanna trees and the resilience of the savanna state. In the third and final study within this dissertation I approach the well-researched encroachment phenomenon from a new perspective: I search for an early warning indicator of the process to be used as a prevention tool for savanna conservation. In order to perform all this work I developed a mathematical ecohydrological model of Ordinary Differential Equations (ODEs) with three variables: soil moisture content, grass cover and tree cover.
Facilitation: Results showed that the removal of grass cover through grazing was detrimental to trees under arid conditions, contrary to expectation based on resource competition. The reason was that grasses preserved moisture in the soil through infiltration and shading, thus ameliorating the harsh conditions for trees in accordance with the Stress Gradient Hypothesis. The exclusion of grasses from the model further demonstrated this: tree cover was lower in the absence of grasses, indicating that the benefits of grass facilitation outweighed the costs of grass competition for trees. Thus, facilitation expanded the climatic range where savannas persisted into drier conditions.
Rainfall variability: By adjusting the model to current rainfall patterns in East Africa, I simulated conditions of increasing inter-annual rainfall variability for two distinct mean rainfall scenarios: semi-arid and mesic. Alternative states of tree-less grassland and tree-dominated savanna emerged in both cases. Increasing variability reduced semi-arid savanna tree cover to the point that at high variability the savanna state was eliminated, because variability intensified resource competition and strengthened the fire disturbance during high rainfall years. Mesic savannas, on the other hand, became more resilient along the variability gradient: increasing rainfall variability created more opportunities for the rapid growth of trees to overcome the fire disturbance, boosting the chances of savannas persisting and thus increasing mesic savanna resilience.
Preventing encroachment: The breakdown in the grass-fire feedback caused by heavy grazing promoted the expansion of woody cover. This could be irreversible due to the presence of alternative states of encroached and open savanna, which I found along a simulated grazing gradient. When I simulated different short term heavy grazing treatments followed by a reduction to the original grazing conditions, certain cases converged to the encroached state. Utilising woody cover changes only during the heavy grazing treatment, I developed an early warning indicator which identified these cases with a high risk of such hysteresis and successfully distinguished them from those with a low risk. Furthermore, after validating the indicator on encroachment data, I demonstrated that it appeared early enough for encroachment to be prevented through realistic grazing-reduction treatments.
Though this dissertation is rooted in the theory of savanna dynamics, its results can have significant applications in savanna conservation. Facilitation has only recently become a topic of interest within savanna literature. Given the threat of increasing droughts and a general anticipation of drier conditions in parts of Africa, insights stemming from this research may provide clues for preserving arid savannas. The impacts of rainfall variability on savannas have not yet been thoroughly studied, either. Conflicting results appear as a result of the lack of a robust theoretical understanding of plant interactions under variable conditions. . My work and other recent studies argue that such conditions may increase the importance of fast resource acquisition creating a ‘temporal niche’. Woody encroachment has been extensively studied as phenomenon, though not from the perspective of its early identification and prevention. The development of an encroachment forecasting tool, as the one presented in this work, could protect both the savanna biome and societies dependent upon it for (economic) survival. All studies which follow are bound by the attempt to broaden the horizons of savanna-related research in order to deal with extreme conditions and phenomena; be it through the enhancement of the coexistence debate or the study of an imminent external threat or the development of a management-oriented tool for the conservation of savannas.
Molekulare Charakterisierung des Centrosom-assoziierten Proteins CP91 in Dictyostelium discoideum
(2016)
Das Dictyostelium-Centrosom ist ein Modell für acentrioläre Centrosomen. Es besteht aus einer dreischichtigen Kernstruktur und ist von einer Corona umgeben, welche Nukleationskomplexe für Mikrotubuli beinhaltet. Die Verdoppelung der Kernstruktur wird einmal pro Zellzyklus am Übergang der G2 zur M-Phase gestartet. Durch eine Proteomanalyse isolierter Centrosomen konnte CP91 identifiziert werden, ein 91 kDa großes Coiled-Coil Protein, das in der centrosomalen Kernstruktur lokalisiert. GFP-CP91 zeigte fast keine Mobilität in FRAP-Experimenten während der Interphase, was darauf hindeutet, dass es sich bei CP91 um eine Strukturkomponente des Centrosoms handelt. In der Mitose hingegen dissoziieren das GFP-CP91 als auch das endogene CP91 ab und fehlen an den Spindelpolen von der späten Prophase bis zur Anaphase. Dieses Verhalten korreliert mit dem Verschwinden der zentralen Schicht der Kernstruktur zu Beginn der Centrosomenverdopplung. Somit ist CP91 mit großer Wahrscheinlichkeit ein Bestandteil dieser Schicht. CP91-Fragmente der N-terminalen bzw. C-terminalen Domäne (GFP-CP91 N-Terminus, GFP-CP91 C-Terminus) lokalisieren als GFP-Fusionsproteine exprimiert auch am Centrosom, zeigen aber nicht die gleiche mitotische Verteilung des Volllängenproteins. Das CP91-Fragment der zentralen Coiled-Coil Domäne (GFP-CP91cc) lokalisiert als GFP-Fusionsprotein exprimiert, als ein diffuser cytosolische Cluster, in der Nähe des Centrosoms. Es zeigt eine partiell ähnliche mitotische Verteilung wie das Volllängenprotein. Dies lässt eine regulatorische Domäne innerhalb der Coiled-Coil Domäne vermuten. Die Expression der GFP-Fusionsproteine unterdrückt die Expression des endogenen CP91 und bringt überzählige Centrosomen hervor. Dies war auch eine markante Eigenschaft nach der Unterexpression von CP91 durch RNAi. Zusätzlich zeigte sich in CP91-RNAi Zellen eine stark erhöhte Ploidie verursacht durch schwere Defekte in der Chromosomensegregation verbunden mit einer erhöhten Zellgröße und Defekten im Abschnürungsprozess während der Cytokinese. Die Unterexpression von CP91 durch RNAi hatte auch einen direkten Einfluss auf die Menge an den centrosomalen Proteinen CP39, CP55 und CEP192 und dem Centromerprotein Cenp68 in der Interphase. Die Ergebnisse deuten darauf hin, dass CP91 eine zentrale centrosomale Kernkomponente ist und für den Zusammenhalt der beiden äußeren Schichten der Kernstruktur benötigt wird. Zudem spielt CP91 eine wichtige Rolle für eine ordnungsgemäße Centrosomenbiogenese und, unabhängig davon, bei dem Abschnürungsprozess der Tochterzellen während der Cytokinese.
In this Thesis, the properties of aqueous hemicellulose polysaccharides are investigated using computer simulations. The high swelling capacity of materials composed of these molecules allows the generation of directed motion in plant materials entirely controlled by water uptake.
To explore the molecular origin of this swelling capacity, a computational model with atomistic resolution for hemicellulose polysaccharides is build and validated in comparison with experiments. Using this model, simulations of small polysaccharides are employed to gain an understanding of the interactions of these molecules with water, the influence of water on their conformational freedom, and the swelling capacity quantified in terms of osmotic pressure. It is revealed that the branched hemicellulose polysaccharides show different hydration characteristics compared to linear polysaccharides.
To study swelling properties on length and time scales that exceed the limitations imposed by atomistic simulations, a procedure to obtain transferable coarse-grain models is developed. The transferability of the coarse-grain models over both different degrees of polymerization as well as different solute concentrations is demonstrated. Therefore, the procedure allows the construction of large coarse-grained systems based on small atomistic reference systems. Finally, the coarse-grain model is applied to demonstrate that linear and branched polysaccharides show a different swelling behavior when coupled to a water bath.
In freshwater sciences, nitrogen gained increasing attention in the past as an important resource potentially influencing phytoplankton growth and thus eutrophication. Most studies and all management approaches, however, are still restricted to dissolved inorganic nitrogen (DIN = nitrate + nitrite + ammonium) since dissolved organic nitrogen (DON) was considered to be refractory for most of the photoautotrophs. In the meantime this assumption has been disproved for all aquatic systems. While research on DON in marine ecosystems substantially increased, in freshwater a surprisingly small number of investigations has been carried out on DON utilization by phytoplankton or even the occurrence and seasonal development of total DON or its compounds in lakes. Therefore, our present knowledge on DON utilization by phytoplankton is often based on single species experiments using a sole, usually low molecular weight DON component, often in unnaturally high amounts mainly carried out with marine phytoplankton species. Thus, we know that some phytoplankton species can take up different DON fractions if they are available in high concentrations and as sole nitrogen source. This does not necessarily imply that phytoplankton would perform likewise in natural environments. In addition, it will be difficult to draw conclusions on the behavior of freshwater phytoplankton from experiments with marine phytoplankton since the nutrient regime in marine environments differs from that of freshwater. In the light of the parallel availability of inorganic and organic nitrogen species in natural freshwater ecosystems, several questions must be raised: "If inorganic nitrogen is available, would phytoplankton really rely on an organic nitrogen source? Could a connection be detected between the seasonal development of DON and changes in the phytoplankton community composition as found for inorganic nitrogen? And if we reduce the input of inorganic nitrogen in lakes and rivers would the importance of DON as nitrogen source for phytoplankton increase, counteracting all management efforts or even leading to undesired effects due to changes in phytoplankton physiology and biodiversity?" I experimentally addressed the questions whether those DON compounds differentially influence growth, physiology and composition of phytoplankton both as sole available nitrogen source and in combination with other nitrogen compounds. I hypothesized that all offered DON - compounds (urea, natural organic matter (NOM), dissolved free and combined amino acids (DFAA, DCAA)) could be utilized by phytoplankton at natural concentrations. However, I assumed that the availability would decrease with increasing compound complexity. I furthermore hypothesized that the occurrence of low DIN concentrations would not affect the utilization of DON negatively. The nitrogen source, whatsoever, would have an impact on phytoplankton physiology as well as community composition. To investigate these questions and assumptions I conducted bioassays with algae monocultures as well as phytoplankton communities testing the utilization of various DON compounds by several freshwater phytoplankton species. Especially the potential utilization of NOM, a complex DON compound mainly consisting of humic substances is of interest, since it is usually regarded to be refractory. In order to be able to use natural concentrations of DON - compounds for my experiments the concentration of total DON and some DON - compounds (urea, humic substances, heigh molecular weight substances) was assessed in Lake Müggelsee. All compounds were able to support algae growth in the low natural concentrations supplied. However, I found that the offered DON compounds differ in their availability to various algae species, both, as sole nitrogen source or in combination with low DIN concentrations. As expected, the availability decreased with increasing complexity of the nitrogen compound. Furthermore, I could show that changes in algal physiology (nitrogen storage, metabolism) occur depending on the utilized nitrogen source. Especially the secondary photosynthetic pigment composition, heterocyst frequency and C:N - ratio of the algae were affected. The uptake and usage of certain nitrogen compounds might be more costly, potentially resulting in those physiology changes. Whereas laboratory experiments with single species revealed strong effects of DON, algal responses to DON in a multi-species situation remain unclear. Experiments with phytoplankton communities from Lake Müggelsee revealed that the nitrogen pool composition does influence the phytoplankton community structure. The findings furthermore show that several species combined might utilize the supplied nitrogen completely different than monocultures in the laboratory. Thus, besides the actual ability of algae to use the offered nitrogen sources other factors, such as interspecific competition, may be of importance. I further investigated, if the results of the laboratory experiments, can be verified in the field. Here, I surveyed the seasonal development of several dissolved organic matter (DOM) components (urea, high molecular weight substances (HMWS), humic substances (HS)) and associated parameters (Specific UV-absorption (SUVA), C:N - ratio) in Lake Müggelsee between 2011 and 2013. Furthermore, data from the long term measurements series of Lake Müggelsee such as physical (temperature, light, pH, O2) and chemical parameters (nitrogen, phosphorous, silica, inorganic carbon), zooplankton and phytoplankton data were used to investigate how much of the variability of the phytoplankton composition in Lake Müggelsee can be explained by DON/DOM concentration and composition, relative to the other groups of explanatory variables. The results show that DON mainly consists of rather complex compounds such as humic substances and biopolymers (80 %) and that only slight seasonal trends are detectable. Using variance partitioning I could show, that the usually investigated nutrients (DIN, silica, inorganic carbon, phosphorous) and abiotic factors together explain most of the algae composition as was to be expected (57.1 % of modeled variance). However, DOM and the associated parameters uniquely explain 10.3 % of the variance and thus slightly more than zooplankton with 9.3 %. I could therefore prove, that the composition of DOM (nitrogen and carbon) is connected to the algae composition in an eutrophic lake such as Lake Müggelsee. DON - compounds such as urea, however, could not be correlated with the occurrence of specific phytoplankton species. Overall, the results of this study imply that DON can be a valuable nitrogen source for freshwater phytoplankton. DON is used by various species even when DIN is available in low concentrations. Through the reduction of DIN in lakes and rivers, the DON:DIN ratio might be changed, resulting even in an increased importance of DON as phytoplankton nitrogen source. My work suggests that not only N2-fixation but also DON utilization might compensate for reduced N - input. Changes from DIN to DON as main nitrogen source might also promote certain, potentially undesired algae species and influence the biodiversity of a limnic ecosystem through changes in the phytoplankton community structure. Thus, DON, especially urea, should be included in calculations concerning total available nitrogen and when determining nitrogen threshold values. Furthermore, the input-reduction of DON, for example from waste-water treatment plants should also be evaluated and the results of my thesis should find consideration when planning to reduce the nitrogen input in freshwater.