@phdthesis{Massie2011,
  author    = {Massie, Thomas Michael},
  title     = {Dynamic behavior of phytoplankton populations far from steady state : chemostat experiments and mathematical modeling},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-58102},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Nature changes continuously and is only seemingly at equilibrium. Environmental parameters like temperature, humidity or insolation may strongly fluctuate on scales ranging from seconds to millions of years. Being part of an ecosystem, species have to cope with these environmental changes. For ecologists, it is of special interest how individual responses to environmental changes affect the dynamics of an entire population - and, if this behavior is predictable. In this context, the demographic structure of a population plays a decisive role since it originates from processes of growth and mortality. These processes are fundamentally influenced by the environment. But, how exactly does the environment influence the behavior of populations? And what does the transient behavior look like? As a result from environmental influences on demography, so called cohorts form. They are age or size classes that are disproportionally represented in the demographic distribution of a population. For instance, if most old and young individuals die due to a cold spell, the population finally consists of mainly middle-aged individuals. Hence, the population got synchronized. Such a population tends to show regular fluctuations in numbers (denoted as oscillations) since the alternating phases of individual growth and population growth (due to reproduction) are now performed synchronously by the majority of the population.That is, one time the population growths, and the other time it declines due to mortality. Synchronous behavior is one of the most pervasive phenomena in nature. Gravitational synchrony in the solar system; fireflies flashing in unison; coordinate firing of pacemaker cells in the heart; electrons in a superconductor marching in lockstep. Whatever scale one looks at, in animate as well as inanimate systems, one is likely to encounter synchrony. In experiments with phytoplankton populations, I could show that this principle of synchrony (as used by physicists) could well-explain the oscillations observed in the experiments, too. The size of the fluctuations depended on the strength by which environmental parameters changed as well as on the demographic state of a population prior to this change. That is, two population living in different habitats can be equally influenced by an environmental change, however, the resulting population dynamics may be significantly different when both populations differed in their demographic state before. Moreover, specific mechanisms relevant for the dynamic behavior of populations, appear only when the environmental conditions change. In my experiments, the population density declined by 50\% after ressource supply was doubled. This counter-intuitive behavior can be explained by increasing ressource consumption. The phytoplankton cells grew larger and enhanced their individual constitution. But at the same time, reproduction was delayed and the population density declined due to the losses by mortality. Environmental influences can also synchronize two or more populations over large distances, which is denoted as Moran effect. Assume two populations living on two distant islands. Although there is no exchange of individuals between them, both populations show a high similarity when comparing their time series. This is because the globally acting climate synchronizes the regionally acting weather on both island. Since the weather fluctuations influence the population dynamics, the Moran effect states that the synchrony between the environment equals the one between the populations. My experiments support this theory and also explain deviations arising when accounting for differences in the populations and the habitats they are living in. Moreover, model simulations and experiments astonishingly show that the synchrony between the populations can be higher than between the environment, when accounting for differences in the environmental fluctuations ("noise color").},
  language  = {de}
}
@phdthesis{AndradeLinares2011,
  author    = {Andrade Linares, Diana Roc{\´i}o},
  title     = {Characterization of tomato root-endophytic fungi and analysis of their effects on plant development, on fruit yield and quality and on interaction with the pathogen Verticillium dahliae},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51375},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Non-mycorrhizal fungal endophytes are able to colonize internally roots without causing visible disease symptoms establishing neutral or mutualistic associations with plants. These fungi known as non-clavicipitaceous endophytes have a broad host range of monocot and eudicot plants and are highly diverse. Some of them promote plant growth and confer increased abiotic-stress tolerance and disease resistance. According to such possible effects on host plants, it was aimed to isolate and to characterize native fungal root endophytes from tomato (Lycopersicon esculentum Mill.) and to analyze their effects on plant development, plant resistance and fruit yield and quality together with the model endophyte Piriformospora indica. Fifty one new fungal strains were isolated from desinfected tomato roots of four different crop sites in Colombia. These isolates were roughly characterized and fourteen potential endophytes were further analyzed concerning their taxonomy, their root colonization capacity and their impact on plant growth. Sequencing of the ITS region from the ribosomal RNA gene cluster and in-depth morphological characterisation revealed that they correspond to different phylogenetic groups among the phylum Ascomycota. Nine different morphotypes were described including six dark septate endophytes (DSE) that did not correspond to the Phialocephala group. Detailed confocal microscopy analysis showed various colonization patterns of the endophytes inside the roots ranging from epidermal penetration to hyphal growth through the cortex. Tomato pot experiments under glass house conditions showed that they differentially affect plant growth depending on colonization time and inoculum concentration. Three new isolates (two unknown fungal endophyte DSE48, DSE49 and one identified as Leptodontidium orchidicola) with neutral or positiv effects were selected and tested in several experiments for their influence on vegetative growth, fruit yield and quality and their ability to diminish the impact of the pathogen Verticillium dahliae on tomato plants. Although plant growth promotion by all three fungi was observed in young plants, vegetative growth parameters were not affected after 22 weeks of cultivation except a reproducible increase of root diameter by the endophyte DSE49. Additionally, L. orchidicola increased biomass and glucose content of tomato fruits, but only at an early date of harvest and at a certain level of root colonization. Concerning bioprotective effects, the endophytes DSE49 and L. orchidicola decreased significantly disease symptoms caused by the pathogen V. dahliae, but only at a low dosis of the pathogen. In order to analyze, if the model root endophytic fungus Piriformospora indica could be suitable for application in production systems, its impact on tomato was evaluated. Similarly to the new fungal isolates, significant differences for vegetative growth parameters were only observable in young plants and, but protection against V. dahliae could be seen in one experiment also at high dosage of the pathogen. As the DSE L. orchidicola, P. indica increased the number and biomass of marketable tomatoes only at the beginning of fruit setting, but this did not lead to a significant higher total yield. If the effects on growth are due to a better nutrition of the plant with mineral element was analyzed in barley in comparison to the arbuscular mycorrhizal fungus Glomus mosseae. While the mycorrhizal fungus increased nitrogen and phosphate uptake of the plant, no such effect was observed for P. indica. In summary this work shows that many different fungal endophytes can be also isolated from roots of crops and, that these isolates can have positive effects on early plant development. This does, however, not lead to an increase in total yield or in improvement of fruit quality of tomatoes under greenhouse conditions.},
  language  = {en}
}
@phdthesis{Kittner2011,
  author    = {Kittner, Madeleine},
  title     = {Folding and aggregation of amyloid peptides},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53570},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Aggregation of the Amyloid β (Aβ) peptide to amyloid fibrils is associated with the outbreak of Alzheimer's disease. Early aggregation intermediates in form of soluble oligomers are of special interest as they are believed to be the major toxic components in the process. These oligomers are of disordered and transient nature. Therefore, their detailed molecular structure is difficult to access experimentally and often remains unknown. In the present work extensive, fully atomistic replica exchange molecular dynamics simulations were performed to study the preaggregated, monomer states and early aggregation intermediates (dimers, trimers) of Aβ(25-35) and Aβ(10-35)-NH2 in aqueous solution. The folding and aggregation of Aβ(25-35) were studied at neutral pH and 293 K. Aβ(25-35) monomers mainly adopt β-hairpin conformations characterized by a β-turn formed by residues G29 and A30, and a β-sheet between residues N27-K28 and I31-I32 in equilibrium with coiled conformations. The β-hairpin conformations served as initial configurations to model spontaneous aggregation of Aβ(25-35). As expected, within the Aβ(25-35) dimer and trimer ensembles many different poorly populated conformations appear. Nevertheless, we were able to distinguish between disordered and fibril-like oligomers. Whereas disordered oligomers are rather compact with few intermolecular hydrogen bonds (HBs), fibril-like oligomers are characterized by the formation of large intermolecular β-sheets. In most of the fibril-like dimers and trimers individual peptides are fully extended forming in- or out-of-register antiparallel β-sheets. A small amount of fibril-like trimers contained V-shaped peptides forming parallel β-sheets. The dimensions of extended and V-shaped oligomers correspond well to the diameters of two distinct morphologies found for Aβ(25-35) fibrils. The transition from disordered to fibril-like Aβ(25-35) dimers is unfavorable but driven by energy. The lower energy of fibril-like dimers arises from favorable intermolecular HBs and other electrostatic interactions which compete with a loss in entropy. Approximately 25 \% of the entropic cost correspond to configurational entropy. The rest relates to solvent entropy, presumably caused by hydrophobic and electrostatic effects. In contrast to the transition towards fibril-like dimers the first step of aggregation is driven by entropy. Here, we compared structural and thermodynamic properties of the individual monomer, dimer and trimer ensembles to gain qualitative information about the aggregation process. The β-hairpin conformation observed for monomers is successively dissolved in dimer and trimer ensembles while instead intermolecular β-sheets are formed. As expected upon aggregation the configurational entropy decreases. Additionally, the solvent accessible surface area (SASA), especially the hydrophobic SASA, decreases yielding a favorable solvation free energy which overcompensates the loss in configurational entropy. In summary, the hydrophobic effect, possibly combined with electrostatic effects, yields an increase in solvent entropy which is believed to be one major driving force towards aggregation. Spontaneous folding of the Aβ(10-35)-NH2 monomer was modeled using two force fields, GROMOS96 43a1 and OPLS/AA, and compared to primary NMR data collected at pH 5.6 and 283 K taken from the literature. Unexpectedly, the two force fields yielded significantly different main conformations. Comparison between experimental and calculated nuclear Overhauser effect (NOE) distances is not sufficient to distinguish between the different force fields. Additionally, the comparison with scalar coupling constants suggest that the chosen protonation in both simulations corresponds to a pH lower than in the experiment. Based on this analysis we were unable to determine which force field yields a better description of this system. Dimerization of Aβ(10-35)-NH2 was studied at neutral pH and 300 K. Dimer conformations arrange in many distinct, poorly populated and rather complex alignments or interlocking patterns which are rather stabilized by side chain interactions than by specific intermolecular hydrogen bonds. Similar to Aβ(25-35) dimers, transition towards β-sheet-rich, fibril-like Aβ(10-35) dimers is driven by energy competing with a loss in entropy. Here, transition is mediated by favorable peptide-solvent and solvent-solvent interactions mainly arising from electrostatic interactions.},
  language  = {en}
}