@phdthesis{Kopka2008,
  author    = {Kopka, Joachim},
  title     = {Applied metabolome analysis : exploration, development and application of gas chromatography-mass spectrometry based metabolite profiling technologies},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40597},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {The uptake of nutrients and their subsequent chemical conversion by reactions which provide energy and building blocks for growth and propagation is a fundamental property of life. This property is termed metabolism. In the course of evolution life has been dependent on chemical reactions which generate molecules that are common and indispensable to all life forms. These molecules are the so-called primary metabolites. In addition, life has evolved highly diverse biochemical reactions. These reactions allow organisms to produce unique molecules, the so-called secondary metabolites, which provide a competitive advantage for survival. The sum of all metabolites produced by the complex network of reactions within an organism has since 1998 been called the metabolome. The size of the metabolome can only be estimated and may range from less than 1,000 metabolites in unicellular organisms to approximately 200,000 in the whole plant kingdom. In current biology, three additional types of molecules are thought to be important to the understanding of the phenomena of life: (1) the proteins, in other words the proteome, including enzymes which perform the metabolic reactions, (2) the ribonucleic acids (RNAs) which constitute the so-called transcriptome, and (3) all genes of the genome which are encoded within the double strands of desoxyribonucleic acid (DNA). Investigations of each of these molecular levels of life require analytical technologies which should best enable the comprehensive analysis of all proteins, RNAs, et cetera. At the beginning of this thesis such analytical technologies were available for DNA, RNA and proteins, but not for metabolites. Therefore, this thesis was dedicated to the implementation of the gas chromatography - mass spectrometry technology, in short GC-MS, for the in-parallel analysis of as many metabolites as possible. Today GC-MS is one of the most widely applied technologies and indispensable for the efficient profiling of primary metabolites. The main achievements and research topics of this work can be divided into technological advances and novel insights into the metabolic mechanisms which allow plants to cope with environmental stresses. Firstly, the GC-MS profiling technology has been highly automated and standardized. The major technological achievements were (1) substantial contributions to the development of automated and, within the limits of GC-MS, comprehensive chemical analysis, (2) contributions to the implementation of time of flight mass spectrometry for GC-MS based metabolite profiling, (3) the creation of a software platform for reproducible GC-MS data processing, named TagFinder, and (4) the establishment of an internationally coordinated library of mass spectra which allows the identification of metabolites in diverse and complex biological samples. In addition, the Golm Metabolome Database (GMD) has been initiated to harbor this library and to cope with the increasing amount of generated profiling data. This database makes publicly available all chemical information essential for GC-MS profiling and has been extended to a global resource of GC-MS based metabolite profiles. Querying the concentration changes of hundreds of known and yet non-identified metabolites has recently been enabled by uploading standardized, TagFinder-processed data. Long-term technological aims have been pursued with the central aims (1) to enhance the precision of absolute and relative quantification and (2) to enable the combined analysis of metabolite concentrations and metabolic flux. In contrast to concentrations which provide information on metabolite amounts, flux analysis provides information on the speed of biochemical reactions or reaction sequences, for example on the rate of CO2 conversion into metabolites. This conversion is an essential function of plants which is the basis of life on earth. Secondly, GC-MS based metabolite profiling technology has been continuously applied to advance plant stress physiology. These efforts have yielded a detailed description of and new functional insights into metabolic changes in response to high and low temperatures as well as common and divergent responses to salt stress among higher plants, such as Arabidopsis thaliana, Lotus japonicus and rice (Oryza sativa). Time course analysis after temperature stress and investigations into salt dosage responses indicated that metabolism changed in a gradual manner rather than by stepwise transitions between fixed states. In agreement with these observations, metabolite profiles of the model plant Lotus japonicus, when exposed to increased soil salinity, were demonstrated to have a highly predictive power for both NaCl accumulation and plant biomass. Thus, it may be possible to use GC-MS based metabolite profiling as a breeding tool to support the selection of individual plants that cope best with salt stress or other environmental challenges.},
  language  = {en}
}
@phdthesis{Knebe2008,
  author    = {Knebe, Alexander},
  title     = {Computational cosmology},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41147},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {"Computational Cosmology" is the modeling of structure formation in the Universe by means of numerical simulations. These simulations can be considered as the only "experiment" to verify theories of the origin and evolution of the Universe. Over the last 30 years great progress has been made in the development of computer codes that model the evolution of dark matter (as well as gas physics) on cosmic scales and new research discipline has established itself. After a brief summary of cosmology we will introduce the concepts behind such simulations. We further present a novel computer code for numerical simulations of cosmic structure formation that utilizes adaptive grids to efficiently distribute the work and focus the computing power to regions of interests, respectively. In that regards we also investigate various (numerical) effects that influence the credibility of these simulations and elaborate on the procedure of how to setup their initial conditions. And as running a simulation is only the first step to modelling cosmological structure formation we additionally developed an object finder that maps the density field onto galaxies and galaxy clusters and hence provides the link to observations. Despite the generally accepted success of the cold dark matter cosmology the model still inhibits a number of deviations from observations. Moreover, none of the putative dark matter particle candidates have yet been detected. Utilizing both the novel simulation code and the halo finder we perform and analyse various simulations of cosmic structure formation investigating alternative cosmologies. These include warm (rather than cold) dark matter, features in the power spectrum of the primordial density perturbations caused by non-standard inflation theories, and even modified Newtonian dynamics. We compare these alternatives to the currently accepted standard model and highlight the limitations on both sides; while those alternatives may cure some of the woes of the standard model they also inhibit difficulties on their own. During the past decade simulation codes and computer hardware have advanced to such a stage where it became possible to resolve in detail the sub-halo populations of dark matter halos in a cosmological context. These results, coupled with the simultaneous increase in observational data have opened up a whole new window on the concordance cosmogony in the field that is now known as "Near-Field Cosmology". We will present an in-depth study of the dynamics of subhaloes and the development of debris of tidally disrupted satellite galaxies.1 Here we postulate a new population of subhaloes that once passed close to the centre of their host and now reside in the outer regions of it. We further show that interactions between satellites inside the radius of their hosts may not be negliable. And the recovery of host properties from the distribution and properties of tidally induced debris material is not as straightforward as expected from simulations of individual satellites in (semi-)analytical host potentials.},
  language  = {en}
}