@phdthesis{Wenk2020,
  author    = {Wenk, Sebastian},
  title     = {Engineering formatotrophic growth in Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {V, 107},
  year      = {2020},
  abstract  = {To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli - which cannot naturally grow on formate - via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli.   In the third chapter, I present the establishment of the serine threonine cycle (STC) - a synthetic formate assimilation pathway - in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) - a short, linear formate assimilation route - in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source.},
  language  = {en}
}
@phdthesis{Schimpf2020,
  author    = {Schimpf, Stefan},
  title     = {Herkunft und Ablagerungsmilieu quart{\"a}rer Sedimente im Einzugsgebiet des Heihe, NW China},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 186},
  year      = {2020},
  abstract  = {Der zentralasiatische Naturraum, wie er sich uns heute pr{\"a}sentiert, ist das Ergebnis eines Zusammenwirkens vieler verschiedener Faktoren {\"u}ber Jahrmillionen hinweg. Im aktuellen Kontext des Klimawandels zeigt sich jedoch, wie stark sich Stofffl{\"u}sse auch kurzfristig {\"a}ndern und dabei das Gesicht der Landschaft verwandeln k{\"o}nnen. Die Gobi-W{\"u}ste in der Inneren Mongolei (China), als Teil der gleichnamigen Trockenregionen Nordwestchinas, ist aufgrund der Ausgestaltung ihrer landschaftspr{\"a}genden Elemente sowie ihrer Landschaftsdynamik, im Zusammenhang mit der Lage zum Tibet-Plateau, in den Fokus der klimageschichtlichen Grundlagenforschung ger{\"u}ckt. Als großes Langzeitarchiv unterschiedlichster fluvialer, lakustriner und {\"a}olischer Sedimente stellt sie eine bedeutende Lokalit{\"a}t zur Rekonstruktion von lokalen und regionalen Stofffl{\"u}ssen dar.. Andererseits ist die Gobi-W{\"u}ste zugleich auch eine bedeutende Quelle f{\"u}r den {\"u}berregionalen Staubtransport, da sie aufgrund der klimatischen Bedingungen insbesondere der Erosion durch Ausblasung preisgegeben wird. Vor diesem Hintergrund erfolgten zwischen 2011 und 2014, im Rahmen des BMBF-Verbundprogramms WTZ Zentralasien - Monsundynamik \& Geo{\"o}kosysteme (F{\"o}rderkennzeichen 03G0814), mehrere deutsch-chinesische Expeditionen in das Ejina-Becken (Innere Mongolei) und das Qilian Shan-Vorland. Im Zuge dieser Expeditionen wurden f{\"u}r eine Bestimmung potenzieller Sedimentquellen erstmals zahlreiche Oberfl{\"a}chenproben aus dem gesamten Einzugsgebiet des Heihe (schwarzer Fluss) gesammelt. Zudem wurden mit zwei Bohrungen im inneren des Ejina-Beckens, erg{\"a}nzende Sedimentbohrkerne zum bestehenden Bohrkern D100 (siehe W{\"u}nnemann (2005)) abgeteuft, um weit reichende, erg{\"a}nzende Informationen zur Landschaftsgeschichte und zum {\"u}berregionalen Sedimenttransfer zu erhalten. Gegenstand und Ziel der vorliegenden Doktorarbeit ist die sedimentologisch-mineralogische Charakterisierung des Untersuchungsgebietes in Bezug auf potenzielle Sedimentquellen und Stofffl{\"u}sse des Ejina-Beckens sowie die Rekonstruktion der Ablagerungsgeschichte eines dort erbohrten, 19m langen Sedimentbohrkerns (GN100). Schwerpunkt ist hierbei die Kl{\"a}rung der Sedimentherkunft innerhalb des Bohrkerns sowie die Ausweisung von Herkunftssignalen und m{\"o}glichen Sedimentquellen bzw. Sedimenttransportpfaden. Die methodische Herangehensweise basiert auf einem Multi-Proxy-Ansatz zur Charakterisierung der klastischen Sedimentfazies anhand von Gel{\"a}ndebeobachtungen, lithologisch-granulometrischen und mineralogisch-geochemischen Analysen sowie statistischen Verfahren. F{\"u}r die mineralogischen Untersuchungen der Sedimente wurde eine neue, rasterelektronenmikroskopische Methode zur automatisierten Partikelanalyse genutzt und den traditionellen Methoden gegen{\"u}bergestellt. Die synoptische Betrachtung der granulometrischen, geochemischen und mineralogischen Befunde der Oberfl{\"a}chensedimente ergibt f{\"u}r das Untersuchungsgebiet ein logisches Kaskadenmodell mit immer wiederkehrenden Prozessbereichen und {\"a}hnlichen Prozesssignalen. Die umfangreichen granulometrischen Analysen deuten dabei auf abnehmende Korngr{\"o}ßen mit zunehmender Entfernung vom Qilian Shan hin und erm{\"o}glichen die Identifizierung von vier texturellen Signalen: den fluvialen Sanden, den D{\"u}nensanden, den Stillwassersedimenten und St{\"a}uben. Diese Ergebnisse k{\"o}nnen als Interpretationsgrundlage f{\"u}r die Korngr{\"o}ßenanalysen des Bohrkerns genutzt werden. Somit ist es m{\"o}glich, die Ablagerungsgeschichte der Bohrkernsedimente zu rekonstruieren und in Verbindung mit eigenen und literaturbasierten Datierungen in einen Gesamtkontext einzuh{\"a}ngen. F{\"u}r das Untersuchungsgebiet werden somit vier Ablagerungsphasen ausgewiesen, die bis in die Zeit des letzten glazialen Maximums (LGM) zur{\"u}ckreichen. W{\"a}hrend dieser Ablagerungsphasen kam es im Zuge unterschiedlicher Aktivit{\"a}ts- und Stabilit{\"a}tsphasen zu einer kontinuierlichen Progradation und {\"U}berpr{\"a}gung des Schwemmf{\"a}chers. Eine besonders aktive Phase kann zwischen 8 ka und 4 ka BP festgestellt werden, w{\"a}hrend der es aufgrund zunehmender fluvialer Aktivit{\"a}ten zu einer deutlich verst{\"a}rkten Schwemmf{\"a}cherdynamik gekommen zu sein scheint. In den Abschnitten davor und danach waren es vor allem {\"a}olische Prozesse, die zu einer {\"U}berpr{\"a}gung des Schwemmf{\"a}chers gef{\"u}hrt haben. Hinsichtlich der mineralogischen Herkunftssignale gibt es eine große Variabilit{\"a}t. Dies spiegelt die enorme Heterogenit{\"a}t der Geologie des Untersuchungsgebietes wider, wodurch die r{\"a}umlichen Signale nicht sehr stark ausgepr{\"a}gt sind. Dennoch, k{\"o}nnen f{\"u}r das Einzugsgebiet drei gr{\"o}ßere Bereiche deklariert werden, die als Herkunftsgebiet in Frage kommen. Das {\"o}stliche Qilian Shan Vorland zeichnet sich dabei durch deutlich h{\"o}here Chloritgehalte als prim{\"a}re Quelle f{\"u}r die Sedimente im Ejina-Becken aus. Sie unterscheiden sich insbesondere durch stark divergierende Chloritgehalte in der Tonmineral- und Gesamtmineralfraktion, was das {\"o}stliche Qilian Shan Vorland als prim{\"a}re Quelle f{\"u}r die Sedimente im Ejina-Becken auszeichnet. Dies steht in Zusammenhang mit den Gr{\"u}nschiefern, Ophioliten und Serpentiniten in diesem Bereich. Geochemisch deutet vor allem das Cr/Rb-Verh{\"a}ltnis eine große Variabilit{\"a}t innerhalb des Einzugsgebietes an. Auch hier ist es das {\"o}stliche Vorland, welches aufgrund seines hohen Anteils an mafischen Gesteinen reich an Chromiten und Spinellen ist und sich somit vom restlichen Untersuchungsgebiet abhebt. Die zeitliche aber auch die generelle Variabilit{\"a}t der Sedimentherkunft l{\"a}sst sich in den Bohrkernsedimenten nicht so deutlich nachzeichnen. Die mineralogisch-sedimentologischen Eigenschaften der erbohrten klastischen Sedimente zeugen zwar von zwischenzeitlichen {\"A}nderungen bei der Sedimentherkunft, diese sind jedoch nicht so deutlich ausgepr{\"a}gt, wie es die Quellsignale in den Oberfl{\"a}chensedimenten vermuten lassen. Ein Grund daf{\"u}r scheint die starke Vermischung unterschiedlichster Sedimente w{\"a}hrend des Transportes zu sein. Die Kombination der Korngr{\"o}ßenergebnisse mit den Befunden der Gesamt- und Schwermineralogie deuten darauf hin, dass es zwischenzeitlich eine Phase mit {\"u}berwiegend {\"a}olischen Prozessen gegeben hat, die mit einem Sedimenteintrag aus dem westlichen Bei Shan in Verbindung stehen. Neben der Zunahme ultrastabiler Schwerminerale wie Zirkon und Granat und der Abnahme opaker Schwerminerale, weisen vor allem die heutigen Verh{\"a}ltnisse darauf hin. Der Vergleich der traditionellen Schwermineralanalyse mit der Computer-Controlled-Scanning-Electron-Microscopy (kurz: CCSEM), die eine automatisierte Partikelauswertung der Proben erm{\"o}glicht, zeigt den deutlichen Vorteil der modernen Analysemethode. Neben einem zeitlichen Vorteil, den man durch die automatisierte Abarbeitung der vorbereiteten Proben erlangen kann, steht vor allem die deutlich gr{\"o}ßere statistische Signifikanz des Ergebnisses im Vordergrund. Zudem k{\"o}nnen mit dieser Methode auch chemische Variet{\"a}ten einiger Schwerminerale bestimmt werden, die eine noch feinere Klassifizierung und sicherere Aussagen zu einer m{\"o}glichen Sedimentherkunft erm{\"o}glichen. Damit ergeben sich außerdem verbesserte Aussagen zu Zusammensetzungen und Entstehungsprozessen der abgelagerten Sedimente. Die Studie verdeutlicht, dass die Sedimentherkunft innerhalb des Untersuchungsgebietes sowie die ablaufenden Prozesse zum Teil stark von lokalen Gegebenheiten abh{\"a}ngen. Die Heterogenit{\"a}t der Geologie und die Gr{\"o}ße des Einzugsgebietes sowie die daraus resultierende Komplexit{\"a}t der Sedimentgenese, machen exakte Zuordnungen zu klar definierten Sedimentquellen sehr schwer. Dennoch zeigen die Ergebnisse, dass die Sedimentzufuhr in das Ejina-Becken in erster Linie durch fluviale klastische Sedimente des Heihe aus dem Qilian Shan erfolgt sein muss. Die Untersuchungsergebnisse zeigen jedoch ebenso die Notwendigkeit einer erg{\"a}nzenden Bearbeitung angrenzender Untersuchungsgebiete, wie beispielsweise den Gobi-Altai im Norden oder den Beishan im Westen, sowie die Verdichtung der Oberfl{\"a}chenbeprobung zur feineren Aufl{\"o}sung von lokalen Sedimentquellen.},
  language  = {de}
}
@phdthesis{Mueller2008,
  author    = {M{\"u}ller, Melanie J. I.},
  title     = {Bidirectional transport by molecular motors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18715},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.},
  language  = {en}
}
@phdthesis{Lenz2016,
  author    = {Lenz, Josefine},
  title     = {Thermokarst dynamics in central-eastern Beringia},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-101364},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XII, 128, A-47},
  year      = {2016},
  abstract  = {Widespread landscape changes are presently observed in the Arctic and are most likely to accelerate in the future, in particular in permafrost regions which are sensitive to climate warming. To assess current and future developments, it is crucial to understand past environmental dynamics in these landscapes. Causes and interactions of environmental variability can hardly be resolved by instrumental records covering modern time scales. However, long-term environmental variability is recorded in paleoenvironmental archives. Lake sediments are important archives that allow reconstruction of local limnogeological processes as well as past environmental changes driven directly or indirectly by climate dynamics. This study aims at reconstructing Late Quaternary permafrost and thermokarst dynamics in central-eastern Beringia, the terrestrial land mass connecting Eurasia and North America during glacial sea-level low stands. In order to investigate development, processes and influence of thermokarst dynamics, several sediment cores from extant lakes and drained lake basins were analyzed to answer the following research questions: 1. When did permafrost degradation and thermokarst lake development take place and what were enhancing and inhibiting environmental factors? 2. What are the dominant processes during thermokarst lake development and how are they reflected in proxy records? 3. How did, and still do, thermokarst dynamics contribute to the inventory and properties of organic matter in sediments and the carbon cycle? Methods applied in this study are based upon a multi-proxy approach combining sedimentological, geochemical, geochronological, and micropaleontological analyses, as well as analyses of stable isotopes and hydrochemistry of pore-water and ice. Modern field observations of water quality and basin morphometrics complete the environmental investigations. The investigated sediment cores reveal permafrost degradation and thermokarst dynamics on different time scales. The analysis of a sediment core from GG basin on the northern Seward Peninsula (Alaska) shows prevalent terrestrial accumulation of yedoma throughout the Early to Mid Wisconsin with intermediate wet conditions at around 44.5 to 41.5 ka BP. This first wetland development was terminated by the accumulation of a 1-meter-thick airfall tephra most likely originating from the South Killeak Maar eruption at 42 ka BP. A depositional hiatus between 22.5 and 0.23 ka BP may indicate thermokarst lake formation in the surrounding of the site which forms a yedoma upland till today. The thermokarst lake forming GG basin initiated 230 ± 30 cal a BP and drained in Spring 2005 AD. Four years after drainage the lake talik was still unfrozen below 268 cm depth. A permafrost core from Mama Rhonda basin on the northern Seward Peninsula preserved a full lacustrine record including several lake phases. The first lake generation developed at 11.8 cal ka BP during the Lateglacial-Early Holocene transition; its old basin (Grandma Rhonda) is still partially preserved at the southern margin of the study basin. Around 9.0 cal ka BP a shallow and more dynamic thermokarst lake developed with actively eroding shorelines and potentially intermediate shallow water or wetland phases (Mama Rhonda). Mama Rhonda lake drainage at 1.1 cal ka BP was followed by gradual accumulation of terrestrial peat and top-down refreezing of the lake talik. A significant lower organic carbon content was measured in Grandma Rhonda deposits (mean TOC of 2.5 wt\%) than in Mama Rhonda deposits (mean TOC of 7.9 wt\%) highlighting the impact of thermokarst dynamics on biogeochemical cycling in different lake generations by thawing and mobilization of organic carbon into the lake system. Proximal and distal sediment cores from Peatball Lake on the Arctic Coastal Plain of Alaska revealed young thermokarst dynamics since about 1,400 years along a depositional gradient based on reconstructions from shoreline expansion rates and absolute dating results. After its initiation as a remnant pond of a previous drained lake basin, a rapidly deepening lake with increasing oxygenation of the water column is evident from laminated sediments, and higher Fe/Ti and Fe/S ratios in the sediment. The sediment record archived characterizing shifts in depositional regimes and sediment sources from upland deposits and re-deposited sediments from drained thaw lake basins depending on the gradually changing shoreline configuration. These changes are evident from alternating organic inputs into the lake system which highlights the potential for thermokarst lakes to recycle old carbon from degrading permafrost deposits of its catchment. The lake sediment record from Herschel Island in the Yukon (Canada) covers the full Holocene period. After its initiation as a thermokarst lake at 11.7 cal ka BP and intense thermokarst activity until 10.0 cal ka BP, the steady sedimentation was interrupted by a depositional hiatus at 1.6 cal ka BP which likely resulted from lake drainage or allochthonous slumping due to collapsing shore lines. The specific setting of the lake on a push moraine composed of marine deposits is reflected in the sedimentary record. Freshening of the maturing lake is indicated by decreasing electrical conductivity in pore-water. Alternation of marine to freshwater ostracods and foraminifera confirms decreasing salinity as well but also reflects episodical re-deposition of allochthonous marine sediments. Based on permafrost and lacustrine sediment records, this thesis shows examples of the Late Quaternary evolution of typical Arctic permafrost landscapes in central-eastern Beringia and the complex interaction of local disturbance processes, regional environmental dynamics and global climate patterns. This study confirms that thermokarst lakes are important agents of organic matter recycling in complex and continuously changing landscapes.},
  language  = {en}
}
@phdthesis{Frenzel2015,
  author    = {Frenzel, Sabine},
  title     = {Die Rolle der Umamirezeptoruntereinheit Tas1r1 jenseits ihrer gustatorischen Bedeutung},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-79502},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XV, 172},
  year      = {2015},
  abstract  = {Aminos{\"a}uren sind lebensnotwendige Molek{\"u}le f{\"u}r alle Organismen. Ihre Erkennung im K{\"o}rper erm{\"o}glicht eine bedarfsgerechte Regulation ihrer Aufnahme und ihrer Verwertung. Welcher Chemosensor f{\"u}r diese Erkennung jedoch hauptverantwortlich ist, ist bisher unklar. In der vorliegenden Arbeit wurde die Rolle der Umamigeschmacksrezeptoruntereinheit Tas1r1 jenseits ihrer gustatorischen Bedeutung f{\"u}r die Aminos{\"a}uredetektion in der Mundh{\"o}hle untersucht. In der histologischen Tas1r1-Expressionsanalyse nichtgustatorischer Gewebe der Mauslinie Tas1r1-Cre/ROSA26-tdRFP wurde {\"u}ber die Detektion des Reporterproteins tdRFP die Expression des Tas1r1 in allen untersuchten Geweben (Speiser{\"o}hre, Magen, Darm, Bauchspeicheldr{\"u}se, Leber, Niere, Muskel- und Fettgewebe, Milz, Thymus, Lymphknoten, Lunge sowie Hoden) nachgewiesen. Mit Ausnahme von D{\"u}nndarm und Hoden gelang hierbei der Nachweis erstmals spezifisch auf zellul{\"a}rer Ebene. Caecum und Lymphknoten wurden zudem neu als Expressionsorte des Tas1r1 identifiziert. Trotz der beobachteten weiten Verbreitung des Tas1r1 im Organismus - unter anderem auch in Geweben, die f{\"u}r den Proteinstoffwechsel besonders relevant sind - waren im Zuge der durchgef{\"u}hrten Untersuchung potentieller extraoraler Funktionen des Rezeptors durch ph{\"a}notypische Charakterisierung der Mauslinie Tas1r1-BLiR nur schwache Auswirkungen auf Aminos{\"a}urestoffwechsel bzw. Stickstoffhaushalt im Falle eines Tas1r1-Knockouts detektierbar. W{\"a}hrend sich Ern{\"a}hrungsverhalten, Gesamtphysiologie, Gewebemorphologie sowie Futterverdaulichkeit unver{\"a}ndert zeigten, war die renale Stickstoffausscheidung bei Tas1r1-Knockout-M{\"a}usen auf eiweißarmer sowie auf eiweißreicher Di{\"a}t signifikant verringert. Eine {\"U}berdeckung der Auswirkungen des Tas1r1-Knockouts aufgrund kompensatorischer Effekte durch den Aminos{\"a}uresensor CaSR oder den Peptidsensor Gpr93 war nicht nachweisbar. Es bleibt offen, ob andere Mechanismen oder andere Chemosensoren an einer Kompensation beteiligt sind oder aber Tas1r1 in extraoralem Gewebe andere Funktionen als die der Aminos{\"a}uredetektion {\"u}bernimmt. Unterschiede im extraoralen Expressionsmuster der beiden Umamirezeptor-untereinheiten Tas1r1 und Tasr3 lassen Spekulationen {\"u}ber andere Partner, Liganden und Funktionen zu.},
  language  = {de}
}
@phdthesis{Kempa2004,
  author    = {Kempa, Stefan},
  title     = {Analysen zur Stressantwort von Arabidopsis thaliana unter Schwefelmangelbedingungen : Studien zur Funktion der Dehydroascorbatreduktase in vivo},
  address   = {Potsdam},
  pages     = {123 S. : graph. Darst.},
  year      = {2004},
  language  = {de}
}
@phdthesis{Meinke2006,
  author    = {Meinke, Anja},
  title     = {Nikotineffekte auf r{\"a}umliche Aufmerksamkeitsprozesse bei Nichtrauchern},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7659},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {Nikotin in den unterschiedlichsten Darreichungsformen verringert bei verschiedenen Spezies im r{\"a}umlichen Hinweisreizparadigma die Kosten invalider Hinweisreize. Welcher Teilprozess genau durch Nikotin beeinflusst wird, ist bislang nicht untersucht worden. Die g{\"a}ngige Interpretation ist, daß Nikotin das Losl{\"o}sen von Aufmerksamkeit von einem bisher beachteten Ort erleichtert. In f{\"u}nf Studien, drei elektrophysiologischen und zwei behavioralen wurden drei m{\"o}gliche Mechanismen der Nikotinwirkung an Nichtrauchern untersucht. Experiment 1 und 2 gingen der Frage nach, ob Nikotin eine Modulation sensorischer gain Kontrolle bewirkt. Dazu wurden ereigniskorrelierte Potentiale (EKP) im Posner-Paradigma erhoben und die Wirkung von Nikotin auf die aufmerksamkeitsassoziierten Komponenten P1 und N1 betrachtet. Nikotin verringerte die Kosten invalider Hinweisreize bei Aufmerksamkeitslenkung durch endogene Hinweisreize, nicht aber bei exogenen Hinweisreizen. Die P1 und N1 Komponenten zeigten sich unbeeinflusst von Nikotin, damit findet also die Annahme einer Wirkung auf sensorische Suppression keine Unterst{\"u}tzung. In Experiment 3 und 4 wurde untersucht, ob Nikotin einen Effekt auf kostentr{\"a}chtige unwillk{\"u}rliche Aufmerksamkeitsverschiebungen, Distraktionen, hat. In Experiment 3 wurden in einem r{\"a}umlichen Daueraufmerksamkeitsparadigma Distraktionen durch deviante Stimulusmerkmale ausgel{\"o}st und die Wirkung von Nikotin auf eine distraktionsassoziierte Komponente des EKP, die P3a, betrachtet. In Experiment 4 wurde in einem Hinweisreizparadigma durch zus{\"a}tzliche Stimuli eine Distraktion ausgel{\"o}st und die Nikotinwirkung auf die Reaktionszeitkosten untersucht. Nikotin zeigte keinen Einfluss auf Distraktionskosten in beiden Studien und auch keine Wirkung auf die P3a Komponente in Experiment 3. In Experiment 4 wurde zus{\"a}tzlich die Wirkung von Nikotin auf das Losl{\"o}sen von Aufmerksamkeit untersucht, indem die Schwierigkeit des Losl{\"o}sens variiert wurde. Auch hier zeigte sich keine Nikotinwirkung. Allerdings konnte in beiden Studien weder die h{\"a}ufig berichtete generelle Reaktionszeitverk{\"u}rzung noch die Verringerung der Kosten invalider Hinweisreize repliziert werden, so dass zum Einen keine Aussage {\"u}ber die Wirkung von Nikotin auf Distraktionen oder den Aufmerksamkeitslosl{\"o}seprozess gemacht werden k{\"o}nnen, zum Anderen sich die Frage stellte, unter welchen Bedingungen Nikotin einen differentiellen Effekt {\"u}berhaupt zeigt. Im letzten Experiment wurde hierzu die H{\"a}ufigkeit der Reaktionsanforderung einerseits und die zeitlichen Aspekte der Aufmerksamkeitslenkung andererseits variiert und der Effekt des Nikotins auf den Validit{\"a}tseffekt, die Reaktionszeitdifferenz zwischen valide und invalide vorhergesagten Zielreizen, betrachtet. Nikotin verringerte bei Individuen, bei denen Aufmerksamkeitslenkung in allen Bedingungen evident war, in der Tendenz den Validit{\"a}tseffekt in der ereignis{\"a}rmsten Bedingung, wenn nur selten willentliche Aufmerksamkeitsausrichtung notwendig war. Dies k{\"o}nnte als Hinweis gedeutet werden, dass Nikotin unter Bedingungen, die große Anforderungen an die Vigilanz stellen, die top-down Zuweisung von Aufmerksamkeitsressourcen unterst{\"u}tzt.},
  subject      = {Nicotin},
  language  = {de}
}
@phdthesis{Loeffler2005,
  author    = {L{\"o}ffler, Frank},
  title     = {Numerical simulations of neutron star - black hole mergers},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7743},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Collisions of black holes and neutron stars, named mixed binaries in the following, are interesting because of at least two reasons. Firstly, it is expected that they emit a large amount of energy as gravitational waves, which could be measured by new detectors. The form of those waves is expected to carry information about the internal structure of such systems. Secondly, collisions of such objects are the prime suspects of short gamma ray bursts. The exact mechanism for the energy emission is unknown so far. In the past, Newtonian theory of gravitation and modifications to it were often used for numerical simulations of collisions of mixed binary systems. However, near to such objects, the gravitational forces are so strong, that the use of General Relativity is necessary for accurate predictions. There are a lot of problems in general relativistic simulations. However, systems of two neutron stars and systems of two black holes have been studies extensively in the past and a lot of those problems have been solved. One of the remaining problems so far has been the use of hydrodynamic on excision boundaries. Inside excision regions, no evolution is carried out. Such regions are often used inside black holes to circumvent instabilities of the numerical methods near the singularity. Methods to handle hydrodynamics at such boundaries have been described and tests are shown in this work. One important test and the first application of those methods has been the simulation of a collapsing neutron star to a black hole. The success of these simulations and in particular the performance of the excision methods was an important step towards simulations of mixed binaries. Initial data are necessary for every numerical simulation. However, the creation of such initial data for general relativistic situations is in general very complicated. In this work it is shown how to obtain initial data for mixed binary systems using an already existing method for initial data of two black holes. These initial data have been used for evolutions of such systems and problems encountered are discussed in this work. One of the problems are instabilities due to different methods, which could be solved by dissipation of appropriate strength. Another problem is the expected drift of the black hole towards the neutron star. It is shown, that this can be solved by using special gauge conditions, which prevent the black hole from moving on the computational grid. The methods and simulations shown in this work are only the starting step for a much more detailed study of mixed binary system. Better methods, models and simulations with higher resolution and even better gauge conditions will be focus of future work. It is expected that such detailed studies can give information about the emitted gravitational waves, which is important in view of the newly built gravitational wave detectors. In addition, these simulations could give insight into the processes responsible for short gamma ray bursts.},
  subject      = {Relativistische Astrophysik},
  language  = {en}
}
@phdthesis{Schauer2006,
  author    = {Schauer, Nicolas},
  title     = {Quantitative trait loci (QTL) for metabolite accumulation and metabolic regulation : metabolite profiling of interspecific crosses of tomato},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7643},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {The advent of large-scale and high-throughput technologies has recently caused a shift in focus in contemporary biology from decades of reductionism towards a more systemic view. Alongside the availability of genome sequences the exploration of organisms utilizing such approach should give rise to a more comprehensive understanding of complex systems. Domestication and intensive breeding of crop plants has led to a parallel narrowing of their genetic basis. The potential to improve crops by conventional breeding using elite cultivars is therefore rather limited and molecular technologies, such as marker assisted selection (MAS) are currently being exploited to re-introduce allelic variance from wild species. Molecular breeding strategies have mostly focused on the introduction of yield or resistance related traits to date. However given that medical research has highlighted the importance of crop compositional quality in the human diet this research field is rapidly becoming more important. Chemical composition of biological tissues can be efficiently assessed by metabolite profiling techniques, which allow the multivariate detection of metabolites of a given biological sample. Here, a GC/MS metabolite profiling approach has been applied to investigate natural variation of tomatoes with respect to the chemical composition of their fruits. The establishment of a mass spectral and retention index (MSRI) library was a prerequisite for this work in order to establish a framework for the identification of metabolites from a complex mixture. As mass spectral and retention index information is highly important for the metabolomics community this library was made publicly available. Metabolite profiling of tomato wild species revealed large differences in the chemical composition, especially of amino and organic acids, as well as on the sugar composition and secondary metabolites. Intriguingly, the analysis of a set of S. pennellii introgression lines (IL) identified 889 quantitative trait loci of compositional quality and 326 yield-associated traits. These traits are characterized by increases/decreases not only of single metabolites but also of entire metabolic pathways, thus highlighting the potential of this approach in uncovering novel aspects of metabolic regulation. Finally the biosynthetic pathway of the phenylalanine-derived fruit volatiles phenylethanol and phenylacetaldehyde was elucidated via a combination of metabolic profiling of natural variation, stable isotope tracer experiments and reverse genetic experimentation.},
  subject      = {Tomate},
  language  = {en}
}
@phdthesis{Unterstab2005,
  author    = {Unterstab, Gunhild},
  title     = {Charakterisierung der viralen Genprodukte p10 und P des Borna Disease Virus},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6905},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Das Borna Disease Virus (BDV, Bornavirus) besitzt ein einzelstr{\"a}ngiges RNA-Genom negativer Polarit{\"a}t und ist innerhalb der Ordnung Mononegavirales der Prototyp einer eigenen Virusfamilie, die der Bornaviridae. Eine außergew{\"o}hnliche Eigenschaft des Virus ist seine nukle{\"a}re Transkription und Replikation, eine weitere besteht in seiner F{\"a}higkeit, als neurotropes Virus sowohl in vivo als auch in vitro persistente Infektionen zu etablieren. Die zugrunde liegenden Mechanismen sowohl der Replikation als auch der Persistenz sind derzeit noch unzureichend verstanden, auch deshalb, weil das Virus noch relativ „jung" ist: Erste komplette Sequenzen des RNA-Genoms wurden 1994 publiziert und erst vor einigen Monaten gelang die Generierung rekombinanter Viren auf der Basis klonierter cDNA. Im Mittelpunkt dieser Arbeit standen das p10 Protein und das Phosphoprotein (P), die von der gemeinsamen Transkriptionseinheit II in {\"u}berlappenden Leserahmen kodiert werden. Als im Kern der Wirtszelle replizierendes Virus ist das Bornavirus auf zellul{\"a}re Importmechanismen angewiesen, um den Kernimport aller an der Replikation beteiligten viralen Proteine zu gew{\"a}hrleisten. Das p10 Protein ist ein negativer Regulator der viralen RNA-abh{\"a}ngigen RNA-Polymerase (L). In vitro Importexperimente zeigten, dass p10 {\"u}ber den klassischen Importin alpha/beta abh{\"a}ngigen Kernimportweg in den Nukleus transportiert wird. Dies war unerwartet, da p10 kein vorhersagbares klassisches Kernlokalisierungssignal (NLS) besitzt und weist darauf hin, dass der zellul{\"a}re Importapparat offensichtlich flexibler ist als allgemein angenommen. Die ersten 20 N-terminalen AS vermitteln sowohl Kernimport als auch die Bindung an den Importrezeptor Importin alpha. Durch Di-Alanin-Austauschmutagenese wurden die f{\"u}r diesen Transportprozess essentiellen AS identifiziert und die Bedeutung hydrophober und polarer AS-Reste demonstriert. Die F{\"a}higkeit des Bornavirus, persistente Infektionen zu etablieren, wirft die Frage auf, wie das Virus die zellul{\"a}ren antiviralen Abwehrmechanismen, insbesondere das Typ I Interferon (IFN)-System, unterwandert. Das virale P Protein wurde in dieser Arbeit als potenter Antagonist der IFN-Induktion charakterisiert. Es verhindert die Phosphorylierung des zentralen Transkriptionsfaktors IRF3 durch die zellul{\"a}re Kinase TBK1 und somit dessen Aktivierung. Der Befund, dass P mit TBK1 Komplexe bildet und zudem auch als Substrat f{\"u}r die zellul{\"a}re Kinase fungiert, erlaubt es, erstmalig einen Mechanismus zu postulieren, in dem ein virales Protein (BDV-P) als putatives TBK1-Pseudosubstrat die IRF3-Aktivierung kompetitiv hemmt.},
  subject      = {Interferon <beta->},
  language  = {de}
}
@phdthesis{Andersen2005,
  author    = {Andersen, Audr{\´e}e},
  title     = {Surfactant dynamics at interfaces : a series of second harmonic generation experiments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6553},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Adsorption layers of soluble surfactants enable and govern a variety of phenomena in surface and colloidal sciences, such as foams. The ability of a surfactant solution to form wet foam lamellae is governed by the surface dilatational rheology. Only systems having a non-vanishing imaginary part in their surface dilatational modulus, E, are able to form wet foams. The aim of this thesis is to illuminate the dissipative processes that give rise to the imaginary part of the modulus. There are two controversial models discussed in the literature. The reorientation model assumes that the surfactants adsorb in two distinct states, differing in their orientation. This model is able to describe the frequency dependence of the modulus E. However, it assumes reorientation dynamics in the millisecond time regime. In order to assess this model, we designed a SHG pump-probe experiment that addresses the orientation dynamics. Results obtained reveal that the orientation dynamics occur in the picosecond time regime, being in strong contradiction with the two states model. The second model regards the interface as an interphase. The adsorption layer consists of a topmost monolayer and an adjacent sublayer. The dissipative process is due to the molecular exchange between both layers. The assessment of this model required the design of an experiment that discriminates between the surface compositional term and the sublayer contribution. Such an experiment has been successfully designed and results on elastic and viscoelastic surfactant provided evidence for the correctness of the model. Because of its inherent surface specificity, surface SHG is a powerful analytical tool that can be used to gain information on molecular dynamics and reorganization of soluble surfactants. They are central elements of both experiments. However, they impose several structural elements of the model system. During the course of this thesis, a proper model system has been identified and characterized. The combination of several linear and nonlinear optical techniques, allowed for a detailed picture of the interfacial architecture of these surfactants.},
  subject      = {Tensid},
  language  = {en}
}
@phdthesis{Hoffmann2007,
  author    = {Hoffmann, Toni},
  title     = {Cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O'Kane and Al'Shehbaz and Arabidopsis thaliana (L.) Heynhold},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15259},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Imranulhaq2008,
  author    = {Imran ul-haq, Muhammad},
  title     = {Synthesis of fluorinated polymers in supercritical carbon dioxide (scCO₂)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19868},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {For the first time stabilizer-free vinylidene fluoride (VDF) polymerizations were carried out in homogeneous phase with supercritical CO₂. Polymerizations were carried out at 140°C, 1500 bar and were initiated with di-tert-butyl peroxide (DTBP). In-line FT-NIR (Fourier Transform- Near Infrared) spectroscopy showed that complete monomer conversion may be obtained. Molecular weights were determined via size-exclusion chromatography (SEC) and polymer end group analysis by 1H-NMR spectroscopy. The number average molecular weights were below 104 g∙mol-1 and polydispersities ranged from 3.1 to 5.7 depending on DTBP and VDF concentration. To allow for isothermal reactions high CO₂ contents ranging from 61 to 83 wt.\% were used. The high-temperature, high-pressure conditions were required for homogeneous phase polymerization. These conditions did not alter the amount of defects in VDF chaining. Scanning electron microscopy (SEM) indicated that regular stack-type particles were obtained upon expansion of the homogeneous polymerization mixture. To reduce the required amount of initiator, further VDF polymerizations using chain transfer agents (CTAs) to control molecular weights were carried out in homogeneous phase with supercritical carbon dioxide (scCO₂) at 120 °C and 1500 bar. Using perfluorinated hexyl iodide as CTA, polymers of low polydispersity ranging from 1.5 to 1.2 at the highest iodide concentration of 0.25 mol·L-1 were obtained. Electrospray ionization- mass spectroscopy (ESI-MS) indicates the absence of initiator derived end groups, supporting livingness of the system. The "livingness" is based on the labile C-I bond. However, due to the weakness of the C-I bond perfluorinated hexyl iodide also contributes to initiation. To allow for kinetic analyses of VDF polymerizations the CTA should not contribute to initiation. Therefore, additional CTAs were applied: BrCCl3, C6F13Br and C6F13H. It was found that C6F13H does not contribute to initiation. At 120°C and 1500 bar kp/kt0.5~ 0.64 (L·mol-1·s-1)0.5 was derived. The chain transfer constant (CT) at 120°C has been determined to be 8·10-1, 9·10-2 and 2·10-4 for C6F13I, C6F13Br and C6F13H, respectively. These CT values are associated with the bond energy of the C-X bond. Moreover, the labile C-I bond allows for functionalization of the polymer to triazole end groups applying click reactions. After substitution of the iodide end group by an azide group 1,3 dipolar cycloadditions with alkynes yield polymers with 1,2,3 triazole end groups. Using symmetrical alkynes the reactions may be carried out in the absence of any catalyst. This end-functionalized poly (vinylidene fluoride) (PVDF) has higher thermal stability as compared to the normal PVDF. PVDF samples from homogeneous phase polymerizations in supercritical CO₂ and subsequent expansion to ambient conditions were analyzed with respect to polymer end groups, crystallinity, type of polymorphs and morphology. Upon expansion the polymer was obtained as white powder. Scanning electron microscopy (SEM) showed that DTBP derived polymer end groups led to stack-type particles whereas sponge- or rose-type particles were obtained in case of CTA fragments as end groups. Fourier-Transform Infrared spectroscopy and wide angle X-ray diffraction indicated that the type of polymorph, α or β crystal phase was significantly affected by the type of end group. The content of β-phase material, which is responsible for piezoelectricity of PVDF, is the highest for polymer with DTBP-derived end groups. In addition, the crystallinity of the material, as determined via differential scanning calorimetry is affected by the end groups and polymer molecular weights. For example, crystallinity ranges from around 26 \% for DTBP-derived end groups to a maximum of 62 \% for end groups originating from perfluorinated hexyl iodide for polymers with Mn ~2200 g·mol-1. Expansion of the homogeneous polymerization mixture results in particle formation by a non-optimized RESS (Rapid Expansion from Supercritical Solution) process. Thus, it was tested how polymer end groups affect the particles size distribution obtained from RESS process under controlled conditions (T = 50°C and P = 200 bar). In all RESS experiments, small primary PVDF with diameters less than 100 nm without the use of liquid solvents, surfactants, or other additives were produced. A strong correlation between particle size and particle size distribution with polymer end groups and molecular weight of the original material was observed. The smallest particles were found for RESS of PVDF with Mn~ 4000 g·mol-1 and PFHI (C6F13I) - derived end groups.},
  language  = {en}
}
@phdthesis{Miteva2007,
  author    = {Miteva, Rositsa Stoycheva},
  title     = {Electron acceleration at localized wave structures in the solar corona},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14775},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Nerlich2007,
  author    = {Nerlich, Annika},
  title     = {Die Rolle der Phosphatidylserin Decarboxylase f{\"u}r die mitochondriale Phospholipid-Biosynthese in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14522},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Die durch Phosphatidylserin Decarboxylase (PSD) katalysierte Decarboxylierung von Phosphatidylserin (PS) zu Phosphatidylethanolamin (PE) ist f{\"u}r Mitochondrien in Hefe und M{\"a}usen von essentieller Bedeutung. Im Rahmen der vorliegenden Dissertation wurde erstmals die Rolle dieses PE-Syntheseweges in Pflanzen untersucht. Die drei in Arabidopsis identifizierten PSD Gene atPSD1, atPSD2, atPSD3 codieren f{\"u}r Enzyme, die in Membranen der Mitochondrien (atPSD1), der Tonoplasten (atPSD2) und des Endoplasmatischen Retikulums (atPSD3) lokalisiert sind. Der Beitrag der einzelnen PSDs zur PE-Synthese wurde anhand von psd Null-Mutanten untersucht. Dabei stellte sich atPSD3 als das Enzym mit der h{\"o}chsten Aktivit{\"a}t heraus. Alternativ zum PSD-Weg wird in Arabidopsis PE auch mittels Aminoalkohol-phosphotransferase synthetisiert. Der Verlust der gesamten PSD-Aktivit{\"a}t, wie es in der erzeugten psd Dreifachmutante der Fall ist, wirkt sich ausschließlich auf die Lipidzusammensetzung in der Mitochondrienmembran aus. Demzufolge wird extramitochondriales PE haupts{\"a}chlich {\"u}ber die Aminoalkoholphosphotransferase synthetisiert. Die ver{\"a}nderte Lipidzusammensetzung der Mitochondrienmembran hatte jedoch keinen Einfluss auf die Anzahl, Gr{\"o}ße und Ultrastruktur der Mitochondrien sowie auf das ADP/ATP-Verh{\"a}ltnis und die Respiration. Neben der Bereitstellung von Reduktions{\"a}quivalenten beeinflusst die Funktionalit{\"a}t der Mitochondrien auch die Bildung von Bl{\"u}ten- und Staubbl{\"a}ttern. Diese Bl{\"u}tenorgane waren in der psd Dreifachmutante stark ver{\"a}ndert, und der Bl{\"u}tenph{\"a}notyp {\"a}hnelte der APETALA3-Mutante. Dieses hom{\"o}otische Gen ist f{\"u}r die Ausbildung von Bl{\"u}ten- und Staubbl{\"a}ttern verantwortlich. F{\"u}r die Erzeugung der Mutanten psd2-1 und psd3-1 wurde ein T-DNA Vektor verwendet, der den Promotor des APETALA3 Gens enthielt, welcher in den Mutanten psd2-1, psd3-1 sowie psd2-1psd3-1 und der psd1psd2-1psd3-1 Dreifachmutante eine vergleichbare Co-Suppression des APETALA3 Gens hervorruft. Der Bl{\"u}tenph{\"a}notyp trat jedoch nur in der psd Dreifachmutante auf, da nur in ihr die Kombination von geringen Funktionst{\"o}rungen der Mitochondrien, hervorgerufen durch ver{\"a}nderte Lipidzusammensetzung, mit der Co-Suppression von APETALA3 auftritt.},
  language  = {de}
}
@phdthesis{NickeltCzycykowski2008,
  author    = {Nickelt-Czycykowski, Iliya Peter},
  title     = {Aktive Regionen der Sonnenoberfl{\"a}che und ihre zeitliche Variation in zweidimensionaler Spektro-Polarimetrie},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-25524},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Die Arbeit beschreibt die Analyse von Beobachtungen zweier Sonnenflecken in zweidimensionaler Spektro-Polarimetrie. Die Daten wurden mit dem Fabry-P{\´e}rot-Interferometer der Universit{\"a}t G{\"o}ttingen am Vakuum-Turm-Teleskop auf Teneriffa erfasst. Von der aktiven Region NOAA 9516 wurde der volle Stokes-Vektor des polarisierten Lichts in der Absorptionslinie bei 630,249 nm in Einzelaufnahmen beobachtet, und von der aktiven Region NOAA 9036 wurde bei 617,3 nm Wellenl{\"a}nge eine 90-min{\"u}tige Zeitserie des zirkular polarisierten Lichts aufgezeichnet. Aus den reduzierten Daten werden Ergebniswerte f{\"u}r Intensit{\"a}t, Geschwindigkeit in Beobachtungsrichtung, magnetische Feldst{\"a}rke sowie verschiedene weitere Plasmaparameter abgeleitet. Mehrere Ans{\"a}tze zur Inversion solarer Modellatmosph{\"a}ren werden angewendet und verglichen. Die teilweise erheblichen Fehlereinfl{\"u}sse werden ausf{\"u}hrlich diskutiert. Das Frequenzverhalten der Ergebnisse und Abh{\"a}ngigkeiten nach Ort und Zeit werden mit Hilfe der Fourier- und Wavelet-Transformation weiter analysiert. Als Resultat l{\"a}sst sich die Existenz eines hochfrequenten Bandes f{\"u}r Geschwindigkeitsoszillationen mit einer zentralen Frequenz von 75 Sekunden (13 mHz) best{\"a}tigen. In gr{\"o}ßeren photosph{\"a}rischen H{\"o}hen von etwa 500 km entstammt die Mehrheit der damit zusammenh{\"a}ngenden Schockwellen den dunklen Anteilen der Granulen, im Unterschied zu anderen Frequenzbereichen. Die 75-Sekunden-Oszillationen werden ebenfalls in der aktiven Region beobachtet, vor allem in der Lichtbr{\"u}cke. In den identifizierten B{\"a}ndern oszillatorischer Power der Geschwindigkeit sind in einer dunklen, penumbralen Struktur sowie in der Lichtbr{\"u}cke ausgepr{\"a}gte Strukturen erkennbar, die sich mit einer Horizontalgeschwindigkeit von 5-8 km/s in die ruhige Sonne bewegen. Diese zeigen einen deutlichen Anstieg der Power, vor allem im 5-Minuten-Band, und stehen m{\"o}glicherweise in Zusammenhang mit dem Ph{\"a}nomen der „Evershed-clouds". Eingeschr{\"a}nkt durch ein sehr geringes Signal-Rausch-Verh{\"a}ltnis und hohe Fehlereinfl{\"u}sse werden auch Magnetfeldvariationen mit einer Periode von sechs Minuten am {\"U}bergang von Umbra zu Penumbra in der N{\"a}he einer Lichtbr{\"u}cke beobachtet. Um die beschriebenen Resultate zu erzielen, wurden bestehende Visualisierungsverfahren der Frequenzanalyse verbessert oder neu entwickelt, insbesondere f{\"u}r Ergebnisse der Wavelet-Transformation.},
  language  = {de}
}
@phdthesis{Kellermann2011,
  author    = {Kellermann, Thorsten},
  title     = {Accurate numerical relativity simulations of non-vacuumspace-times in two dimensions and applications to critical collapse},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59578},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {This Thesis puts its focus on the physics of neutron stars and its description with methods of numerical relativity. In the first step, a new numerical framework the Whisky2D code will be developed, which solves the relativistic equations of hydrodynamics in axisymmetry. Therefore we consider an improved formulation of the conserved form of these equations. The second part will use the new code to investigate the critical behaviour of two colliding neutron stars. Considering the analogy to phase transitions in statistical physics, we will investigate the evolution of the entropy of the neutron stars during the whole process. A better understanding of the evolution of thermodynamical quantities, like the entropy in critical process, should provide deeper understanding of thermodynamics in relativity. More specifically, we have written the Whisky2D code, which solves the general-relativistic hydrodynamics equations in a flux-conservative form and in cylindrical coordinates. This of course brings in 1/r singular terms, where r is the radial cylindrical coordinate, which must be dealt with appropriately. In the above-referenced works, the flux operator is expanded and the 1/r terms, not containing derivatives, are moved to the right-hand-side of the equation (the source term), so that the left hand side assumes a form identical to the one of the three-dimensional (3D) Cartesian formulation. We call this the standard formulation. Another possibility is not to split the flux operator and to redefine the conserved variables, via a multiplication by r. We call this the new formulation. The new equations are solved with the same methods as in the Cartesian case. From a mathematical point of view, one would not expect differences between the two ways of writing the differential operator, but, of course, a difference is present at the numerical level. Our tests show that the new formulation yields results with a global truncation error which is one or more orders of magnitude smaller than those of alternative and commonly used formulations. The second part of the Thesis uses the new code for investigations of critical phenomena in general relativity. In particular, we consider the head-on-collision of two neutron stars in a region of the parameter space where two final states a new stable neutron star or a black hole, lay close to each other. In 1993, Choptuik considered one-parameter families of solutions, S[P], of the Einstein-Klein-Gordon equations for a massless scalar field in spherical symmetry, such that for every P > P⋆, S[P] contains a black hole and for every P < P⋆, S[P] is a solution not containing singularities. He studied numerically the behavior of S[P] as P → P⋆ and found that the critical solution, S[P⋆], is universal, in the sense that it is approached by all nearly-critical solutions regardless of the particular family of initial data considered. All these phenomena have the common property that, as P approaches P⋆, S[P] approaches a universal solution S[P⋆] and that all the physical quantities of S[P] depend only on |P - P⋆|. The first study of critical phenomena concerning the head-on collision of NSs was carried out by Jin and Suen in 2007. In particular, they considered a series of families of equal-mass NSs, modeled with an ideal-gas EOS, boosted towards each other and varied the mass of the stars, their separation, velocity and the polytropic index in the EOS. In this way they could observe a critical phenomenon of type I near the threshold of black-hole formation, with the putative solution being a nonlinearly oscillating star. In a successive work, they performed similar simulations but considering the head-on collision of Gaussian distributions of matter. Also in this case they found the appearance of type-I critical behaviour, but also performed a perturbative analysis of the initial distributions of matter and of the merged object. Because of the considerable difference found in the eigenfrequencies in the two cases, they concluded that the critical solution does not represent a system near equilibrium and in particular not a perturbed Tolmann-Oppenheimer-Volkoff (TOV) solution. In this Thesis we study the dynamics of the head-on collision of two equal-mass NSs using a setup which is as similar as possible to the one considered above. While we confirm that the merged object exhibits a type-I critical behaviour, we also argue against the conclusion that the critical solution cannot be described in terms of equilibrium solution. Indeed, we show that, in analogy with what is found in, the critical solution is effectively a perturbed unstable solution of the TOV equations. Our analysis also considers fine-structure of the scaling relation of type-I critical phenomena and we show that it exhibits oscillations in a similar way to the one studied in the context of scalar-field critical collapse.},
  language  = {en}
}
@phdthesis{Berger2012,
  author    = {Berger, Florian},
  title     = {Different modes of cooperative transport by molecular motors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60319},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors' velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.},
  language  = {en}
}
@phdthesis{Kluth2012,
  author    = {Kluth, Oliver},
  title     = {Einfluss von Glucolipotoxizit{\"a}t auf die Funktion der β-Zellen diabetessuszeptibler und -resistenter Mausst{\"a}mme},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-61961},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Ziel der vorliegenden Arbeit war es, die Auswirkungen von Glucose- und Lipidtoxizit{\"a}t auf die Funktion der β-Zellen von Langerhans-Inseln in einem diabetesresistenten (B6.V-Lepob/ob, ob/ob) sowie diabetessuszeptiblen (New Zealand Obese, NZO) Mausmodell zu untersuchen. Es sollten molekulare Mechanismen identifiziert werden, die zum Untergang der β-Zellen in der NZO-Maus f{\"u}hren bzw. zum Schutz der β-Zellen der ob/ob-Maus beitragen. Zun{\"a}chst wurde durch ein geeignetes di{\"a}tetisches Regime in beiden Modellen durch kohlenhydratrestriktive Ern{\"a}hrung eine Adipositas(Lipidtoxizit{\"a}t) induziert und anschließend durch F{\"u}tterung einer kohlenhydrathaltigen Di{\"a}t ein Zustand von Glucolipotoxizit{\"a}t erzeugt. Dieses Vorgehen erlaubte es, in der NZO-Maus in einem kurzen Zeitfenster eine Hyperglyk{\"a}mie sowie einen β-Zelluntergang durch Apoptose auszul{\"o}sen. Im Vergleich dazu blieben ob/ob-M{\"a}use l{\"a}ngerfristig normoglyk{\"a}misch und wiesen keinen β-Zelluntergang auf. Die Ursache f{\"u}r den β-Zellverlust war die Inaktivierung des Insulin/IGF-1-Rezeptor-Signalwegs, wie durch Abnahme von phospho-AKT, phospho-FoxO1 sowie des β-zellspezifischen Transkriptionsfaktors PDX1 gezeigt wurde. Mit Ausnahme des Effekts einer Dephosphorylierung von FoxO1, konnten ob/ob-M{\"a}use diesen Signalweg aufrechterhalten und dadurch einen Verlust von β-Zellen abwenden. Die glucolipotoxischen Effekte wurden in vitro an isolierten Inseln beider St{\"a}mme und der β-Zelllinie MIN6 best{\"a}tigt und zeigten, dass ausschließlich die Kombination hoher Glucose und Palmitatkonzentrationen (Glucolipotoxizit{\"a}t) negative Auswirkungen auf die NZO-Inseln und MIN6-Zellen hatte, w{\"a}hrend ob/ob-Inseln davor gesch{\"u}tzt blieben. Die Untersuchung isolierter Inseln ergab, dass beide St{\"a}mme unter glucolipotoxischen Bedingungen keine Steigerung der Insulinexpression aufweisen und sich bez{\"u}glich ihrer Glucose-stimulierten Insulinsekretion nicht unterscheiden. Mit Hilfe von Microarray- sowie immunhistologischen Untersuchungen wurde gezeigt, dass ausschließlich ob/ob-M{\"a}use nach Kohlenhydratf{\"u}tterung eine kompensatorische transiente Induktion der β-Zellproliferation aufwiesen, die in einer nahezu Verdreifachung der Inselmasse nach 32 Tagen m{\"u}ndete. Die hier erzielten Ergebnisse lassen die Schlussfolgerung zu, dass der β-Zelluntergang der NZO-Maus auf eine Beeintr{\"a}chtigung des Insulin/IGF-1-Rezeptor-Signalwegs sowie auf die Unf{\"a}higkeit zur β- Zellproliferation zur{\"u}ckgef{\"u}hrt werden kann. Umgekehrt erm{\"o}glichen der Erhalt des Insulin/IGF-1-Rezeptor-Signalwegs und die Induktion der β-Zellproliferation in der ob/ob-Maus den Schutz vor einer Hyperglyk{\"a}mie und einem Diabetes.},
  language  = {de}
}
@phdthesis{Hoffmann2011,
  author    = {Hoffmann, Anne},
  title     = {Comparative aerosol studies based on multi-wavelength Raman LIDAR at Ny-{\AA}lesund, Spitsbergen},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52426},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {The Arctic is a particularly sensitive area with respect to climate change due to the high surface albedo of snow and ice and the extreme radiative conditions. Clouds and aerosols as parts of the Arctic atmosphere play an important role in the radiation budget, which is, as yet, poorly quantified and understood. The LIDAR (Light Detection And Ranging) measurements presented in this PhD thesis contribute with continuous altitude resolved aerosol profiles to the understanding of occurrence and characteristics of aerosol layers above Ny-{\AA}lesund, Spitsbergen. The attention was turned to the analysis of periods with high aerosol load. As the Arctic spring troposphere exhibits maximum aerosol optical depths (AODs) each year, March and April of both the years 2007 and 2009 were analyzed. Furthermore, stratospheric aerosol layers of volcanic origin were analyzed for several months, subsequently to the eruptions of the Kasatochi and Sarychev volcanoes in summer 2008 and 2009, respectively. The Koldewey Aerosol Raman LIDAR (KARL) is an instrument for the active remote sensing of atmospheric parameters using pulsed laser radiation. It is operated at the AWIPEV research base and was fundamentally upgraded within the framework of this PhD project. It is now equipped with a new telescope mirror and new detection optics, which facilitate atmospheric profiling from 450m above sea level up to the mid-stratosphere. KARL provides highly resolved profiles of the scattering characteristics of aerosol and cloud particles (backscattering, extinction and depolarization) as well as water vapor profiles within the lower troposphere. Combination of KARL data with data from other instruments on site, namely radiosondes, sun photometer, Micro Pulse LIDAR, and tethersonde system, resulted in a comprehensive data set of scattering phenomena in the Arctic atmosphere. The two spring periods March and April 2007 and 2009 were at first analyzed based on meteorological parameters, like local temperature and relative humidity profiles as well as large scale pressure patterns and air mass origin regions. Here, it was not possible to find a clear correlation between enhanced AOD and air mass origin. However, in a comparison of two cloud free periods in March 2007 and April 2009, large AOD values in 2009 coincided with air mass transport through the central Arctic. This suggests the occurrence of aerosol transformation processes during the aerosol transport to Ny-{\AA}lesund. Measurements on 4 April 2009 revealed maximum AOD values of up to 0.12 and aerosol size distributions changing with altitude. This and other performed case studies suggest the differentiation between three aerosol event types and their origin: Vertically limited aerosol layers in dry air, highly variable hygroscopic boundary layer aerosols and enhanced aerosol load across wide portions of the troposphere. For the spring period 2007, the available KARL data were statistically analyzed using a characterization scheme, which is based on optical characteristics of the scattering particles. The scheme was validated using several case studies. Volcanic eruptions in the northern hemisphere in August 2008 and June 2009 arose the opportunity to analyze volcanic aerosol layers within the stratosphere. The rate of stratospheric AOD change was similar within both years with maximum values above 0.1 about three to five weeks after the respective eruption. In both years, the stratospheric AOD persisted at higher rates than usual until the measurements were stopped in late September due to technical reasons. In 2008, up to three aerosol layers were detected, the layer structure in 2009 was characterized by up to six distinct and thin layers which smeared out to one broad layer after about two months. The lowermost aerosol layer was continuously detected at the tropopause altitude. Three case studies were performed, all revealed rather large indices of refraction of m = (1.53-1.55) - 0.02i, suggesting the presence of an absorbing carbonaceous component. The particle radius, derived with inversion calculations, was also similar in both years with values ranging from 0.16 to 0.19 μm. However, in 2009, a second mode in the size distribution was detected at about 0.5 μm. The long term measurements with the Koldewey Aerosol Raman LIDAR in Ny-{\AA}lesund provide the opportunity to study Arctic aerosols in the troposphere and the stratosphere not only in case studies but on longer time scales. In this PhD thesis, both, tropospheric aerosols in the Arctic spring and stratospheric aerosols following volcanic eruptions have been described qualitatively and quantitatively. Case studies and comparative studies with data of other instruments on site allowed for the analysis of microphysical aerosol characteristics and their temporal evolution.},
  language  = {en}
}