@phdthesis{Oehlschlaeger2001,
  author    = {Oehlschl{\"a}ger, Susanne},
  title     = {Zur Habitatwahl, Nahrungs{\"o}kologie und Brutbiologie des Wiederhopfes (Upupa epops) Linn{\´e} 1958 auf den ehemaliegen Truppen{\"u}bungspl{\"a}tzen bei J{\"u}terbog, Brandenburg},
  pages     = {70, XXIII S.},
  year      = {2001},
  language  = {de}
}
@phdthesis{Otto2013,
  author    = {Otto, Sebastian},
  title     = {Zulassungskonforme und schnelle massenspektronomische Analytik und pr{\"a}klinische Pharmakokinetik neuer Wirkstoffkandidaten},
  address   = {Potsdam},
  pages     = {143 S.},
  year      = {2013},
  language  = {de}
}
@phdthesis{Kiemel2023,
  author    = {Kiemel, Katrin},
  title     = {Zooplankton adaptations and community dynamics in space and time},
  school      = {Universit{\"a}t Potsdam},
  year      = {2023},
  abstract  = {In times of ongoing biodiversity loss, understanding how communities are structured and what mechanisms and local adaptations underlie the patterns we observe in nature is crucial for predicting how future ecological and anthropogenic changes might affect local and regional biodiversity. Aquatic zooplankton are a group of primary consumers that represent a critical link in the food chain, providing nutrients for the entire food web. Thus, understanding the adaptability and structure of zooplankton communities is essential. In this work, the genetic basis for the different temperature adaptations of two seasonally shifted (i.e., temperature-dependent) occurring freshwater rotifers of a formerly cryptic species complex (Brachionus calyciflorus) was investigated to understand the overall genetic diversity and evolutionary scenario for putative adaptations to different temperature regimes. Furthermore, this work aimed to clarify to what extent the different temperature adaptations may represent a niche partitioning process thus enabling co-existence. The findings were then embedded in a metacommunity context to understand how zooplankton communities assemble in a kettle hole metacommunity located in the northeastern German "Uckermark" and which underlying processes contribute to the biodiversity patterns we observe. Using a combined approach of newly generated mitochondrial resources (genomes/cds) and the analysis of a candidate gene (Heat Shock Protein 40kDa) for temperature adaptation, I showed that the global representatives of B. calyciflorus s.s.. are genetically more similar than B. fernandoi (average pairwise nucleotide diversity: 0.079 intraspecific vs. 0.257 interspecific) indicating that both species carry different standing genetic variation. In addition to differential expression in the thermotolerant B. calyciflorus s.s. and thermosensitive B. fernandoi, the HSP 40kDa also showed structural variation with eleven fixed and six positively selected sites, some of which are located in functional areas of the protein. The estimated divergence time of ~ 25-29 Myr combined with the fixed sites and a prevalence of ancestral amino acids in B. calyciflorus s.s. indicate that B. calyciflorus s.s. remained in the ancestral niche, while B. fernandoi partitioned into a new niche. The comparison of mitochondrial and nuclear markers (HPS 40kDa, ITS1, COI) revealed a hybridisation event between the two species. However, as hybridisation between the two species is rare, it can be concluded that the temporally isolated niches (i.e., seasonal-shifted occurrence) they inhabit based on their different temperature preferences most likely represent a pre-zygotic isolation mechanism that allows sympatric occurrence while maintaining species boundaries. To determine the processes underlying zooplankton community assembly, a zooplankton metacommunity comprising 24 kettle holes was sampled over a two-year period. Active (i.e., water samples) and dormant communities (i.e., dormant eggs hatched from sediment) were identified using a two-fragment DNA metabarcoding approach (COI and 18S). Species richness and diversity as well as community composition were analysed considering spatial, temporal and environmental parameters. The analysis revealed that environmental filtering based on parameters such as pH, size and location of the habitat patch (i.e., kettle hole) and surrounding field crops largely determined zooplankton community composition (explained variance: Bray-Curtis dissimilarities: 10.5\%; Jaccard dissimilarities: 12.9\%), indicating that adaptation to a particular habitat is a key feature of zooplankton species in this system. While the spatial configuration of the kettle holes played a minor role (explained variance: Bray-Curtis dissimilarities: 2.8\% and Jaccard dissimilarities: 5.5\%), the individual kettle hole sites had a significant influence on the community composition. This suggests monopolisation/priority effects (i.e., dormant communities) of certain species in individual kettle holes. As environmental filtering is the dominating process structuring zooplankton communities, this system could be significantly influenced by future land-use change, pollution and climate change.},
  language  = {en}
}
@phdthesis{Meyer2018,
  author    = {Meyer, Susann},
  title     = {Wirkung und Wirkungsweise von Ectoin auf DNA-Molek{\"u}le},
  school      = {Universit{\"a}t Potsdam},
  pages     = {103},
  year      = {2018},
  language  = {de}
}
@phdthesis{CamaraMattosMartins2011,
  author    = {Camara Mattos Martins, Marina},
  title     = {What are the downstream targets of trehalose-6-phosphate signalling in plants?},
  address   = {Potsdam},
  pages     = {164 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{Mofina2012,
  author    = {Mofina, Sabine},
  title     = {Weighing the Role of the Hypoxia Inducible Factor-1a in Tumor and Stroma for tumorigenesis},
  address   = {Potsdam},
  pages     = {IX, 132 S.},
  year      = {2012},
  language  = {en}
}
@phdthesis{Edner2008,
  author    = {Edner, Christoph},
  title     = {Wechselwirkungen zwischen Glucan, Wasser-Dikinase (GWD) und Glucan-Hydrolasen beim Abbau transitorischer Balttst{\"a}rke},
  address   = {Potsdam},
  pages     = {vi, 107 S. : graph. Darst.},
  year      = {2008},
  language  = {de}
}
@phdthesis{Warsinke2006,
  author    = {Warsinke, Axel},
  title     = {Von Enzymen zu biomimetischen Polymeren : neue Perspektiven f{\"u}r die Bioanalytik},
  address   = {Potsdam},
  pages     = {Getr. Z{\"a}hlung},
  year      = {2006},
  language  = {de}
}
@phdthesis{Mittag2011,
  author    = {Mittag, Sonnhild},
  title     = {Vom Rosetta-Stone-Protein NitFhit zur Tumorsuppressorwirkung der humanen Nitrilase1},
  address   = {Potsdam},
  pages     = {113 S.},
  year      = {2011},
  language  = {de}
}
@phdthesis{Yang2017,
  author    = {Yang, Lei},
  title     = {Verification of systemic mRNAs mobility and mobile functions},
  school      = {Universit{\"a}t Potsdam},
  pages     = {125},
  year      = {2017},
  language  = {en}
}
@phdthesis{Brueggemann2008,
  author    = {Br{\"u}ggemann, Clemens},
  title     = {Vergleichend-{\"o}kologische Untersuchungen an Laufk{\"a}ferz{\"o}nosen (Coleoptera: Carabidae) unterschiedlich strukturierter Buchenw{\"a}lder des Nationalparks Hainich (Th{\"u}ringen) unter besonderer Ber{\"u}cksichtigung der chrono-{\"o}kologischen Einnischung und der stenotopen Waldart Carabus irregularis},
  pages     = {IV, 169 S.},
  year      = {2008},
  language  = {de}
}
@phdthesis{Wolters2001,
  author    = {Wolters, Steffen},
  title     = {Vegetationsgeschichtliche Untersuchungen zur sp{\"a}tglazialen und holoz{\"a}nen Landschaftsentwicklung in der D{\"o}britzer Heide (Brandenburg)},
  pages     = {179 S. : Anh.},
  year      = {2001},
  language  = {de}
}
@phdthesis{Zimmermann2017,
  author    = {Zimmermann, Heike Hildegard},
  title     = {Vegetation changes and treeline dynamics in northern Siberia since the last interglacial revealed by sedimentary ancient DNA metabarcoding and organelle genome assembly of modern larches},
  school      = {Universit{\"a}t Potsdam},
  pages     = {138},
  year      = {2017},
  language  = {en}
}
@phdthesis{Czech2013,
  author    = {Czech, Andreas},
  title     = {Variations in the tRNA pool of mammalian cells upon differentiation and oxidative stress},
  address   = {Potsdam},
  pages     = {98 S.},
  year      = {2013},
  language  = {en}
}
@phdthesis{Pfautsch2007,
  author    = {Pfautsch, Simone},
  title     = {Variabilit{\"a}t in den Genen des Haupthistokompatibilit{\"a}tskomplexes (MHC II B) bei Entenv{\"o}geln (Anseriformes)},
  address   = {Potsdam},
  pages     = {Getr. Z{\"a}hlung : Ill., graph. Darst.},
  year      = {2007},
  language  = {de}
}
@phdthesis{Lehmann2018,
  author    = {Lehmann, Andreas},
  title     = {Variability in human life history traits},
  school      = {Universit{\"a}t Potsdam},
  pages     = {110},
  year      = {2018},
  language  = {de}
}
@phdthesis{Boehme2005,
  author    = {B{\"o}hme, Carsten},
  title     = {Validierung der Messung der Oberfl{\"a}chenkontur der Lendenwirbels{\"a}ule},
  pages     = {Vii, 57 Bl.},
  year      = {2005},
  language  = {de}
}
@phdthesis{Becher2003,
  author    = {Becher, Martina},
  title     = {Untersuchungen zur Zinkhyperakkumulation in Arabidopsis halleri auf physiologischer und molekularbiologischer Ebene},
  pages     = {102, X, XIV S. : graph. Darst.},
  year      = {2003},
  language  = {de}
}
@phdthesis{Geigenberger2006,
  author    = {Geigenberger, Peter Ludwig},
  title     = {Untersuchungen zur Regulation der Kohlenstoffspeicherung in Pflanzen},
  publisher = {Golm},
  pages     = {45 S. : graph. Darst.},
  year      = {2006},
  language  = {de}
}
@phdthesis{Pruefer2014,
  author    = {Pr{\"u}fer, Nicole},
  title     = {Untersuchungen zur pro-inflammatorischen Wirkung von Serum-Amyloid A in glatten Gef{\"a}ßmuskelzellen},
  pages     = {XIII, 98},
  year      = {2014},
  language  = {de}
}
@phdthesis{Fuenfhaus2013,
  author    = {F{\"u}nfhaus, Anne},
  title     = {Untersuchungen zur molekularen Pathogenese der amerikanischen Faulbrut der Honigbiene},
  address   = {Potsdam},
  pages     = {136 S.},
  year      = {2013},
  language  = {de}
}
@phdthesis{Maimann2000,
  author    = {Maimann, Stefanie},
  title     = {Untersuchungen zur in vivo-Funktion der Cystathionin ß-layase in der Methioninbiosynthese h{\"o}herer Pflanzen},
  pages     = {124 S.},
  year      = {2000},
  language  = {de}
}
@phdthesis{Duwenig1996,
  author    = {Duwenig, Elke},
  title     = {Untersuchungen zur Funktion von alpha-1,4-Glucan-Phosphorylasen in h{\"o}heren Pflanzen},
  address   = {Potsdam},
  pages     = {117 S. : Ill.},
  year      = {1996},
  language  = {de}
}
@phdthesis{Jeske1992,
  author    = {Jeske, Kerstin},
  title     = {Untersuchungen zur Entstehung morphogenetisch unterschiedlicher Kallustypen bei Beta vulgaris L.},
  pages     = {107 Bl. : Ill., graph. Darst.},
  year      = {1992},
  language  = {de}
}
@phdthesis{Reschke2013,
  author    = {Reschke, Stefan},
  title     = {Untersuchungen zur Bildung und Modifizierung des Molybd{\"a}ncofaktors und dessen Einbau in Molybdoenzyme},
  address   = {Potsdam},
  pages     = {133 S.},
  year      = {2013},
  language  = {de}
}
@phdthesis{Dombrowski1992,
  author    = {Dombrowski, Mike},
  title     = {Untersuchungen zum Verhalten der Deutschen Schabe, Blattella germanica L. gegen{\"u}ber pflanzlichen Repellents},
  pages     = {133 Bl. : Ill. + Thesen (1 Ex.)},
  year      = {1992},
  language  = {de}
}
@phdthesis{Wenzel2007,
  author    = {Wenzel, Kathrin},
  title     = {Untersuchungen zum Citramalatstoffwechsel in Arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {VI, 146 S.: Ill., graph. Darst.},
  year      = {2007},
  language  = {de}
}
@phdthesis{Wenzel2007,
  author    = {Wenzel, Kathrin},
  title     = {Untersuchungen zum Citramalatstoffwechsel in Arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {146 S., II-V, : graph. Darst.},
  year      = {2007},
  language  = {de}
}
@phdthesis{Bergmueller2003,
  author    = {Bergm{\"u}ller, Eveline},
  title     = {Untersuchungen zu physiologischen Bedeutung von Tocopherol (Vitamin E) und zum Lipid-Metabolismus in Arabidopsis thaliana},
  pages     = {107 S.},
  year      = {2003},
  language  = {de}
}
@phdthesis{Kreft2002,
  author    = {Kreft, Oliver},
  title     = {Untersuchungen zu in vivo-Funktion der Cystathionin y-Synthase in der Methioninbiosynthese h{\"o}herer Pflanzen},
  pages     = {103 S.},
  year      = {2002},
  language  = {de}
}
@phdthesis{Voigt1994,
  author    = {Voigt, Manfred},
  title     = {Untersuchungen und Vorschl{\"a}ge zur Verbesserung der Klassifikation des somatischen Entwicklungsstandes Neugeborener unter besonderer Ber{\"u}cksichtigung des Geburtsgewichtes : Mehrdimensionale Analyse der Beziehungsstruktur zwischen anthropometrischen Maßen der Eltern - besonders der M{\"u}tter - und ihrer Neugeborenen ; Hauptbd.},
  pages     = {111 Bl.},
  year      = {1994},
  language  = {de}
}
@phdthesis{Voigt1994,
  author    = {Voigt, Manfred},
  title     = {Untersuchungen und Vorschl{\"a}ge zur Verbesserung der Klassifikation des somatischen Entwicklungsstandes Neugeborener unter besonderer Ber{\"u}cksichtigung des Geburtsgewichtes : Mehrdimensionale Analyse der Beziehungsstruktur zwischen anthropometrischen Maßen der Eltern - besonders der M{\"u}tter - und ihrer Neugeborenen ; Anlagenbd.},
  pages     = {102 S.},
  year      = {1994},
  language  = {de}
}
@phdthesis{Lehmann2000,
  author    = {Lehmann, Claudia},
  title     = {Untersuchungen des Selenoenzyms Phospholipidhydroperoxid-Glutathionperoxidase an modifizierten Elektroden},
  pages     = {99 S.},
  year      = {2000},
  language  = {de}
}
@phdthesis{Apel2009,
  author    = {Apel, Wiebke},
  title     = {Untersuchung und Ver{\"a}nderung der Genexpression und Proteinstabilit{\"a}t in Plastiden h{\"o}herer Pflanzen},
  address   = {Potsdam},
  pages     = {112 S.},
  year      = {2009},
  language  = {de}
}
@phdthesis{Schmidt2013,
  author    = {Schmidt, Stefanie},
  title     = {Untersuchung des Einflusses der stressregulierten rei1 homologen Proteine auf die Physiologie und den Metabolismus von Arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {106, XXII S.},
  year      = {2013},
  language  = {de}
}
@phdthesis{Schimkat2006,
  author    = {Schimkat, Jan},
  title     = {Untersuchung der Populationsdynamik von Regionalbest{\"a}nden ostziehender Weißst{\"o}rche (Ciconia ciconia) mittels eines Simulationsmodells},
  address   = {Potsdam},
  pages     = {128 S. : graph. Darst.},
  year      = {2006},
  language  = {de}
}
@phdthesis{Wiegand2012,
  author    = {Wiegand, Kathlen},
  title     = {Untersuchung der Auswirkung von Trockenstress auf verschiedene K{\"u}rbisgew{\"a}chse unter spezieller Betrachtung des Phloems},
  address   = {Potsdam},
  pages     = {102 S.},
  year      = {2012},
  language  = {de}
}
@phdthesis{ShahnejatBushehri2016,
  author    = {Shahnejat-Bushehri, Sara},
  title     = {Unravelling the role of the Arabidopsis NAC transcription factor JUNGBRUNNEN1 (JUB1) for the regulation of growth and stress responses},
  school      = {Universit{\"a}t Potsdam},
  pages     = {155},
  year      = {2016},
  language  = {en}
}
@phdthesis{Nguyen2022,
  author    = {Nguyen, Van Thanh},
  title     = {Unravelling the mysteries of the Annamites},
  school      = {Universit{\"a}t Potsdam},
  pages     = {116},
  year      = {2022},
  abstract  = {The Annamites mountain range of Southeast Asia which runs along the border of Viet Nam and Laos is an important biodiversity hotspot with high levels of endemism. However, that biodiversity is threatened by unsustainable hunting, and many protected areas across the region have been emptied of their wildlife. To better protect the unique species in the Annamites, it is crucial to have a better understanding of their ecology and distribution. Additionally, basic genetic information is needed to provide conservation stakeholders with essential information to facilitate conservation breeding and counteract the illegal wildlife trade. To date, this baseline information is lacking for many Annamites species. This thesis aims to assess the effectiveness of using non-invasive collection methods, i.e. camera-trap surveys and leech-derived wildlife host DNA, in order to improve and enhance our understanding of ecology, distribution, and genetic diversity of the Annamites terrestrial mammals. In chapter 1, we analysed data from a systematic landscape camera-trap survey using single-species occupancy models to assess the ecology and distribution of two little-known Annamite endemics, the Annamite dark muntjac (Muntiacus rooseveltorum / truongsonensis) and Annamite striped rabbit (Nesolagus timminsi), in multiple protected areas across the Annamites. This chapter provided the first in-depth information on their ecology, as well as distribution patterns at large spatial scales. Most notably, we found that the Annamite dark muntjac was predominantly found at higher elevations, while responses to elevation varied among study areas for the Annamite striped rabbit. We estimated occupancy probabilities for both endemics by using their responses to environmental and anthropogenic influences and used this information to make recommendations for targeted conservation actions. We discuss how the approach we used for these two Annamites endemics can be expanded for other little-known and threatened species in other tropical regions. As is the case with ecology and distribution, very little is known about the genetic diversity of the Annamite striped rabbit and other mammals of the Annamites. This poor understanding is mainly attributed to the lack of a comprehensive DNA sample collection that covers the species' entire distribution range, which is believed to be a consequence of the low density of mammals or the remoteness of species' habitat. In order to overcome the difficulties when trying to collect DNA samples from elusive mammals, we applied invertebrate-derived DNA (iDNA) sampling via hematophagous leeches to indirectly obtain genetic materials of their terrestrial host mammals. In chapter 2, leech-derived DNA was used to study the genetic diversity of the Annamite striped rabbit population. By analysing the DNA extracted from leech samples collected at multiple study areas of the central Annamites, we found a genetic variation with five haplotypes among nine obtained sequences. Despite this diversity, we found no clear phylogeographic pattern among the lagomorph's populations in central Annamites. The findings have direct conservation implications for the species, as local stakeholders are currently establishing a conservation rescue and breeding facility for Annamite endemic species. Thus our results suggested that Annamite striped rabbits from multiple protected areas in central Annamites can be used as founders for the breeding program. In chapter 3, the genetic material of six mammals, which are frequently found in Indochina's illegal wildlife trade, was extracted from leeches collected at six study sites across the Anamites. Species-specific genetic markers were used to obtain DNA fragments that were analysed together with Genbank reference sequences from other parts of the species' distribution range. Our results showed that invertebrate-derived DNA can be used to fill the sampling gaps and provide genetic reference data that is needed for conservation breeding programmes or to counteract the illegal wildlife trade. Overal, this dissertation provides the first insights in the ecology, distribution, and genetics of rare and threatened species of the Annamites by utilising camera traps and leech-derived DNA as two non-invasive collection methods. This information is essential for improving conservation efforts of local stakeholders and managers, especially for the Annamite endemics. Results in this dissertation also show the effectiveness of both non-invasive methods for studying terrestrial mammals at a landscape level. By expanding the application of these methods to other protected areas across the Annamites, we will further our understanding of ecology, distribution, and genetics of Annamite endemics. With such landscape-scale surveys, we are able to provide stakeholders with an overview of the current status of wildlife in the Annamites which supports efforts to protect these secretive species from illegal hunting and thus their extinction.},
  language  = {en}
}
@phdthesis{Sedaghatmehr2017,
  author    = {Sedaghatmehr, Mastoureh},
  title     = {Unraveling the regulatory mechanisms of heat stress memory in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {176},
  year      = {2017},
  language  = {en}
}
@phdthesis{Zhang2018,
  author    = {Zhang, Yunming},
  title     = {Understanding the functional specialization of poly(A) polymerases in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {131},
  year      = {2018},
  language  = {de}
}
@phdthesis{Weiss2017,
  author    = {Weiß, Lina},
  title     = {Understanding the emergence and maintenance of biodiversity in grasslands},
  school      = {Universit{\"a}t Potsdam},
  pages     = {153},
  year      = {2017},
  language  = {en}
}
@phdthesis{Ogden2022,
  author    = {Ogden, Michael},
  title     = {Uncovering the interplay between nutrient availability and cellulose biosynthesis inhibitor activity},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XI, 124},
  year      = {2022},
  abstract  = {All plant cells are surrounded by a dynamic, carbohydrate-rich extracellular matrix known as the cell wall. Nutrient availability affects cell wall composition via uncharacterized regulatory mechanisms, and cellulose deficient mutants develop a hypersensitive root response to growth on high concentrations of nitrate. Since cell walls account for the bulk of plant biomass, it is important to understand how nutrients regulate cell walls. This could provide important knowledge for directing fertilizer treatments and engineering plants with higher nutrient use efficiency. The direct effect of nitrate on cell wall synthesis was investigated through growth assays on varying concentrations of nitrate, measuring cellulose content of roots and shoots, and assessing cellulose synthase activity (CESA) using live cell imaging with spinning disk confocal microscopy. A forward genetic screen was developed to isolate mutants impaired in nutrient-mediated cell wall regulation, revealing that cellulose biosynthesis inhibitor (CBI) activity is modulated by nutrient availability. Various non-CESA mutants were isolated that displayed CBI resistance, with the majority of mutations causing perturbation of mitochondria-localized proteins. To investigate mitochondrial involvement, the CBI mechanism of action was investigated using a reverse genetic screen, a targeted pharmacological screen, and -omics approaches. The results generated suggest that CBI-induced cellulose inhibition is due to off-target effects. This provides the groundwork to investigate uncharacterized processes of CESA regulation and adds valuable knowledge to the understanding of CBI activity, which could be harnessed to develop new and improved herbicides.},
  language  = {en}
}
@phdthesis{Sarlet2023,
  author    = {Sarlet, Adrien},
  title     = {Tuning the viscoelasticity of Escherichia coli biofilms},
  school      = {Universit{\"a}t Potsdam},
  pages     = {143},
  year      = {2023},
  abstract  = {Biofilms are heterogeneous structures made of microorganisms embedded in a self-secreted extracellular matrix. Recently, biofilms have been studied as sustainable living materials with a focus on the tuning of their mechanical properties. One way of doing so is to use metal ions. In particular biofilms have been shown to stiffen in presence of some metal cations and to soften in presence of others. However, the specificity and the determinants of those interactions vary between species. While Escherichia coli is a widely studied model organism, little is known concerning the response of its biofilms to metal ions. In this work, we aimed at tuning the mechanics of E. coli biofilms by acting on the interplay between matrix composition and metal cations. To do so, we worked with E. coli strains producing a matrix composed of curli amyloid fibres or phosphoethanolamine-cellulose (pEtN-cellulose) fibres or both. The viscoelastic behaviour of the resulting biofilms was investigated with rheology after incubation with one of the following metal ion solutions: FeCl3, AlCl3, ZnCl2 and CaCl2 or ultrapure water. We observed that the strain producing both fibres stiffen by a factor of two when exposed to the trivalent metal cations Al(III) and Fe(III) while no such response is observed for the bivalent cations Zn(II) and Ca(II). Strains producing only one matrix component did not show any stiffening in response to either cation, but even a small softening. In order to investigate further the contribution of each matrix component to the mechanical properties, we introduced additional bacterial strains producing curli fibres in combination with non-modified cellulose, non-modified cellulose only or neither component. We measured biofilms produced by those different strains with rheology and without any solution. Since rheology does not preserve the architecture of the matrix, we compared those results to the mechanical properties of biofilms probed with the non-destructive microindentation. The microindentation results showed that biofilm stiffness is mainly determined by the presence of curli amyloid fibres in the matrix. However, this clear distinction between biofilm matrices containing or not containing curli is absent from the rheology results, i.e. following partial destruction of the matrix architecture. In addition, rheology also indicated a negative impact of curli on biofilm yield stress and flow stress. This suggests that curli fibres are more brittle and therefore more affected by the mechanical treatments. Finally, to examine the molecular interactions between the biofilms and the metal cations, we used Attenuated total reflectance - Fourier transform infrared spectroscopy (ATR-FTIR) to study the three E.coli strains producing a matrix composed of curli amyloid fibres, pEtN-cellulose fibres or both. We measured biofilms produced by those strains in presence of each of the aforementioned metal cation solutions or ultrapure water. We showed that the three strains cannot be distinguished based on their FTIR spectra and that metal cations seem to have a non-specific effect on bacterial membranes in absence of pEtN-cellulose. We subsequently conducted similar experiments on purified curli or pEtN-cellulose fibres. The spectra of the pEtN-cellulose fibres revealed a non-valence-specific interaction between metal cations and the phosphate of the pEtN-modification. Altogether, these results demonstrate that the mechanical properties of E. coli biofilms can be tuned via incubation with metal ions. While the mechanism involving curli fibres remains to be determined, metal cations seem to adsorb onto pEtN-cellulose and this is not valence-specific. This work also underlines the importance of matrix architecture to biofilm mechanics and emphasises the specificity of each matrix composition.},
  language  = {en}
}
@phdthesis{Mohr2001,
  author    = {Mohr, Silvia},
  title     = {Trophic interactions between two Brachionus species and protozoans},
  pages     = {79 S.},
  year      = {2001},
  language  = {en}
}
@phdthesis{Wanner2000,
  author    = {Wanner, Susanne C.},
  title     = {Transport, retention, and turnover of particulate organic matter (POM) in the lowland River Spree (Germany)},
  pages     = {101 S.},
  year      = {2000},
  language  = {en}
}
@phdthesis{Pieritz2010,
  author    = {Pieritz, Janin},
  title     = {Transport von Proteinen und mikro RNAs im Pholoem von Brassica napus und Arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {105 S.},
  year      = {2010},
  language  = {de}
}
@phdthesis{Rogalski2008,
  author    = {Rogalski, Marcelo},
  title     = {Translation in plastids : elucidation of decoding mechanisms and functions of ribosomal components},
  address   = {Potsdam},
  pages     = {Getr. Z{\"a}hl. : Ill., graph. Darst.},
  year      = {2008},
  language  = {en}
}
@phdthesis{Zhang2009,
  author    = {Zhang, Gong},
  title     = {Transient ribosomal attenuation as a generic mechanism to coordinate protein biosynthesis and biogenesis},
  address   = {Potsdam},
  pages     = {114 S.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Loiacono2017,
  author    = {Loiacono, Filomena Vanessa},
  title     = {Transfer of chloroplast RNA editing events between species},
  school      = {Universit{\"a}t Potsdam},
  pages     = {155},
  year      = {2017},
  language  = {en}
}
@phdthesis{Soja2014,
  author    = {Soja, Aleksandra Maria},
  title     = {Transcriptomic and metabolomic analysis of Arabidopsis thaliana during abiotic stress},
  pages     = {134},
  year      = {2014},
  language  = {en}
}
@phdthesis{Hameed2010,
  author    = {Hameed, Muhammad Waqar},
  title     = {Transcriptional and translational control of mitochondrial gene expression in plants},
  address   = {Potsdam},
  pages     = {III, 118 Bl. : graph. Darst.},
  year      = {2010},
  language  = {en}
}
@phdthesis{Najafabadi2009,
  author    = {Najafabadi, Masood Soltani},
  title     = {Transcription factor networks in the initial ohase of drouht stress in rice (Oryza sativa L.)},
  address   = {Potsdam},
  pages     = {II, 144 S. : Ill., graph. Darst.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Ebert2008,
  author    = {Ebert, Berit},
  title     = {Transcript, protein and metabolite analysis of Arabidopsis thaliana Trichomes},
  pages     = {IX, 173 S.},
  year      = {2008},
  language  = {en}
}
@phdthesis{Chai2008,
  author    = {Chai, Yan},
  title     = {Traffic of molecular motors},
  pages     = {87 S.},
  year      = {2008},
  language  = {en}
}
@phdthesis{Jehle2019,
  author    = {Jehle, Franziska},
  title     = {Tracking self-assembly of hierarchically structured soft matter},
  school      = {Universit{\"a}t Potsdam},
  pages     = {88},
  year      = {2019},
  language  = {en}
}
@phdthesis{Wutke2016,
  author    = {Wutke, Saskia},
  title     = {Tracing Changes in Space and Time},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 84},
  year      = {2016},
  abstract  = {The horse is a fascinating animal symbolizing power, beauty, strength and grace. Among all the animal species domesticated the horse had the largest impact on the course of human history due to its importance for warfare and transportation. Studying the process of horse domestication contributes to the knowledge about the history of horses and even of our own species. Research based on molecular methods has increasingly focused on the genetic basis of horse domestication. Mitochondrial DNA (mtDNA) analyses of modern and ancient horses detected immense maternal diversity, probably due to many mares that contributed to the domestic population. However, mtDNA does not provide an informative phylogeographic structure. In contrast, Y chromosome analyses displayed almost complete uniformity in modern stallions but relatively high diversity in a few ancient horses. Further molecular markers that seem to be well suited to infer the domestication history of horses or genetic and phenotypic changes during this process are loci associated with phenotypic traits. This doctoral thesis consists of three different parts for which I analyzed various single nucleotide polymorphisms (SNPs) associated with coat color, locomotion or Y chromosomal variation of horses. These SNPs were genotyped in 350 ancient horses from the Chalcolithic (5,000 BC) to the Middle Ages (11th century). The distribution of the samples ranges from China to the Iberian Peninsula and Iceland. By applying multiplexed next-generation sequencing (NGS) I sequenced short amplicons covering the relevant positions: i) eight coat-color-associated mutations in six genes to deduce the coat color phenotype; ii) the so-called 'Gait-keeper' SNP in the DMRT3 gene to screen for the ability to amble; iii) 16 SNPs previously detected in ancient horses to infer the corresponding haplotype. Based on these data I investigated the occurrence and frequencies of alleles underlying the respective phenotypes as well as Y chromosome haplotypes at different times and regions. Also, selection coefficients for several Y chromosome lineages or phenotypes were estimated. Concerning coat color differences in ancient horses my work constitutes the most comprehensive study to date. I detected an increase of chestnut horses in the Middle Ages as well as differential selection for spotted and solid phenotypes over time which reflects changing human preferences. With regard to ambling horses, the corresponding allele was present in medieval English and Icelandic horses. Based on these results I argue that Norse settlers, who frequently invaded parts of Britain, brought ambling individuals to Iceland from the British Isles which can be regarded the origin of this trait. Moreover, these settlers appear to have selected for ambling in Icelandic horses. Relating to the third trait, the paternal diversity, these findings represent the largest ancient dataset of Y chromosome variation in non-humans. I proved the existence of several Y chromosome haplotypes in early domestic horses. The decline of Y chromosome variation coincides with the movement of nomadic peoples from the Eurasian steppes and later with different breeding practices in the Roman period. In conclusion, positive selection was estimated for several phenotypes/lineages in different regions or times which indicates that these were preferred by humans. Furthermore, I could successfully infer the distribution and dispersal of horses in association with human movements and actions. Thereby, a better understanding of the influence of people on the changing appearance and genetic diversity of domestic horses could be gained. My results also emphasize the close relationship of ancient genetics and archeology or history and that only in combination well-founded conclusions can be reached.},
  language  = {en}
}
@phdthesis{KnoxBrown2021,
  author    = {Knox-Brown, Patrick Frank},
  title     = {Towards understanding the sequence-structure-function relationship of intrinsically disordered LEA_4 proteins from Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {172, XI},
  year      = {2021},
  abstract  = {Water-deficits can cause lethal damage to organisms, which is rooted in cellular dehydration. Many plant species, but also other organisms have developed mechanisms to tolerate such stresses, such as the expression of LEA proteins. Many studies report on physiological protective functions of LEA proteins but lack information about their precise mechanisms on a molecular level. Most LEA proteins are intrinsically disordered in dilute solution but may adopt a distinct secondary structure upon changes in solvent conditions. Understanding the molecular mechanism of how LEA proteins contribute to the counteraction of cellular damage during water-deficits may in the long-term pave the way for breeding crops that are resistant to the effects of global warming. The objective of the work at hand is to improve the biophysical understanding of the sequencestructure-function relationship of LEA proteins as membrane stabilizers, based on the LEA_4 family of the model plant A. thaliana. This is pursued by using a combination of spectroscopic and scattering techniques, supported by bioinformatics and computational analyses. Eight out of the 18 LEA_4 proteins are experimentally assessed revealing that a coil-helix transition in response to water-deficit is a common feature, as predicted for the entire family. In addition, they all stabilize simple membrane models during a freeze/ thaw cycle. Three-dimensional structure prediction of representative members suggests that their completely folded states are represented by a sequential arrangement of alpha-helical segments connected by unstructured linkers, which is experimentally verified for the LEA_4 protein COR15A. The unstructured linker region of COR15A represents a conserved motif among its closest homologs and is, therefore, of particular interest. Facilitating a set of seven designed and investigated COR15A mutants uncovers a complex interplay of transient interactions between the amphipathic alpha-helical segments, mediated by the linker, which fine-tunes folding transitions and structural ensembles upon reduced water-availability. Finally, alpha-helicity is also induced in COR15A upon temperature decrease, which is enhanced in the presence of osmolytes. In addition, high solution osmolarity induced secondary structure is followed by oligomerization of COR15A. Interestingly, the functionality of COR15A, in terms of liposome stabilization, strongly correlates with its alpha-helix ratio in the folded state. The present work significantly improves the understanding of the sequence-structure-function relationship for LEA_4 proteins and offers novel findings on folding mechanisms and oligomerization of COR15A.},
  language  = {en}
}
@phdthesis{Sun2011,
  author    = {Sun, Xiaoliang},
  title     = {Towards understanding the dynamics of biological systems from -Omics data},
  address   = {Potsdam},
  pages     = {114 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{MartinezJaime2017,
  author    = {Mart{\´i}nez Jaime, Silvia},
  title     = {Towards the understanding of protein function and regulation},
  school      = {Universit{\"a}t Potsdam},
  pages     = {131},
  year      = {2017},
  language  = {en}
}
@phdthesis{Santos2010,
  author    = {Santos, Francisca dos},
  title     = {Towards a mechanistic understanding of species and community responses to climate change : the role of disturbances interaction},
  address   = {Potsdam},
  pages     = {89 S.},
  year      = {2010},
  language  = {en}
}
@phdthesis{Lachmuth2011,
  author    = {Lachmuth, Susanne},
  title     = {Towards a mechanistic understanding of how demography, genetic differentiation and environmental factors interact to generate the invasion dynamics of senecio inaequidens},
  address   = {Potsdam},
  pages     = {172 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{Morozova2007,
  author    = {Morozova, Daria},
  title     = {Tolerance limits and survival potential of methanogenic archaea from Siberian permafrost under extreme liveing conditions},
  address   = {Potsdam},
  pages     = {VI, 97 S. : graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Lukas2014,
  author    = {Lukas, Marcus},
  title     = {To breath or not to breathe - carbon budget regulation in Daphnia},
  address   = {Potsdam},
  pages     = {132 S.},
  year      = {2014},
  language  = {en}
}
@phdthesis{Rocha2011,
  author    = {Rocha, Marcia Rosa},
  title     = {Time series analysis reveals links between functional traits, population dynamics and ecosystem functions in a diverse phytoplankton community},
  address   = {Potsdam},
  pages     = {126 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{Fiedler2013,
  author    = {Fiedler, Sebastian},
  title     = {Thermodynamic stability of the a-Helical membrane-interacting protein mistic in detergent micelles},
  address   = {Potsdam},
  pages     = {99 S.},
  year      = {2013},
  language  = {en}
}
@phdthesis{Jin2015,
  author    = {Jin, Chenyu},
  title     = {Theoretical and experimental study of capillary effect on melting},
  pages     = {97},
  year      = {2015},
  language  = {en}
}
@phdthesis{UlbrichtJones2017,
  author    = {Ulbricht-Jones, Elena Sofia},
  title     = {The virescent and narrow leaf phenotype of a plastome-genome-incompatible Oenothera hybrid is associated with the plastid gene accD and fatty acid synthesis},
  school      = {Universit{\"a}t Potsdam},
  pages     = {124},
  year      = {2017},
  language  = {en}
}
@phdthesis{Seibert,
  author    = {Seibert, Tanja Stefanie},
  title     = {The T6P pathway in Solanum tuberosum},
  pages     = {212},
  language  = {en}
}
@phdthesis{Fichtner2017,
  author    = {Fichtner, Franziska},
  title     = {The role of Trehalose 6-Phosphate synthase 1 and trehalose 6-phosphate in plant metabolism and development},
  school      = {Universit{\"a}t Potsdam},
  pages     = {225},
  year      = {2017},
  language  = {en}
}
@phdthesis{Radloff2018,
  author    = {Radloff, Katrin},
  title     = {The role of the fatty acid profile and its modulation by cytokines in the systemic inflammation in cancer cachexia},
  school      = {Universit{\"a}t Potsdam},
  pages     = {156},
  year      = {2018},
  language  = {en}
}
@phdthesis{Heyneke2015,
  author    = {Heyneke, Elmien},
  title     = {The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism},
  school      = {Universit{\"a}t Potsdam},
  pages     = {135},
  year      = {2015},
  language  = {en}
}
@phdthesis{Peng2023,
  author    = {Peng, Maolin},
  title     = {The role of prion-like domains in plant temperatur sensing},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XVI, 121},
  year      = {2023},
  language  = {en}
}
@phdthesis{CruzCenteno2009,
  author    = {Cruz Centeno, Danilo da},
  title     = {The role of malate in the development of tomato fruit},
  address   = {Potsdam},
  pages     = {IV, 113 Bl. : Ill., graph. Darst.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Haensel2007,
  author    = {H{\"a}nsel, Ulrike},
  title     = {The role of hemicelluloses in plant growth and development},
  address   = {Potsdam},
  pages     = {VIII, 133 S. : graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Qin2022,
  author    = {Qin, Miaojing},
  title     = {The role of heat shock proteins (HSP23s and HSP70-4) for heat stress memory in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {138},
  year      = {2022},
  abstract  = {Heat is a significant climatic condition that threatens crop growth and survival. Extreme temperature occurrences in nature are becoming more severe, more frequent and longer-lasting, all of which have deleterious repercussions for agricultural production. As a result, it is critical to learn more about the mechanisms that lead to increased heat tolerance in plants. To endure and survive, higher plants have evolved complex mechanisms to respond to various amounts of heat stress. Plants have a thermal tolerance that permits them to survive rapid and dramatic temperature rises for a limited time. Plants can also be primed to withstand heat stress (HS) that would otherwise be lethal by exposing them to short, moderate, and non-lethal HS (referred to as a priming stimulus) before being exposed to severe HS. A prepared acquired thermotolerance in primed plants can be maintained for a long time under optimal circumstances, implying that plants can store information during this period. Several studies have shown that acquired thermotolerance (thermopriming) refers to the increased resistance of cells, tissues, and organisms to elevated temperatures after prior heat exposure. Maintenance of acquired thermotolerance (thermomemory) is associated with the synthesis of specialized stress proteins involved in cellular protection and accelerated tissue repair, such as heat shock proteins (HSPs). Recent studies showed a main role of heat shock proteins for turnover of protein quality components, e.g. HSP21 in the chloroplast in the regulation of thermomemory. As an important organelle, mitochondrial function is critical for plant cell responses to heat. However, it is still unknown what the molecular and physiological involvement of HSPs is in mitochondrial function and thermomemory. In our study, we showed that thermopriming induces transcript and protein levels of two mitochondrial small heat shock proteins, HSP23.5 (AT5G51440) and HSP23.6 (AT4G25200), which last for 2-3 days throughout the thermomemory phase. The morphological analysis of HSP23.5/6 transgenic plants demonstrated HSP23.5/6 function redundantly in heat stress. We showed that hsp23.5/6 double knockout plants had abnormalities in thermomemory at the seedling stage, and that mature hsp23.5/6 4 plants are more sensitive to both basal thermotolerance and thermomemory. Heat treatment significantly impacted the respiration rate of hsp23.5/6 seedlings compared to WT, indicating mitochondrial dysfunction dependent on HSP23.5 and HSP23.6. In addition, we tested and confirmed the chaperone activity of HSP23.6 toward the model substrate protein malate dehydrogenase (MDH) in vitro, indicating that HSP23.6 potentially contributes to the maintenance of cellular viability. Furthermore, we discovered a novel HSP23.6 client protein, CIB22, a mitochondrial complex-I subunit protein. According to experimental data (BiFC and Co-IP), HSP23.6 and CIB22 interact in plant cells. We also identified a heat response phenotype in the cib22 mutant compared to WT, as well as CIB22 protein degradation in the hsp23.5/6 mutant when exposed to heat. Our findings suggest that the two mitochondrial-localized heat shock proteins play a role in thermotolerance, presumably by influencing mitochondrial function and structure. More broadly, to identify novel genetic components associated with thermomemory in plants, we performed proteome profiling for Arabidopsis WT (Col-0) seedlings during thermomemory. Multiple time point samples of priming and triggering with controls were collected and analyzed to reveal the dynamic proteome changes during the memory phase in Arabidopsis cells. Among the top memory-associated proteins, we discovered that HSP70-4 was significantly upregulated after priming and remains high (at least 2-fold) for the next four days. By morphologically analyzing their heat stress behaviors, we were able to verify that HSP70-4 is involved in plant heat stress response. More intriguingly, we discovered that following priming, HSP70-4-GFP creates cytosolic foci that persist for a few days into the recovery period. We propose that these foci are linked to SGs due to cycloheximide (CHX) repressing the GFP-foci signal when exposed to heat. These findings indicate an HSP70-4-mediated transcription and translation control link (module) during basal thermotolerance and thermomemory, as well as its potential role(s) in heat stress response. To summarize, our research provides new insight into the role of heat shock proteins in controlling heat stress tolerance and memory.},
  language  = {de}
}
@phdthesis{Schulz2014,
  author    = {Schulz, Elisa},
  title     = {The role of flavonols and anthocyanins in the cold an UV-B acclimation of Arabidopsis thaliana (L.)},
  pages     = {159},
  year      = {2014},
  language  = {en}
}
@phdthesis{Buehler2023,
  author    = {B{\"u}hler, Miriam},
  title     = {The role of (xeno)hormone-activated GPER1 for centrosome amplification and whole chromosomal instability in colon cell lines},
  school      = {Universit{\"a}t Potsdam},
  pages     = {IX, 144},
  year      = {2023},
  abstract  = {The G protein-coupled estrogen receptor (GPER1) is acknowledged as an important mediator of estrogen signaling. Given the ubiquitous expression of GPER1, it is likely that the receptor plays a role in a variety of malignancies, not only in the classic hormonally regulated tissues (e.g., breast, ovary, and prostate), but also in the colon. As colorectal cancer (CRC) is the third most common cancer in both men and women worldwide and environmental factors and dietary habits are important risk factors, it is increasingly recognized that natural and synthetic hormones and their associated receptors might play a role in CRC. Through oral consumption, environmental contaminants with endocrine activity are in contact with the gastrointestinal mucosa, where they might exert their toxic effects. Although GPER1 has been shown to be engaged in physiological and pathophysiological processes, its role in CRC remains poorly understood. Thus, pro- as well as anti-tumorigenic effects are described in the literature. This thesis has uncovered novel roles of GPER1 in mediating major CRC-associated phenotypes in transformed and non-transformed colon cell lines. Exposure to the estrogens 17β-estradiol (E2), bisphenol-A (BPA) and diethylstilbestrol (DES) but also the androgen dihydrotestosterone (DHT) resulted in GPER1-dependent induction of supernumerary centrosomes, whole chromosomal instability (w-CIN) and aneuploidy. Indeed, both knockdown and inhibition of GPER1 attenuated the generation of (xeno)hormone-driven supernumerary centrosomes and karyotype instability. Mechanistically, (xeno)hormone-induced centrosome amplification was associated with transient multipolar mitosis and the generation of so called anaphase "lagging" chromosomes. The results of this thesis propose a GPER1/PKA/AKAP9-pathway in regulating centrosome numbers in colorectal cancer cells and the involvement of the centriolar protein centrin. Remarkably, exposure to (xeno)hormones resulted in atypical enlargement and unexpected phosphorylation of the centriole marker centrin in interphase. These findings provide a novel role for GPER1 in key CRC-prone lesions and shed light on underlying mechanisms that involve GPER1 function in the colon. Elucidating to what extent centrosomal proteins are involved in the GPER1-mediated aneugenic effect will be an important task for future studies. The present study was intended to lay a first foundation to understand the molecular basis and potential risk factors of CRC which might help to reduce the use of laboratory animals. Since numerous animal experiments are conducted in biomedical research, the development of alternative methods is indispensable. The Federal Institute for Risk Assessment (BfR) as the German Center for the Protection of Laboratory Animals (Bf3R) addresses this issue by uncovering underlying mechanisms leading to colorectal cancer as necessary prerequisite in order to develop alternative methods.},
  language  = {en}
}
@phdthesis{Merwe2008,
  author    = {Merwe, Johanna van der},
  title     = {The role and regulation of the tricarboxylic acid cycle in Solanum lycopersicum roots},
  address   = {Potsdam},
  pages     = {X, 112 Doppels., [10] S.. : Ill., graph. Darst.},
  year      = {2008},
  language  = {en}
}
@phdthesis{Tschoep2009,
  author    = {Tschoep, Hendrik},
  title     = {The response of growth and primary metabolism to a mild but sustained nitrogen limitation in arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {176 S.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Bauer2011,
  author    = {Bauer, Barbara},
  title     = {The relevance of species traits for predicting the dynamics of diverse plankton communities},
  address   = {Potsdam},
  pages     = {190 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{Wagner2007,
  author    = {Wagner, Kerstin},
  title     = {The regulation of phopholipase activity by lipid membrane structure},
  address   = {Potsdam},
  pages     = {105 S. :graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Zupok2015,
  author    = {Zupok, Arkadiusz},
  title     = {The psbB-operon is a major locus for plastome-genome incompatibility in Oenothera},
  school      = {Universit{\"a}t Potsdam},
  pages     = {108},
  year      = {2015},
  language  = {en}
}
@phdthesis{Hoelscher2020,
  author    = {Hoelscher, Matthijs Pieter},
  title     = {The production of antimicrobial polypeptides in chloroplasts},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiii, 114},
  year      = {2020},
  abstract  = {Plants are an attractive platform for the production of medicinal compounds because of their potential to generate large amounts of biomass cheaply. The use of chloroplast transformation is an attractive way to achieve the recombinant production of proteins in plants, because of the chloroplasts' high capacity to produce foreign proteins in comparison to nuclear transformed plants. In this thesis, the production of two different types of antimicrobial polypeptides in chloroplasts is explored. The first example is the production of the potent HIV entry inhibitor griffithsin. Griffithsin has the potential to prevent HIV infections by blocking the entry of the virus into human cells. Here the use of transplastomic plants as an inexpensive production method for griffithsin was explored. Transplastomic plants grew healthily and were able to accumulate griffithsin to up to 5\% of the total soluble protein. Griffithsin could easily be purified from tobacco leaf tissue and had a similarly high neutralization activity as griffithsin recombinantly produced in bacteria. Griffithsin could be purified from dried tobacco leaves, demonstrating that dried leaves could be used as a storable starting material for griffithsin purification, circumventing the need for immediate purification after harvest. The second example is the production of antimicrobial peptides (AMPs) that have the capacity to kill bacteria and are an attractive alternative to currently used antibiotics that are increasingly becoming ineffective. The production of antimicrobial peptides was considerably more challenging than the production of griffithsin. Small AMPs are prone to degradation in plastids. This problem was overcome by fusing AMPs to generate larger polypeptides. In one approach, AMPs were fused to each other to increase size and combine the mode of action of multiple AMPs. This improved the accumulation of AMPs but also resulted in impaired plant growth. This was solved by the use of two different inducible systems, which could largely restore plant growth. Fusions of multiple AMPs were insoluble and could not be purified. In addition to fusing AMPs to each other, the fusion of AMPs to small ubiquitin-like modifier (SUMO), was tested as an approach to improve the accumulation, facilitate purification, and reduce the toxicity of AMPs to chloroplasts. Fusion of AMPs to SUMO indeed increased accumulation while reducing the toxicity to the plants. SUMO fusions produced inside chloroplasts could be purified, and SUMO could be efficiently cleaved off with the SUMO protease. Such fusions therefore provide a promising strategy for the production of AMPs and other small polypeptides inside chloroplasts.},
  language  = {en}
}
@phdthesis{Kopka2006,
  author    = {Kopka, Claudia},
  title     = {The nucleoside diphosphate kinases - a small gene family involved in the energyphosphotransfer of arabidopsis thaliana},
  address   = {Potsdam},
  pages     = {133 Bl. : graph. Darst.},
  year      = {2006},
  language  = {en}
}
@phdthesis{Sauter2016,
  author    = {Sauter, J{\"o}rg},
  title     = {The molecular origin of plant cell wall swelling},
  school      = {Universit{\"a}t Potsdam},
  pages     = {iii, 127 S.},
  year      = {2016},
  abstract  = {In dieser Arbeit werden die Eigenschaften von hydratisierten Hemicellulose Polysacchariden mittels Computersimulation untersucht. Die hohe Quellfähigkeit von Materialien die aus diesen Molek{\"u}len bestehen, erlaubt die Erzeugung von zielgerichteter Bewegung in Planzenmaterialien, ausschließlich gesteuert durch Wasseraufnahme. Um den molekularen Ursprung dieses Quellvermögens zu untersuchen wird, im Vergleich mit Experimenten, ein atomistisches Modell f{\"u}r Hemicellulose Polysaccharide entwickelt und getestet. Unter Verwendung dieses Modells werden Simulationen von kleinen Polysacchariden benutzt um die Wechselwirkungen mit Wasser, den Einfluss von Wasser auf die Konformationsfreiheit der Molek{\"u}le, und die Quellfähigkeit, quantifiziert durch den osmotischen Druck, zu verstehen. Es wird gezeigt, dass verzweigte und lineare Polysaccharide unterschiedliche Hydratisierungseingenschaften im Vergleich zu lineare Polysacchariden aufweisen. Um das Quellverhalten auf Längen- und Zeitskalen untersuchen zu können die {\"u}ber die Begrenzungen atomistischer Simulationen hinausgehen, wurde eine Prozedur entwickelt um {\"u}bertragbare vergröberte Modelle herzuleiten. Die Übertragbarkeit der vegröberten Modelle wird gezeigt, sowohl {\"u}ber unterschiedliche Polysaccharidkonzentrationen als auch {\"u}ber unterschiedliche Polymerlängen. Daher erlaubt die Prozedur die Konstruktion von großen vergröberter Systemen ausgehend von kleinen atomistischen Referenzsystemen. Abschließend wird das vergröberte Modell verwendet um zu zeigen, dass lineare und verzweigte Polysaccharide ein unterschiedliches Quellverhalten aufweisen, wenn sie mit einem Wasserbad gekoppelt werden.},
  language  = {en}
}
@phdthesis{Pham2018,
  author    = {Pham, Phuong Anh},
  title     = {The metabolic significance of the NAD+ salvage pathway and the alternative pathway of respiration in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {186},
  year      = {2018},
  language  = {en}
}
@phdthesis{Kloss2016,
  author    = {Kloß, Lena},
  title     = {The link between genetic diversity and species diversity},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109},
  year      = {2016},
  language  = {en}
}
@phdthesis{Kaptur2021,
  author    = {Kaptur, Joanna Alexandra},
  title     = {The LEUNIG regulatory complex},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  abstract  = {Patterning along the apical-basal (A-B) axis is a crucial step during the early stages of plant embryogenesis and leads to the establishment of two poles of which each will develop their own stem cell niches. The activity of these meristems is responsible for post-embryonic growth, with the shoot apical meristem (SAM) generating the above-ground organs and the root apical meristem (RAM) producing the subterranean structures of the plant. While several transcriptional regulators governing A-B patterning have been identified, precisely how their regulatory function is orchestrated remains elusive. This study focuses on transcriptional co-regulators LEUNIG (LUG) and closely related LEUNIG_HOMOLOG (LUH) and their role in the formation of A-B patterning during embryogenesis as well as their post-embryonic maintenance. A link between the LUG regulatory complex and SAM formation and maintenance comes from the observation that lug mutants heterozygous for the luh allele (lug luh+/-) often have enlarged SAMs resulting from misregulated cell divisions. A more severe phenotype is observed in lug luh double mutants which are embryonically lethal. In this study, a detailed characterisation of lug luh embryo phenotype reveals that these mutants display aberrant cell divisions along the A-B axis, which correlates with defects in auxin distribution, complete loss of apical identity, and altered expression of transcription factors determining basal fate. Like other co-regulators, LUG and LUH lack intrinsic DNA-binding domains and instead must interact with DNA-binding cofactors to ensure recruitment to regulatory elements of target genes. This either involves direct contact between the co-regulators and transcription factors (TFs) or the formation of higher-order complexes with adaptor proteins such as SEUSS (SEU) or related SEUSS-LIKEs (SLKs), which facilitate binding to specific TFs. Results presented in this study provide insight into the molecular framework for the LUG regulatory complex activity during embryogenesis. Both yeast and in planta assays showed that LUG/LUH and SEU/SLKs physically associate with a variety of WUSCHEL-RELATED HOMEOBOX (WOX) TFs including members of the WOX2-module. Furthermore, genetic interactions between members of the WOX2-module and the LUG regulatory complex, support their mutual action during embryogenesis. Based on the reduced activity of HOMEODOMAIN LEUCINE-ZIPPER CLASS III (HD-ZIPIII) promoters in lug luh embryos, a model is proposed in which the LUG regulatory complex functions together with WOX2-module to promote apical identity and subsequent SAM initiation through regulation of the HD-ZIPIIIs. The activity of the LUG complex in promoting basal embryo identity through positive regulation of microRNA165/166 suggests that this complex also has functions that are independent of the WOX2-module. Preliminary work reported in this study further uncovered the role of the LUG regulatory complex in post-embryonic development. While the fasciated inflorescence meristems of lug luh+/- plants displayed defects in auxin transport and altered activity of stem cell markers, embryonically rescued lug luh mutants formed flat and differentiated SAMs. In addition, rescued lug luh mutants exhibited severely disorganised RAM and defects in quiescent center (QC) specification, supporting the involvement of the LUG complex in post-embryonic RAM maintenance.},
  language  = {en}
}
@phdthesis{Wojciechowska2022,
  author    = {Wojciechowska, Izabela},
  title     = {The journey towards the discovery of new protein-metabolite interactions in Arabidopsis thaliana and further functional characterization of selected binding events},
  school      = {Universit{\"a}t Potsdam},
  pages     = {150},
  year      = {2022},
  language  = {en}
}
@phdthesis{vonBismarck2023,
  author    = {von Bismarck, Thekla},
  title     = {The influence of long-term light acclimation on photosynthesis in dynamic light},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 163},
  year      = {2023},
  abstract  = {Photosynthesis converts light into metabolic energy which fuels plant growth. In nature, many factors influence light availability for photosynthesis on different time scales, from shading by leaves within seconds up to seasonal changes over months. Variability of light energy supply for photosynthesis can limit a plant´s biomass accumulation. Plants have evolved multiple strategies to cope with strongly fluctuation light (FL). These range from long-term optimization of leaf morphology and physiology and levels of pigments and proteins in a process called light acclimation, to rapid changes in protein activity within seconds. Therefore, uncovering how plants deal with FL on different time scales may provide key ideas for improving crop yield. Photosynthesis is not an isolated process but tightly integrates with metabolism through mutual regulatory interactions. We thus require mechanistic understanding of how long-term light acclimation shapes both, dynamic photosynthesis and its interactions with downstream metabolism. To approach this, we analyzed the influence of growth light on i) the function of known rapid photosynthesis regulators KEA3 and VCCN1 in dynamic photosynthesis (Chapter 2-3) and ii) the interconnection of photosynthesis with photorespiration (PR; Chapter 4). We approached topic (i) by quantifying the effect of different growth light regimes on photosynthesis and photoprotection by using kea3 and vccn1 mutants. Firstly, we found that, besides photosynthetic capacity, the activities of VCCN1 and KEA3 during a sudden high light phase also correlated with growth light intensity. This finding suggests regulation of both proteins by the capacity of downstream metabolism. Secondly, we showed that KEA3 accelerated photoprotective non-photochemical quenching (NPQ) kinetics in two ways: Directly via downregulating the lumen proton concentration and thereby de-activating pH-dependent NPQ, and indirectly via suppressing accumulation of the photoprotective pigment zeaxanthin. For topic (ii), we analyzed the role of PR, a process which recycles a toxic byproduct of the carbon fixation reactions, in metabolic flexibility in a dynamically changing light environment. For this we employed the mutants hpr1 and ggt1 with a partial block in PR. We characterized the function of PR during light acclimation by tracking molecular and physiological changes of the two mutants. Our data, in contrast to previous reports, disprove a generally stronger physiological relevance of PR under dynamic light conditions. Additionally, the two different mutants showed pronounced and distinct metabolic changes during acclimation to a condition inducing higher photosynthetic activity. This underlines that PR cannot be regarded purely as a cyclic detoxification pathway for 2PG. Instead, PR is highly interconnected with plant metabolism, with GGT1 and HPR1 representing distinct metabolic modulators. In summary, the presented work provides further insight into how energetic and metabolic flexibility is ensured by short-term regulators and PR during long-term light acclimation.},
  language  = {en}
}
@phdthesis{Hobson2001,
  author    = {Hobson, Dagmar},
  title     = {The importance of having a backbone: contribution of RNA backbone groups to the affinity and specificity of the MS2 coat protein-operator complex},
  pages     = {112 S.},
  year      = {2001},
  language  = {en}
}
@phdthesis{Heinze2016,
  author    = {Heinze, Johannes},
  title     = {The impact of soil microbiota on plant species performance and diversity in semi-natural grasslands},
  school      = {Universit{\"a}t Potsdam},
  pages     = {157},
  year      = {2016},
  language  = {en}
}
@phdthesis{Wasiolka2007,
  author    = {Wasiolka, Bernd},
  title     = {The impact of overgrazing on reptile diversity and population dynamics of Pedioplanis l. lineoocellata in the southern Kalahari},
  publisher = {Univ.-Verl.},
  address   = {Potsdam},
  pages     = {v, 101 BL. : Ill., graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Tews2003,
  author    = {Tews, J{\"o}rg},
  title     = {The impact of climate change and land use on woody plants in semiarid savanna : modelling shrub population dynamics in the southern kalahari},
  pages     = {98 S.},
  year      = {2003},
  language  = {en}
}
@phdthesis{Seul2008,
  author    = {Seul, Anait},
  title     = {Tailspike interactions in bacteriophage P22},
  address   = {Potsdam},
  pages     = {65, [9], 5 Bl. : Ill., graph. Darst.},
  year      = {2008},
  language  = {en}
}
@phdthesis{Belkius2017,
  author    = {Belkius, Karolina Dorota},
  title     = {Systems biology approach to investigate the development and degradation of the photosynthetic apparatus during leaf ontogenesis in higher plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {121},
  year      = {2017},
  language  = {en}
}
@phdthesis{Schad2005,
  author    = {Schad, Martina},
  title     = {Systemische Auswirkungen der kompatiblen Interaktion zwischen Golovinomyces orontii und Arabidopsis thaliana auf die molekulare Zusammensetzung von Leitgeweben},
  address   = {Potsdam},
  pages     = {92 Bl. : graph. Darst.},
  year      = {2005},
  language  = {de}
}
@phdthesis{Irgang2012,
  author    = {Irgang, Susann},
  title     = {Systemic characterization of the TOR-signaling pathway in chlamydomonas reinhardtii},
  address   = {Potsdam},
  pages     = {135 S.},
  year      = {2012},
  language  = {en}
}
@phdthesis{Kožul2020,
  author    = {Kožul, Danijela},
  title     = {Systematic identification of loci determining chloroplast and nuclear genome incompatibility in the evening primrose (Oenothera)},
  school      = {Universit{\"a}t Potsdam},
  pages     = {126},
  year      = {2020},
  language  = {en}
}