@phdthesis{Schmitt2014,
  author    = {Schmitt, Clemens Nikolaus Zeno},
  title     = {The role of protein metal complexes in the mechanics of Mytilus californianus byssal threads},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74216},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, 93},
  year      = {2014},
  abstract  = {Protein-metal coordination complexes are well known as active centers in enzymatic catalysis, and to contribute to signal transduction, gas transport, and to hormone function. Additionally, they are now known to contribute as load-bearing cross-links to the mechanical properties of several biological materials, including the jaws of Nereis worms and the byssal threads of marine mussels. The primary aim of this thesis work is to better understand the role of protein-metal cross-links in the mechanical properties of biological materials, using the mussel byssus as a model system. Specifically, the focus is on histidine-metal cross-links as sacrificial bonds in the fibrous core of the byssal thread (Chapter 4) and L-3,4-dihydroxyphenylalanine (DOPA)-metal bonds in the protective thread cuticle (Chapter 5). Byssal threads are protein fibers, which mussels use to attach to various substrates at the seashore. These relatively stiff fibers have the ability to extend up to about 100 \% strain, dissipating large amounts of mechanical energy from crashing waves, for example. Remarkably, following damage from cyclic loading, initial mechanical properties are subsequently recovered by a material-intrinsic self-healing capability. Histidine residues coordinated to transition metal ions in the proteins comprising the fibrous thread core have been suggested as reversible sacrificial bonds that contribute to self-healing; however, this remains to be substantiated in situ. In the first part of this thesis, the role of metal coordination bonds in the thread core was investigated using several spectroscopic methods. In particular, X-ray absorption spectroscopy (XAS) was applied to probe the coordination environment of zinc in Mytilus californianus threads at various stages during stretching and subsequent healing. Analysis of the extended X-ray absorption fine structure (EXAFS) suggests that tensile deformation of threads is correlated with the rupture of Zn-coordination bonds and that self-healing is connected with the reorganization of Zn-coordination bond topologies rather than the mere reformation of Zn-coordination bonds. These findings have interesting implications for the design of self-healing metallopolymers. The byssus cuticle is a protective coating surrounding the fibrous thread core that is both as hard as an epoxy and extensible up to 100 \% strain before cracking. It was shown previously that cuticle stiffness and hardness largely depend on the presence of Fe-DOPA coordination bonds. However, the byssus is known to concentrate a large variety of metals from seawater, some of which are also capable of binding DOPA (e.g. V). Therefore, the question arises whether natural variation of metal composition can affect the mechanical performance of the byssal thread cuticle. To investigate this hypothesis, nanoindentation and confocal Raman spectroscopy were applied to the cuticle of native threads, threads with metals removed (EDTA treated), and threads in which the metal ions in the native tissue were replaced by either Fe or V. Interestingly, replacement of metal ions with either Fe or V leads to the full recovery of native mechanical properties with no statistical difference between each other or the native properties. This likely indicates that a fixed number of metal coordination sites are maintained within the byssal thread cuticle - possibly achieved during thread formation - which may provide an evolutionarily relevant mechanism for maintaining reliable mechanics in an unpredictable environment. While the dynamic exchange of bonds plays a vital role in the mechanical behavior and self-healing in the thread core by allowing them to act as reversible sacrificial bonds, the compatibility of DOPA with other metals allows an inherent adaptability of the thread cuticle to changing circumstances. The requirements to both of these materials can be met by the dynamic nature of the protein-metal cross-links, whereas covalent cross-linking would fail to provide the adaptability of the cuticle and the self-healing of the core. In summary, these studies of the thread core and the thread cuticle serve to underline the important and dynamic roles of protein-metal coordination in the mechanical function of load-bearing protein fibers, such as the mussel byssus.},
  language  = {en}
}
@phdthesis{SchreiberStahnSchenketal.2000,
  author    = {Schreiber, J. and Stahn, R. and Schenk, J{\"o}rg A. and Karsten, U. and Pecher, Gabriele},
  title     = {Binding of tumor antigen mucin (MUC1) derived peptides to the heat shock protein DnaK},
  year      = {2000},
  language  = {en}
}
@phdthesis{Schudoma2011,
  author    = {Schudoma, Christian},
  title     = {Bioinformatic approaches to sequence-structure relationships in RNA loops},
  address   = {Potsdam},
  pages     = {114},
  year      = {2011},
  language  = {en}
}
@phdthesis{Schulte2022,
  author    = {Schulte, Luise},
  title     = {Dynamics of Larix (Mill.) species in Siberia during the last 50,000 years inferred from sedimentary ancient DNA},
  doi       = {10.25932/publishup-55878},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-558782},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 121},
  year      = {2022},
  abstract  = {The deciduous needle tree larch (Larix Mill.) covers more than 80\% of the Asian boreal forests. Only a few Larix species constitute the vast forests and these species differ markedly in their ecological traits, most importantly in their ability to grow on and stabilize underlying permafrost. The pronounced dominance of the summergreen larches makes the Asian boreal forests unique, as the rest of the northern hemisphere boreal forests is almost exclusively dominated by evergreen needle-leaf forests. Global warming is impacting the whole world but is especially pronounced in the arctic and boreal regions. Although adapted to extreme climatic conditions, larch forests are sensitive to varying climatic conditions. By their sheer size, changes in Asian larch forests as range shifts or changes in species composition and the resulting vegetation-climate feedbacks are of global relevance. It is however still uncertain if larch forests will persist under the ongoing warming climate or if they will be replaced by evergreen forests. It is therefore of great importance to understand how these ecosystems will react to future climate warmings and if they will maintain their dominance. One step in the better understanding of larch dynamics is to study how the vast dominant forests developed and why they only established in northern Asia. A second step is to study how the species reacted to past changes in the climate. The first objective of this thesis was to review and identify factors promoting Asian larch dominance. I achieved this by synthesizing and comparing reported larch occurrences and influencing components on the northern hemisphere continents in the present and in the past. The second objective was to find a possibility to directly study past Larix populations in Siberia and specifically their genetic variation, enabling the study of geographic movements. For this, I established chloroplast enrichment by hybridization capture from sedimentary ancient DNA (sedaDNA) isolated from lake sediment records. The third objective was to use the established method to track past larch populations, their glacial refugia during the Last Glacial Maximum (LGM) around 21,000 years before present (ka BP), and their post-glacial migration patterns. To study larch promoting factors, I compared the present state of larch species ranges, areas of dominance, their bioclimatic niches, and the distribution on different extents and thaw depths of permafrost. The species comparison showed that the bioclimatic niches greatly overlap between the American and Asian species and that it is only in the extremely continental climates in which only the Asian larch species can persist. I revealed that the area of dominance is strongly connected to permafrost extent but less linked to permafrost seasonal thaw depths. Comparisons of the paleorecord of larch between the continents suggest differences in the recolonization history. Outside of northern Asia and Alaska, glacial refugial populations of larch were confined to the southern regions and thus recolonization could only occur as migration from south to north. Alaskan larch populations could not establish wide-range dominant forest which could be related to their own genetically depletion as separated refugial population. In Asia, it is still unclear whether or not the northern refugial populations contributed and enhanced the postglacial colonization or whether they were replaced by populations invading from the south in the course of climate warming. Asian larch dominance is thus promoted partly by adaptions to extremely continental climates and by adaptations to grow on continuous permafrost but could be also connected to differences in glacial survival and recolonization history of Larix species. Except for extremely rare macrofossil findings of fossilized cones, traditional methods to study past vegetation are not able to distinguish between larch species or populations. Within the scope of this thesis, I therefore established a method to retrieve genetic information of past larch populations to distinguish between species. Using the Larix chloroplast genome as target, I successfully applied the method of DNA target enrichment by hybridization capture on sedaDNA samples from lake records and showed that it is able to distinguish between larch species. I then used the method on samples from lake records from across Siberia dating back up to 50 ka BP. The results allowed me to address the question of glacial survival and post-glacial recolonization mode in Siberian larch species. The analyzed pattern showed that LGM refugia were almost exclusively constituted by L. gmelinii, even in sites of current L. sibirica distribution. For included study sites, L. sibirica migrated into its extant northern distribution area only in the Holocene. Consequently, the post-glacial recolonization of L. sibirica was not enhanced by northern glacial refugia. In case of sites in extant distribution area of L. gmelinii, the absence of a genetic turn-over point to a continuous population rather than an invasion of southern refugia. The results suggest that climate has a strong influence on the distribution of Larix species and that species may also respond differently to future climate warming. Because species differ in their ecological characteristics, species distribution is also relevant with respect to further feedbacks between vegetation and climate. With this thesis, I give an overview of present and past larch occurrences and evaluate which factors promote their dominance. Furthermore, I provide the tools to study past Larix species and give first important insights into the glacial history of Larix populations.},
  language  = {en}
}
@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{Schulze2005,
  author    = {Schulze, Torsten},
  title     = {Changes in structure and function of the fish community in a mesotrophic lake ecosystem after stocking a non- native top predator},
  pages     = {108 S. : graph. Darst.},
  year      = {2005},
  language  = {en}
}
@phdthesis{Schumacher2019,
  author    = {Schumacher, Julia},
  title     = {Regulation and function of STERILE APETALA in Arabidopsis flower development},
  school      = {Universit{\"a}t Potsdam},
  pages     = {144},
  year      = {2019},
  abstract  = {STERILE APETALA (SAP) is known to be an essential regulator of flower development for over 20 years. Loss of SAP function in the model plant Arabidopsis thaliana is associated with a reduction of floral organ number, size and fertility. In accordance with the function of SAP during early flower development, its spatial expression in flowers is confined to meristematic stages and to developing ovules. However, to date, despite extensive research, the molecular function of SAP and the regulation of its spatio-temporal expression still remain elusive. In this work, amino acid sequence analysis and homology modeling revealed that SAP belongs to the rare class of plant F-box proteins with C-terminal WD40 repeats. In opisthokonts, this type of F-box proteins constitutes the substrate binding subunit of SCF complexes, which catalyze the ubiquitination of proteins to initiate their proteasomal degradation. With LC-MS/MS-based protein complex isolation, the interaction of SAP with major SCF complex subunits was confirmed. Additionally, candidate substrate proteins, such as the growth repressor PEAPOD 1 and 2 (PPD1/2), could be revealed during early stages of flower development. Also INDOLE-3-BUTYRIC ACID RESPONSE 5 (IBR5) was identified among putative interactors. Genetic analyses indicated that, different from substrate proteins, IBR5 is required for SAP function. Protein complex isolation together with transcriptome profiling emphasized that the SCFSAP complex integrates multiple biological processes, such as proliferative growth, vascular development, hormonal signaling and reproduction. Phenotypic analysis of sap mutant and SAP overexpressing plants positively correlated SAP function with plant growth during reproductive and vegetative development. Furthermore, to elaborate on the transcriptional regulation of SAP, publicly available ChIP-seq data of key floral homeotic proteins were reanalyzed. Here, it was shown that the MADS-domain transcription factors APETALA 1 (AP1), APETALA 3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA 3 (SEP3) bind to the SAP locus, which indicates that SAP is expressed in a floral organ-specific manner. Reporter gene analyses in combination with CRISPR/Cas9-mediated deletion of putative regulatory regions further demonstrated that the intron contains major regulatory elements of SAP in Arabidopsis thaliana. In conclusion, these data indicate that SAP is a pleiotropic developmental regulator that acts through tissue-specific destabilization of proteins. The presumed transcriptional regulation of SAP by the floral MADS-domain transcription factors could provide a missing link between the specification of floral organ identity and floral organ growth pathways.},
  language  = {en}
}
@phdthesis{Schumann2022,
  author    = {Schumann, Anne},
  title     = {Development of GIPR antagonists for targeted radiotherapy in neuroendocrine neoplasms},
  school      = {Universit{\"a}t Potsdam},
  pages     = {X, 104},
  year      = {2022},
  abstract  = {Die Theorie der zielgerichteten Radiotherapie basiert auf der {\"U}berexpression von spezifischen Rezeptoren auf der Oberfl{\"a}che von entarteten Zellen. In pr{\"a}klinischen Studien konnte der Gastric inhibitory polypeptide receptor (GIPR) in besonders hoher Dichte in neuroendokrinen Neoplasien (NENs) identifiziert werden, wohingegen er in gesundem Gewebe kaum vorkommt (Waser 2012). Die Verwendung von Somatostatinrezeptor 2 (SSTR2) bindenden Molek{\"u}len, welche mit radioaktiven Isotopen verbunden sind, wird in der klinischen Praxis zur Diagnose und Therapie (Theranostik) von NEN´s eingesetzt, wodurch die Tumorzellen gezielt sichtbar gemacht oder zerst{\"o}rt werden k{\"o}nnen. Das Ziel der vorliegenden Arbeit war die Entwicklung von Molek{\"u}len mit besonders hoher Affinit{\"a}t gegen{\"u}ber dem GIPR zum Einsatz in der zielgerichteten Radiotherapie. Es sollte die Hypothese {\"u}berpr{\"u}ft werden, ob ein neuartiger GIPR Antagonist bei der Detektion von GIPR-positiven Tumoren, bessere Ergebnisse als der GIPR Agonist GIP(1-30) generieren kann. (Reubi 2017). Dar{\"u}ber hinaus wurde auch ein direkter Vergleich mit dem SSTR2 Agonist DOTATATE und Antagonist JR11 f{\"u}r die Detektion von NENs angestellt. Die im Rahmen der Arbeit entwickelten neuen GIPR-bindenden Antagonisten sind nicht von GIP abgeleitet. Die Konjugation mit DOTA erlaubt die Komplexbildung mit diagnostischen (z.B. 111In) und therapeutischen Radionukliden (z.B. 177Lu). Unter der Vielzahl entwickelten Verbindungen, war das Molek{\"u}l 3BP-3775 der vielversprechendste Kandidat f{\"u}r eine klinische Weiterentwicklung. Es zeigte sich ein hohe GIPR Affinit{\"a}t und langanhaltende Rezeptorbindung in vitro und dar{\"u}ber hinaus bei in vivo Versuchen eine starke und persistente Aufnahme in den Tumor. Die geringe Verteilung in den Nieren repr{\"a}sentiert dabei die herausragenden Eigenschaften von 3BP-3775 im Gegensatz zu bereits publizierten Daten mit GIP abgeleiteten Verbindungen (Gourni 2014). Mit 177Lu-3BP-3775 konnte zum ersten Mal eine therapeutische Wirksamkeit eines GIPR-Binders nachgewiesen werden. Mittels in vitro Rezeptor Autoradiographie wurde zudem gezeigt, dass ein neu entwickelter GIPR Antagonist (111In-3BP-3626) eine 6-fach h{\"o}here Bindung an gastroenteropankreatische (GEP) und bronchiale NENs zeigt als der heute klinisch relevanteste SSTR2 Agonist DOTATATE. Zwar war die Bindung des SSTR2 Antagonist JR11 vergleichbar stark, jedoch wurde bei JR11 eine deutlich h{\"o}here Bindung in gesundem Gewebe detektiert, weshalb sich f{\"u}r 3BP-3626 ein zu favorisierendes Tumor-zu-Hintergrund Bindungsverh{\"a}ltnis errechnen ließ. Die Bindung des GIPR Agonisten 111In GIP(1 30) war in allen untersuchten Proben sehr gering. Anhand der Ergebnisse ergab sich folgende Reihenfolge bei der Beurteilung der untersuchten Verbindung und ihrer F{\"a}higkeit NENs gezielt zu detektieren: 111In 3BP 3626 ~ 111In-JR11> 111In-DOTATATE > 111In-GIP(1-30). Die erfolgreiche Entwicklung von neuartigen Molek{\"u}len f{\"u}r zielgerichtete Anwendungen gegen den GIPR bildet das Kernst{\"u}ck der vorliegenden Arbeit. Die erzielten in vitro und in vivo Ergebnisse sind die Grundlage f{\"u}r die Weiterentwicklung des GIPR Antagonisten 3BP-3775 um dessen klinischen Einsatz in der Radiotherapie von GEP- und bronchialen NENs zu realisieren.},
  language  = {en}
}
@phdthesis{Schurr2009,
  author    = {Schurr, Frank Martin},
  title     = {From genes to species ranges : demographic studies of plant dynamics at multiple scales},
  address   = {Potsdam},
  pages     = {277 S. : Ill., graph. Darst. + 1 CD-Rom},
  year      = {2009},
  language  = {en}
}
@phdthesis{Schuster2020,
  author    = {Schuster, Maja},
  title     = {High resolution decoding of the tobacco chloroplast translatome and its dynamics during light-intensity acclimation},
  doi       = {10.25932/publishup-51268},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-512680},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvii, 155},
  year      = {2020},
  abstract  = {Chloroplasts are the photosynthetic organelles in plant and algae cells that enable photoautotrophic growth. Due to their prokaryotic origin, modern-day chloroplast genomes harbor 100 to 200 genes. These genes encode for core components of the photosynthetic complexes and the chloroplast gene expression machinery, making most of them essential for the viability of the organism. The regulation of those genes is predominated by translational adjustments. The powerful technique of ribosome profiling was successfully used to generate highly resolved pictures of the translational landscape of Arabidopsis thaliana cytosol, identifying translation of upstream open reading frames and long non-coding transcripts. In addition, differences in plastidial translation and ribosomal pausing sites were addressed with this method. However, a highly resolved picture of the chloroplast translatome is missing. Here, with the use of chloroplast isolation and targeted ribosome affinity purification, I generated highly enriched ribosome profiling datasets of the chloroplasts translatome for Nicotiana tabacum in the dark and light. Chloroplast isolation was found unsuitable for the unbiased analysis of translation in the chloroplast but adequate to identify potential co-translational import. Affinity purification was performed for the small and large ribosomal subunit independently. The enriched datasets mirrored the results obtained from whole-cell ribosome profiling. Enhanced translational activity was detected for psbA in the light. An alternative translation initiation mechanism was not identified by selective enrichment of small ribosomal subunit footprints. In sum, this is the first study that used enrichment strategies to obtain high-depth ribosome profiling datasets of chloroplasts to study ribosome subunit distribution and chloroplast associated translation. Ever-changing light intensities are challenging the photosynthetic capacity of photosynthetic organism. Increased light intensities may lead to over-excitation of photosynthetic reaction centers resulting in damage of the photosystem core subunits. Additional to an expensive repair mechanism for the photosystem II core protein D1, photosynthetic organisms developed various features to reduce or prevent photodamage. In the long-term, photosynthetic complex contents are adjusted for the efficient use of experienced irradiation. However, the contribution of chloroplastic gene expression in the acclimation process remained largely unknown. Here, comparative transcriptome and ribosome profiling was performed for the early time points of high-light acclimation in Nicotiana tabacum chloroplasts in a genome-wide scale. The time- course data revealed stable transcript level and only minor changes in translational activity of specific chloroplast genes during high-light acclimation. Yet, psbA translation was increased by two-fold in the high light from shortly after the shift until the end of the experiment. A stress-inducing shift from low- to high light exhibited increased translation only of psbA. This study indicate that acclimation fails to start in the observed time frame and only short-term responses to reduce photoinhibition were observed.},
  language  = {en}
}
@phdthesis{Schwager2005,
  author    = {Schwager, Monika},
  title     = {Climate change, variable colony sizes and temporal autocorrelation : consequences of living in changing environments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-5744},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Natural and human induced environmental changes affect populations at different time scales. If they occur in a spatial heterogeneous way, they cause spatial variation in abundance. In this thesis I addressed three topics, all related to the question, how environmental changes influence population dynamics. In the first part, I analysed the effect of positive temporal autocorrelation in environmental noise on the extinction risk of a population, using a simple population model. The effect of autocorrelation depended on the magnitude of the effect of single catastrophic events of bad environmental conditions on a population. If a population was threatened by extinction only, when bad conditions occurred repeatedly, positive autocorrelation increased extinction risk. If a population could become extinct, even if bad conditions occurred only once, positive autocorrelation decreased extinction risk. These opposing effects could be explained by two features of an autocorrelated time series. On the one hand, positive autocorrelation increased the probability of series of bad environmental conditions, implying a negative effect on populations. On the other hand, aggregation of bad years also implied longer periods with relatively good conditions. Therefore, for a given time period, the overall probability of occurrence of at least one extremely bad year was reduced in autocorrelated noise. This can imply a positive effect on populations. The results could solve a contradiction in the literature, where opposing effects of autocorrelated noise were found in very similar population models. In the second part, I compared two approaches, which are commonly used for predicting effects of climate change on future abundance and distribution of species: a "space for time approach", where predictions are based on the geographic pattern of current abundance in relation to climate, and a "population modelling approach" which is based on correlations between demographic parameters and the inter-annual variation of climate. In this case study, I compared the two approaches for predicting the effect of a shift in mean precipitation on a population of the sociable weaver Philetairus socius, a common colonially living passerine bird of semiarid savannahs of southern Africa. In the space for time approach, I compared abundance and population structure of the sociable weaver in two areas with highly different mean annual precipitation. The analysis showed no difference between the two populations. This result, as well as the wide distribution range of the species, would lead to the prediction of no sensitive response of the species to a slight shift in mean precipitation. In contrast, the population modelling approach, based on a correlation between reproductive success and rainfall, predicted a sensitive response in most model types. The inconsistency of predictions was confirmed in a cross-validation between the two approaches. I concluded that the inconsistency was caused, because the two approaches reflect different time scales. On a short time scale, the population may respond sensitively to rainfall. However, on a long time scale, or in a regional comparison, the response may be compensated or buffered by a variety of mechanisms. These may include behavioural or life history adaptations, shifts in the interactions with other species, or differences in the physical environment. The study implies that understanding, how such mechanisms work, and at what time scale they would follow climate change, is a crucial precondition for predicting ecological consequences of climate change. In the third part of the thesis, I tested why colony sizes of the sociable weaver are highly variable. The high variation of colony sizes is surprising, as in studies on coloniality it is often assumed that an optimal colony size exists, in which individual bird fitness is maximized. Following this assumption, the pattern of bird dispersal should keep colony sizes near an optimum. However, I showed by analysing data on reproductive success and survival that for the sociable weaver fitness in relation to colony size did not follow an optimum curve. Instead, positive and negative effects of living in large colonies overlaid each other in a way that fitness was generally close to one, and density dependence was low. I showed in a population model, which included an evolutionary optimisation process of dispersal that this specific shape of the fitness function could lead to a dispersal strategy, where the variation of colony sizes was maintained.},
  subject      = {Populationsbiologie},
  language  = {en}
}
@phdthesis{Schwahn2018,
  author    = {Schwahn, Kevin},
  title     = {Data driven approaches to infer the regulatory mechanism shaping and constraining levels of metabolites in metabolic networks},
  doi       = {10.25932/publishup-42324},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423240},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109},
  year      = {2018},
  abstract  = {Systems biology aims at investigating biological systems in its entirety by gathering and analyzing large-scale data sets about the underlying components. Computational systems biology approaches use these large-scale data sets to create models at different scales and cellular levels. In addition, it is concerned with generating and testing hypotheses about biological processes. However, such approaches are inevitably leading to computational challenges due to the high dimensionality of the data and the differences in the dimension of data from different cellular layers. This thesis focuses on the investigation and development of computational approaches to analyze metabolite profiles in the context of cellular networks. This leads to determining what aspects of the network functionality are reflected in the metabolite levels. With these methods at hand, this thesis aims to answer three questions: (1) how observability of biological systems is manifested in metabolite profiles and if it can be used for phenotypical comparisons; (2) how to identify couplings of reaction rates from metabolic profiles alone; and (3) which regulatory mechanism that affect metabolite levels can be distinguished by integrating transcriptomics and metabolomics read-outs. I showed that sensor metabolites, identified by an approach from observability theory, are more correlated to each other than non-sensors. The greater correlations between sensor metabolites were detected both with publicly available metabolite profiles and synthetic data simulated from a medium-scale kinetic model. I demonstrated through robustness analysis that correlation was due to the position of the sensor metabolites in the network and persisted irrespectively of the experimental conditions. Sensor metabolites are therefore potential candidates for phenotypical comparisons between conditions through targeted metabolic analysis. Furthermore, I demonstrated that the coupling of metabolic reaction rates can be investigated from a purely data-driven perspective, assuming that metabolic reactions can be described by mass action kinetics. Employing metabolite profiles from domesticated and wild wheat and tomato species, I showed that the process of domestication is associated with a loss of regulatory control on the level of reaction rate coupling. I also found that the same metabolic pathways in Arabidopsis thaliana and Escherichia coli exhibit differences in the number of reaction rate couplings. I designed a novel method for the identification and categorization of transcriptional effects on metabolism by combining data on gene expression and metabolite levels. The approach determines the partial correlation of metabolites with control by the principal components of the transcript levels. The principle components contain the majority of the transcriptomic information allowing to partial out the effect of the transcriptional layer from the metabolite profiles. Depending whether the correlation between metabolites persists upon controlling for the effect of the transcriptional layer, the approach allows us to group metabolite pairs into being associated due to post-transcriptional or transcriptional regulation, respectively. I showed that the classification of metabolite pairs into those that are associated due to transcriptional or post-transcriptional regulation are in agreement with existing literature and findings from a Bayesian inference approach. The approaches developed, implemented, and investigated in this thesis open novel ways to jointly study metabolomics and transcriptomics data as well as to place metabolic profiles in the network context. The results from these approaches have the potential to provide further insights into the regulatory machinery in a biological system.},
  language  = {en}
}
@phdthesis{Schwarte2010,
  author    = {Schwarte, Sandra},
  title     = {Genetic variation of photosynthesis and starch metabolism genes in Arabidopsis thaliana},
  address   = {Potsdam},
  year      = {2010},
  language  = {en}
}
@phdthesis{Schwarzer2018,
  author    = {Schwarzer, Christian},
  title     = {Climate change, adaptive divergence and their effects on species interactions in European bog-plant communities},
  school      = {Universit{\"a}t Potsdam},
  pages     = {169},
  year      = {2018},
  language  = {en}
}
@phdthesis{Schaefer2005,
  author    = {Sch{\"a}fer, Arne},
  title     = {Characterization of ammoniumtransporters in Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-5937},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Nitrogen is often a limiting factor for plant growth due to its heterogenous distribution in the soil and to seasonal and diurnal changes in growth rates. In most soils, NH4+ and NO3 - are the predominant sources of inorganic nitrogen that are available for plant nutrition. In this context, plants have evolved mechanisms that enable them to optimize nitrogen acquisition, which include transporters specialized in the uptake of nitrogen and susceptible to a regulation that responds to nitrogen limiting or excess conditions. Although the average NH4+ concentrations of soils are generally 100 to 1000 times lower than those of NO3 - (Marschner, 1995), most plants preferentially take up NH4+ when both forms are present because unlike NO3- , NH4+ has not to be reduced prior to assimilation and thus requires less energy for assimilation (Bloom et al., 1992). Apart from high uptake rates in roots, high intracellular ammonium concentrations also result from quantitatively important internal breakdown of amino acids (Feng et al., 1998), and originates in high quantities during photorespiration (Mattson et al., 1997, Pearson et al., 1998). Thus, NH4+ is a key component of nitrogen metabolism for all plants and can accumulate to varying concentrations in all compartments of the cell, including the cytosol, the vacuole and in the apoplast (Wells and Miller, 2000; Nielsen and Schjoerring, 1998). Two related families of ammonium transporters (AMT1 and AMT2), containing six genes which encode transporter proteins that are specific for ammonium had been identified prior to this thesis and some genes had partially been characterised in Arabidopsis (Gazzarrini et al., 1999; Sohlenkamp et al. 2002; Kaiser et al., 2002). However, these studies were not sufficient to assign physiological functions to the individual transporters and AMT1.4 and AMT1.5 had not been studied prior to this thesis. Given this background, it was considered desirable to acquire a deeper knowledge of the physiological functions of the six Arabidopsis ammonium transporters. To this end, tissue specific expression profiles of the individual wildtype AtAMT genes were performed by quantitative real time PCR (qRT-PCR) and promoter-GUS expression. Modern approaches such as the use of T-DNA insertional mutants and RNAi hairpin constructs were employed to reduce the expression levels of AMT genes. Transcript levels were determined, and physiological, biochemical and developmental analysis such as growth tests on different media and 14C-MA and NH4+ uptake studies with the isolated insertional mutants and RNAi lines were performed to deepen the knowledge of the individual functions of the six AMTs in Arabidopsis. In addition, double mutants of the insertional mutants were created to investigate the extent in which homologous genes could compensate for lost transporter functions. The results described in this thesis show that the six AtAMT genes display a high degree of specifity in their tissue specific expression and are likely to play complementary roles in ammonium uptake into roots, in shoots, and in flowers. AtAMT1.1 is likely to be a 'work horse' for cellular ammonium transport and reassimilation. A major role is probably the recapture of photorespiratory NH3/NH4+ escaping from the cytosol. In roots, it is likely to transport NH4+ from the apoplast into cortical cells. AtAMT1.3 and AtAMT1.5 appear to be specialised in the acquisition of external NH4+ from the soil. Furthermore, AtAMT1.5 plays an additional role in the reassimilation of NH3/NH4+ released during the breakdown of storage proteins in the cotyledons of germinating seedlings. It was difficult to distinguish a specialisation between the transporters AtAMt1.2 and AtAMt1.1, however the root and flower specific expression patterns are different and indicate alternative functions of both. AtAMT1.4 has a very distinct expression which is restricted to the vascular bundels of leaves and to pollen only, where it is likely to be involved in the loading of NH4+ into the cells.The AtAMT2.1 expression pattern is confined to vascular bundels and meristematic active tissues in leaves where ammonium concentrations can reach very high levels. Additionally, the Vmax of AtAMT2 increases with increasing external pH, contrasting to AtAMT1.1. Thus, AtAMT2.1 it might be specialised in ammonium transport in ammonium rich environments, where the functions of other transporters are limited, enabling cells to take up NH4+ over a wide range of concentrations. The root hair expression ascribes an additional role in NH3/NH4+ acquisition where it possibly serves as a transporter that is able to acquire ammonium from basic soils where other transporters become less effective.RNAi lines showing a reduction in AtAMT gene mRNA levels and NH4+ transport kinetics, grew slower and flowering time was delayed. This indicates that NH4+ is a crucial and limiting factor for plant growth.},
  subject      = {Ammonium},
  language  = {en}
}
@phdthesis{Schaefer2019,
  author    = {Sch{\"a}fer, Merlin},
  title     = {Understanding and predicting global change impacts on migratory birds},
  doi       = {10.25932/publishup-43925},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439256},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIV, 153},
  year      = {2019},
  abstract  = {This is a publication-based dissertation comprising three original research stud-ies (one published, one submitted and one ready for submission; status March 2019). The dissertation introduces a generic computer model as a tool to investigate the behaviour and population dynamics of animals in cyclic environments. The model is further employed for analysing how migratory birds respond to various scenarios of altered food supply under global change. Here, ecological and evolutionary time-scales are considered, as well as the biological constraints and trade-offs the individual faces, which ultimately shape response dynamics at the population level. Further, the effect of fine-scale temporal patterns in re-source supply are studied, which is challenging to achieve experimentally. My findings predict population declines, altered behavioural timing and negative carry-over effects arising in migratory birds under global change. They thus stress the need for intensified research on how ecological mechanisms are affected by global change and for effective conservation measures for migratory birds. The open-source modelling software created for this dissertation can now be used for other taxa and related research questions. Overall, this thesis improves our mechanistic understanding of the impacts of global change on migratory birds as one prerequisite to comprehend ongoing global biodiversity loss. The research results are discussed in a broader ecological and scientific context in a concluding synthesis chapter.},
  language  = {en}
}
@phdthesis{Schaelicke2020,
  author    = {Sch{\"a}licke, Svenja},
  title     = {Consumer traits and trait variation under the influence of biochemical food quality},
  school      = {Universit{\"a}t Potsdam},
  pages     = {136},
  year      = {2020},
  abstract  = {The earth's ecosystems undergo considerable changes characterized by human-induced alterations of environmental factors. In order to develop conservation goals for vulnerable ecosystems, research on ecosystem functioning is required.. Therefore, it is crucial to explore organismal interactions, such as trophic interaction or competition, which are decisive for key processes in ecosystems. These interactions are determined by the performance responses of organisms to environmental changes, which in turn, are shaped by the organism's functional traits. Exploring traits, their variation, and the environmental factors that act on them may provide insights on how ecological interactions affect populations, community structures and dynamics, and thus ecosystem functioning. In aquatic ecosystems, global warming intensifies phytoplankton blooms, which are more frequently dominated by cyanobacteria. As cyanobacteria are poor in polyunsaturated fatty acids (PUFA) and sterols, this compositional change alters the biochemical food quality of phytoplankton for consumer species with potential effects on ecological interactions. Within this thesis, I studied the effects of biochemical food quality on consumer traits and performance responses at the phytoplankton-zooplankton interface using different strains of two closely related generalist rotifer species Brachionus calyciflorus and Brachionus fernandoi and three phytoplankton species that differ in their biochemical food quality, i.e. in their content and composition of PUFA and sterols. In a series of laboratory feeding experiments I found that biochemical food quality affected rotifer's performance, i.e. fecundity, survival, and population growth, across a broad range of food quantities. Biochemical food quality constraints, which are often underestimated as influencing environmental factors, had strong impacts on performance responses. I further explored the potential of biochemical food quality in mediating consumer response variation between species and among strains of one species. Co-limitation by food quantity and biochemical food quality resulted in differences in performance responses, which were more pronounced within than between rotifer species. Furthermore, I demonstrated that the body PUFA compositions of rotifer species and strains were differently affected by the dietary PUFA supply, which indicates inter- and intraspecific differences in physiological traits, such as PUFA retention, allocation, and/or bioconversion capacity, within the genus Brachionus. This indicates that dietary PUFA are involved in shaping traits and performance responses of rotifers. This thesis reveals that biochemical food quality is an environmental factor with strong effects on individual traits and performance responses of consumers. Biochemical food quality constraints can further mediate trait and response variation among species or strains. Consequently, they carry the potential to shape ecological interactions and evolutionary processes with effects on community structures and dynamics. Trait-based approaches, which include food quality research, thus may provide further insights into the linkage between functional diversity and the maintenance of crucial ecosystem functions.},
  language  = {en}
}
@phdthesis{Schoene2018,
  author    = {Sch{\"o}ne, Anne-Christin},
  title     = {Degradation of Aliphatic Polyesters at the Air-Water Interface - Capabilities of the Langmuir Monolayer Technique},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109, XXXIX},
  year      = {2018},
  language  = {en}
}
@phdthesis{Schoenheit2011,
  author    = {Sch{\"o}nheit, J{\"o}rg},
  title     = {A phagocyte-specific Irf8 gene enhancer establishes early conventional dendritic cell commitment},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-55482},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Haematopoietic development is a complex process that is strictly hierarchically organized. Here, the phagocyte lineages are a very heterogeneous cell compartment with specialized functions in innate immunity and induction of adaptive immune responses. Their generation from a common precursor must be tightly controlled. Interference within lineage formation programs for example by mutation or change in expression levels of transcription factors (TF) is causative to leukaemia. However, the molecular mechanisms driving specification into distinct phagocytes remain poorly understood. In the present study I identify the transcription factor Interferon Regulatory Factor 8 (IRF8) as the specification factor of dendritic cell (DC) commitment in early phagocyte precursors. Employing an IRF8 reporter mouse, I showed the distinct Irf8 expression in haematopoietic lineage diversification and isolated a novel bone marrow resident progenitor which selectively differentiates into CD8α+ conventional dendritic cells (cDCs) in vivo. This progenitor strictly depends on Irf8 expression to properly establish its transcriptional DC program while suppressing a lineage-inappropriate neutrophile program. Moreover, I demonstrated that Irf8 expression during this cDC commitment-step depends on a newly discovered myeloid-specific cis-enhancer which is controlled by the haematopoietic transcription factors PU.1 and RUNX1. Interference with their binding leads to abrogation of Irf8 expression, subsequently to disturbed cell fate decisions, demonstrating the importance of these factors for proper phagocyte cell development. Collectively, these data delineate a transcriptional program establishing cDC fate choice with IRF8 in its center.},
  language  = {en}
}
@phdthesis{Schoeppler2016,
  author    = {Sch{\"o}ppler, Vanessa},
  title     = {Material properties of Banksia follicles},
  school      = {Universit{\"a}t Potsdam},
  pages     = {119},
  year      = {2016},
  language  = {en}
}