@phdthesis{Raatz2019, author = {Raatz, Michael}, title = {Strategies within predator-prey interactions - from individuals to ecosystems}, doi = {10.25932/publishup-42658}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426587}, school = {Universit{\"a}t Potsdam}, pages = {175}, year = {2019}, abstract = {Predator-prey interactions provide central links in food webs. These interaction are directly or indirectly impacted by a number of factors. These factors range from physiological characteristics of individual organisms, over specifics of their interaction to impacts of the environment. They may generate the potential for the application of different strategies by predators and prey. Within this thesis, I modelled predator-prey interactions and investigated a broad range of different factors driving the application of certain strategies, that affect the individuals or their populations. In doing so, I focused on phytoplankton-zooplankton systems as established model systems of predator-prey interactions. At the level of predator physiology I proposed, and partly confirmed, adaptations to fluctuating availability of co-limiting nutrients as beneficial strategies. These may allow to store ingested nutrients or to regulate the effort put into nutrient assimilation. We found that these two strategies are beneficial at different fluctuation frequencies of the nutrients, but may positively interact at intermediate frequencies. The corresponding experiments supported our model results. We found that the temporal structure of nutrient fluctuations indeed has strong effects on the juvenile somatic growth rate of {\itshape Daphnia}. Predator colimitation by energy and essential biochemical nutrients gave rise to another physiological strategy. High-quality prey species may render themselves indispensable in a scenario of predator-mediated coexistence by being the only source of essential biochemical nutrients, such as cholesterol. Thereby, the high-quality prey may even compensate for a lacking defense and ensure its persistence in competition with other more defended prey species. We found a similar effect in a model where algae and bacteria compete for nutrients. Now, being the only source of a compound that is required by the competitor (bacteria) prevented the competitive exclusion of the algae. In this case, the essential compounds were the organic carbon provided by the algae. Here again, being indispensable served as a prey strategy that ensured its coexistence. The latter scenario also gave rise to the application of the two metabolic strategies of autotrophy and heterotrophy by algae and bacteria, respectively. We found that their coexistence allowed the recycling of resources in a microbial loop that would otherwise be lost. Instead, these resources were made available to higher trophic levels, increasing the trophic transfer efficiency in food webs. The predation process comprises the next higher level of factors shaping the predator-prey interaction, besides these factors that originated from the functioning or composition of individuals. Here, I focused on defensive mechanisms and investigated multiple scenarios of static or adaptive combinations of prey defense and predator offense. I confirmed and extended earlier reports on the coexistence-promoting effects of partially lower palatability of the prey community. When bacteria and algae are coexisting, a higher palatability of bacteria may increase the average predator biomass, with the side effect of making the population dynamics more regular. This may facilitate experimental investigations and interpretations. If defense and offense are adaptive, this allows organisms to maximize their growth rate. Besides this fitness-enhancing effect, I found that co-adaptation may provide the predator-prey system with the flexibility to buffer external perturbations. On top of these rather internal factors, environmental drivers also affect predator-prey interactions. I showed that environmental nutrient fluctuations may create a spatio-temporal resource heterogeneity that selects for different predator strategies. I hypothesized that this might favour either storage or acclimation specialists, depending on the frequency of the environmental fluctuations. We found that many of these factors promote the coexistence of different strategies and may therefore support and sustain biodiversity. Thus, they might be relevant for the maintenance of crucial ecosystem functions that also affect us humans. Besides this, the richness of factors that impact predator-prey interactions might explain why so many species, especially in the planktonic regime, are able to coexist.}, language = {en} } @phdthesis{Rachold2001, author = {Rachold, Volker}, title = {Sediment pathways and budgets of the laptev sea region, siberian articic-implications for arctic land-ocean interactions}, pages = {229 S.}, year = {2001}, 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{Rajasundaram2015, author = {Rajasundaram, Dhivyaa}, title = {Integrative analysis of heterogeneous plant cell wall related data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77652}, school = {Universit{\"a}t Potsdam}, pages = {xii, 205}, year = {2015}, abstract = {Plant cell walls are complex structures that underpin plant growth and are widely exploited in diverse human activities thus placing them with a central importance in biology. Cell walls have been a prominent area of research for a long time, but the chemical complexity and diversity of cell walls not just between species, but also within plants, between cell-types, and between cell wall micro-domains pose several challenges. Progress accelerated several-fold in cell wall biology owing to advances in sequencing technology, aided soon thereafter by advances in omics and imaging technologies. This development provides additional perspectives of cell walls across a rapidly growing number of species, highlighting a myriad of architectures, compositions, and functions. Furthermore, rather than the component centric view, integrative analysis of the different cell wall components across system-levels help to gain a more in-depth understanding of the structure and biosynthesis of the cell envelope and its interactions with the environment. To this end, in this work three case studies are detailed, all pertaining to the integrative analysis of heterogeneous cell wall related data arising from different system-levels and analytical techniques. A detailed account of multiblock methods is provided and in particular canonical correlation and regression methods of data integration are discussed. In the first integrative analysis, by employing canonical correlation analysis - a multivariate statistical technique to study the association between two datasets - novel insight to the relationship between glycans and phenotypic traits is gained. In addition, sparse partial least squares regression approach that adapts Lasso penalization and allows for the selection of a subset of variables was employed. The second case study focuses on an integrative analysis of images obtained from different spectroscopic techniques. By employing yet another multiblock approach - multiple co-inertia analysis, insitu biochemical composition of cell walls from different cell-types is studied thereby highlighting the common and complementary parts of the two hyperspectral imaging techniques. Finally, the third integrative analysis facilitates gene expression analysis of the Arabidopsis root transcriptome and translatome for the identification of cell wall related genes and compare expression patterns of cell wall synthesis genes. The computational analysis considered correlation and variation of expression across cell-types at both system-levels, and also provides insight into the degree of co-regulatory relationships that are preserved between the two processes. The integrative analysis of glycan data and phenotypic traits in cotton fibers using canonical methods led to the identification of specific polysaccharides which may play a major role during fiber development for the final fiber characteristics. Furthermore, this analysis provides a base for future studies on glycan arrays in case of developing cotton fibers. The integrative analysis of images from infrared and Raman spectroscopic approaches allowed the coupling of different analytical techniques to characterize complex biological material, thereby, representing various facets of their chemical properties. Moreover, the results from the co-inertia analysis demonstrated that the study was well adapted as it is relevant for coupling data tables in a symmetric way. Several indicators are proposed to investigate how the global and block scores are related. In addition, studying the root cells of \textit{Arabidopsis thaliana} allowed positing a novel pipeline to systematically investigate and integrate the different levels of information available at the global and single-cell level. The conducted analysis also confirms that previously identified key transcriptional activators of secondary cell wall development display highly conserved patterns of transcription and translation across the investigated cell-types. Moreover, the biological processes that display conserved and divergent patterns based on the cell-type-specific expression and translation levels are identified.}, language = {en} } @phdthesis{Rajkumar2007, author = {Rajkumar, Rajagopal}, title = {Development of a thermometric sensor for fructosyl valine and fructose using molecularly imprinted polymers as a recognition element}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17272}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Nature has always served as a model for mimicking and inspiration to humans in their efforts to improve their life. Researchers have been inspired by nature to produce biomimetic materials with molecular recognition properties by design rather than evolution. Molecular imprinting is one way to prepare such materials. Such smart materials with new functionalities are at the forefront of the development of a relevant number of ongoing and perspective applications ranging from consumer to space industry. Molecularly imprinted polymers were developed by mimicking the natural enzymes or antibodies that serve as host for binding target molecules. These imprints were used as a recognition element to substitute natural biomolecules in biosensors. The concept behind molecular imprinting is to mold a material (with the desired chemical properties) around individual molecules. Upon removal of the molecular templates, one is left with regions in the molded material that fit the shape of the template molecules. Thus, molecular imprinting results in materials that can selectively bind to molecules of interest. Imprinted materials resulted in applications ranging from chemical separation to bioanalytics. In this work attempts were made particularly in the development of molecularly imprinted polymer based thermometric sensors. The main effort was focused towards the development of an covalently imprinted polymer that would be able to selectively bind fructosyl valine (Fru-Val), the N-terminal constituent of hemoglobin A1c ß-chains. Taking into account the known advantages of imprinted polymers, e.g. robustness, thermal and chemical stability, imprinted materials were successfully used as a recognition element in the sensor. One of the serious problems associated with the development of MIP sensors and which lies in the absence of a generic procedure for the transformation of the polymer-template binding event into a detectable signal has been addressed by developing the "thermometric" approach. In general the developed approach gives a new insight on MIP/Analyte interactions.}, language = {en} } @phdthesis{Rakpenthai2022, author = {Rakpenthai, Apidet}, title = {Analysis of the regulation of the sulfur responsive genese, SD11 and SD 12}, year = {2022}, language = {en} } @phdthesis{Ramming2019, author = {Ramming, Anna}, title = {Specific Roles of POLY(A) POLYMERASE1 in the male Gametophyte and Beyond}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2019}, language = {en} } @phdthesis{RamirezAguilar2010, author = {Ram{\´i}rez Aguilar, Santiago Javier}, title = {Regulation of respiration in plants : molecular mechanisms in metabolism and in the mitochondrial electron transport chain}, address = {Potsdam}, pages = {Getr. Z{\"a}hlung : graph. Darst.}, year = {2010}, language = {en} } @phdthesis{Rasul2023, author = {Rasul, Fiaz}, title = {Biostimulant SuperFifty based molecular priming to increase plant strength and stress tolerance}, year = {2023}, language = {en} } @phdthesis{Ratzka2007, author = {Ratzka, Antje}, title = {Cell wall biosynthesis and metabolism in tomato fruit}, address = {Potsdam}, pages = {VII, 88 S. : graph. Darst.}, year = {2007}, language = {en} } @phdthesis{Rauf2012, author = {Rauf, Mamoona}, title = {Exploring the gene regulatory networks of the NAC transcription factors SHYG and ORE1 in Arabidopsis thaliana}, address = {Potsdam}, pages = {172 S.}, year = {2012}, language = {en} } @phdthesis{Rautengarten2007, author = {Rautengarten, Carsten}, title = {Subtilisin-like serine proteases : in Arabidopsis thaliana (L.) Heynh.}, address = {Potsdam}, pages = {VII, 147 S. : graph. Darst.}, year = {2007}, language = {en} } @phdthesis{Razzaq2013, author = {Razzaq, Muhammad Yasar}, title = {Shape-memory investigations of magneto-sensitive polymer nanocomposites}, address = {Potsdam}, pages = {140 S.}, year = {2013}, language = {en} } @phdthesis{Redestig2007, author = {Redestig, Henning}, title = {Approaches for integrative analysis of gene expression data}, address = {Potsdam}, pages = {VIII, 130 S. : Ill., graph. Darst.}, year = {2007}, language = {en} } @phdthesis{Reeg2019, author = {Reeg, Jette}, title = {Simulating the impact of herbicide drift exposure on non-target terrestrial plant communities}, doi = {10.25932/publishup-42907}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429073}, school = {Universit{\"a}t Potsdam}, pages = {178}, year = {2019}, abstract = {In Europe, almost half of the terrestrial landscape is used for agriculture. Thus, semi-natural habitats such as field margins are substantial for maintaining diversity in intensively managed farmlands. However, plants located at field margins are threatened by agricultural practices such as the application of pesticides within the fields. Pesticides are chemicals developed to control for undesired species within agricultural fields to enhance yields. The use of pesticides implies, however, effects on non-target organisms within and outside of the agricultural fields. Non-target organisms are organisms not intended to be sprayed or controlled for. For example, plants occurring in field margins are not intended to be sprayed, however, can be impaired due to herbicide drift exposure. The authorization of plant protection products such as herbicides requires risk assessments to ensure that the application of the product has no unacceptable effects on the environment. For non-target terrestrial plants (NTTPs), the risk assessment is based on standardized greenhouse studies on plant individual level. To account for the protection of plant populations and communities under realistic field conditions, i.e. extrapolating from greenhouse studies to field conditions and from individual-level to community-level, assessment factors are applied. However, recent studies question the current risk assessment scheme to meet the specific protection goals for non-target terrestrial plants as suggested by the European Food Safety Authority (EFSA). There is a need to clarify the gaps of the current risk assessment and to include suitable higher tier options in the upcoming guidance document for non-target terrestrial plants. In my thesis, I studied the impact of herbicide drift exposure on NTTP communities using a mechanistic modelling approach. I addressed main gaps and uncertainties of the current risk assessment and finally suggested this modelling approach as a novel higher tier option in future risk assessments. Specifically, I extended the plant community model IBC-grass (Individual-based community model for grasslands) to reflect herbicide impacts on plant individuals. In the first study, I compared model predictions of short-term herbicide impacts on artificial plant communities with empirical data. I demonstrated the capability of the model to realistically reflect herbicide impacts. In the second study, I addressed the research question whether or not reproductive endpoints need to be included in future risk assessments to protect plant populations and communities. I compared the consequences of theoretical herbicide impacts on different plant attributes for long-term plant population dynamics in the community context. I concluded that reproductive endpoints only need to be considered if the herbicide effect is assumed to be very high. The endpoints measured in the current vegetative vigour and seedling emergence studies had high impacts for the dynamic of plant populations and communities already at lower effect intensities. Finally, the third study analysed long-term impacts of herbicide application for three different plant communities. This study highlighted the suitability of the modelling approach to simulate different communities and thus detecting sensitive environmental conditions. Overall, my thesis demonstrates the suitability of mechanistic modelling approaches to be used as higher tier options for risk assessments. Specifically, IBC-grass can incorporate available individual-level effect data of standardized greenhouse experiments to extrapolate to community-level under various environmental conditions. Thus, future risk assessments can be improved by detecting sensitive scenarios and including worst-case impacts on non-target plant communities.}, language = {en} } @phdthesis{Reichel2016, author = {Reichel, Victoria Eleonore}, title = {Biomedical applications and multifunctional nanostructures based on magnetite nanoparticles synthesized in presence of biological additives}, school = {Universit{\"a}t Potsdam}, pages = {94, XX}, year = {2016}, language = {en} } @phdthesis{Reil2016, author = {Reil, Daniela}, title = {Puumala hantavirus dynamics in bank voles: identification of environmental correlates to predict human infection risk}, school = {Universit{\"a}t Potsdam}, pages = {85}, year = {2016}, language = {en} } @phdthesis{Reinecke2016, author = {Reinecke, Antje Adriana}, title = {Impact of protein structure on the mechanics and assembly of mytilus byssal threads}, school = {Universit{\"a}t Potsdam}, pages = {101}, year = {2016}, language = {en} } @phdthesis{ReynaGonzalez2017, author = {Reyna Gonz{\´a}lez, Emmanuel}, title = {Engineering of the microviridin post-translational modification enzymes for the production of synthetic protease inhibitors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-406979}, school = {Universit{\"a}t Potsdam}, pages = {XI, 91, CI}, year = {2017}, abstract = {Natural products and their derivatives have always been a source of drug leads. In particular, bacterial compounds have played an important role in drug development, for example in the field of antibiotics. A decrease in the discovery of novel leads from natural sources and the hope of finding new leads through the generation of large libraries of drug-like compounds by combinatorial chemistry aimed at specific molecular targets drove the pharmaceutical companies away from research on natural products. However, recent technological advances in genetics, bioinformatics and analytical chemistry have revived the interest in natural products. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of natural products generated by the action of post-translationally modifying enzymes on precursor peptides translated from mRNA by ribosomes. The great substrate promiscuity exhibited by many of the enzymes from RiPP biosynthetic pathways have led to the generation of hundreds of novel synthetic and semisynthetic variants, including variants carrying non-canonical amino acids (ncAAs). The microviridins are a family of RiPPs characterized by their atypical tricyclic structure composed of lactone and lactam rings, and their activity as serine protease inhibitors. The generalities of their biosynthetic pathway have already been described, however, the lack of information on details such as the protease responsible for cleaving off the leader peptide from the cyclic core peptide has impeded the fast and cheap production of novel microviridin variants. In the present work, knowledge on leader peptide activation of enzymes from other RiPP families has been extrapolated to the microviridin family, making it possible to bypass the need of a leader peptide. This feature allowed for the exploitation of the microviridin biosynthetic machinery for the production of novel variants through the establishment of an efficient one-pot in vitro platform. The relevance of this chemoenzymatic approach has been exemplified by the synthesis of novel potent serine protease inhibitors from both rationally-designed peptide libraries and bioinformatically predicted microviridins. Additionally, new structure-activity relationships (SARs) could be inferred by screening microviridin intermediates. The significance of this technique was further demonstrated by the simple incorporation of ncAAs into the microviridin scaffold.}, language = {en} } @phdthesis{Reza2008, author = {Reza, Mohammad}, title = {GC-TOF-MS assessment and genetic modification of the metabolic salt stress reponse in rice (Oryza sativa L.)}, pages = {IV, 154 S.}, year = {2008}, language = {en} } @phdthesis{RianoPachon2008, author = {Ria{\~n}o-Pach{\´o}n, Diego Mauricio}, title = {Identification of transcription factor genes in plants}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-27009}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {In order to function properly, organisms have a complex control mechanism, in which a given gene is expressed at a particular time and place. One way to achieve this control is to regulate the initiation of transcription. This step requires the assembly of several components, i.e., a basal/general machinery common to all expressed genes, and a specific/regulatory machinery, which differs among genes and is the responsible for proper gene expression in response to environmental or developmental signals. This specific machinery is composed of transcription factors (TFs), which can be grouped into evolutionarily related gene families that possess characteristic protein domains. In this work we have exploited the presence of protein domains to create rules that serve for the identification and classification of TFs. We have modelled such rules as a bipartite graph, where families and protein domains are represented as nodes. Connections between nodes represent that a protein domain should (required rule) or should not (forbidden rule) be present in a protein to be assigned into a TF family. Following this approach we have identified putative complete sets of TFs in plant species, whose genome is completely sequenced: Cyanidioschyzon merolae (red algae), Chlamydomonas reinhardtii (green alga), Ostreococcus tauri (green alga), Physcomitrella patens (moss), Arabidopsis thaliana (thale cress), Populus trichocarpa (black cottonwood) and Oryza sativa (rice). The identification of the complete sets of TFs in the above-mentioned species, as well as additional information and reference literature are available at http://plntfdb.bio.uni-potsdam.de/. The availability of such sets allowed us performing detailed evolutionary studies at different levels, from a single family to all TF families in different organisms in a comparative genomics context. Notably, we uncovered preferential expansions in different lineages, paving the way to discover the specific biological roles of these proteins under different conditions. For the basic leucine zipper (bZIP) family of TFs we were able to infer that in the most recent common ancestor (MRCA) of all green plants there were at least four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. Currently, following the approach described above, up to 57 TF and 11 TR families can be identified, which are among the most numerous transcription regulatory families in plants. Three families of putative TFs predate the split between rhodophyta (red algae) and chlorophyta (green algae), i.e., G2-like, PLATZ, and RWPRK, and may have been of particular importance for the evolution of eukaryotic photosynthetic organisms. Nine additional families, i.e., ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP, and WRKY, predate the split between green algae and streptophytes. The identification of putative complete list of TFs has also allowed the delineation of lineage-specific regulatory families. The families SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA significantly differ in size between algae and land plants. The SBP family of TFs is significantly larger in C. reinhardtii, compared to land plants, and appears to have been lost in the prasinophyte O. tauri. The families bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA preferentially expanded with the colonisation of land, and might have played an important role in this great moment in evolution. Later, after the split of bryophytes and tracheophytes, the families MADS, AP2-EREBP, NAC, AUX/IAA, PHD and HRT have significantly larger numbers in the lineage leading to seed plants. We identified 23 families that are restricted to land plants and that might have played an important role in the colonization of this new habitat. Based on the list of TFs in different species we have started to develop high-throughput experimental platforms (in rice and C. reinhardtii) to monitor gene expression changes of TF genes under different genetic, developmental or environmental conditions. In this work we present the monitoring of Arabidopsis thaliana TFs during the onset of senescence, a process that leads to cell and tissue disintegration in order to redistribute nutrients (e.g. nitrogen) from leaves to reproductive organs. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. 76\% of these TFs are down-regulated during senescence, the remaining are up-regulated. The identification of TFs in plants in a comparative genomics setup has proven fruitful for the understanding of evolutionary processes and contributes to the elucidation of complex developmental programs.}, language = {en} } @phdthesis{RibeiroMartins2017, author = {Ribeiro Martins, Renata Filipa}, title = {Deciphering evolutionary histories of Southeast Asian Ungulates}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-404669}, school = {Universit{\"a}t Potsdam}, pages = {vii, 115}, year = {2017}, abstract = {Im Verlauf von Jahrmillionen gestalteten evolution{\"a}re Kr{\"a}fte die Verbreitung und genetische Variabilit{\"a}t von Arten, indem sie die Anpassungsf{\"a}higkeit und {\"U}berlebenswahrscheinlichkeit dieser Arten beeinflussten. Da S{\"u}dostasien eine außerordentlich artenreiche Region darstellt, eignet sie sich besonders, um den Einfluss dieser Kr{\"a}fte zu untersuchen. Historische Klimaver{\"a}nderungen hatten dramatische Auswirkungen auf die Verf{\"u}gbarkeit sowie die Verbreitung von Habitaten in S{\"u}dostasien, weil hierdurch wiederholt das Festland mit sonst isolierten Inseln verbunden wurde. Dies beeinflusste nicht nur, wie Arten in dieser Region verbreitet sind, sondern erm{\"o}glichte auch eine zunehmende genetische Variabilit{\"a}t. Zwar ist es bekannt, dass Arten mit {\"a}hnlicher Evolutionsgeschichte unterschiedliche phylogeographische Muster aufweisen k{\"o}nnen. Die zugrundeliegenden Mechanismen sind jedoch nur gering verstanden. Diese Dissertation behandelt die Phylogeographie von drei Gruppen von Huftieren, welche im S{\"u}den und S{\"u}dosten Asiens vorkommen. Dabei war das vornehmliche Ziel, zu verstehen, wie es zur Ausbildung verschiedener Arten sowie zu einer regionalen Verteilung von genetischer Variabilit{\"a}t kam. Hierf{\"u}r untersuchte ich die mitochondrialen Genome alter Proben. Dadurch war es m{\"o}glich, Populationen des gesamten Verbreitungsgebietes der jeweiligen Arten zu untersuchen - auch solche Populationen, die heutzutage nicht mehr existieren. Entsprechend der einzelnen Huftiergruppen ist diese Arbeit in drei Kapitel unterteilt: Muntjaks (Muntiacus sp.), Hirsche der Gattung Rusa und asiatische Nash{\"o}rner. Alle drei Gruppen weisen eine Aufteilung in unterschiedliche Linien auf, was jeweils direkt auf Ereignisse des Pleistoz{\"a}ns zur{\"u}ckgef{\"u}hrt werden kann. Muntjaks sind eine weit verbreitete Art, die in verschiedensten Habitaten vorkommen kann. Ich wies nach, dass es in der Vergangenheit zu genetischem Austausch zwischen Populationen von verschiedenen Inseln des Sundalandes kam. Dies deutet auf die F{\"a}higkeit von Muntjaks hin, sich an die ehemaligen Landbr{\"u}cken anzupassen. Jedoch zeige ich auch, dass mindestens zwei Hindernisse bei ihrer Verbreitung existierten, wodurch es zu einer Differenzierung von Populationen kam: eine Barriere trennte Populationen des asiatischen Festlands von denen der Sundainseln, die andere isolierte sri-lankische von restlichen Muntjaks. Die zwei untersuchten Rusa-Arten weisen ein anderes Muster auf, was wiederum eine weitere Folge der pleistoz{\"a}nen Landbr{\"u}cken darstellt. Beide Arten sind ausschließlich monophyletisch. Allerdings gibt es Anzeichen f{\"u}r die Hybridisierung dieser Arten auf Java, was durch eine fr{\"u}here Ausbreitung des sambar (R. unicolor) gef{\"o}rdert wurde. Aufgrund dessen fand ich zudem, dass all jene Individuen der anderen Art, R. timorensis, die durch den Menschen auf die {\"o}stlichen Sundainseln gebracht wurden, in Wahrheit Hybride sind. F{\"u}r den dritten Teil war es mir m{\"o}glich, Proben von Vertretern ausgestorbener Populationen vom asiatischen Festland des Sumatra- und des Java-Nashorns (Dicerorhinus sumatrensis und Rhinoceros sondaicus) zu analysieren. Die Ergebnisse meiner Arbeit belegen, dass die genetische Vielfalt dieser historischen Populationen bedeutend gr{\"o}ßer war als die der heutigen Nachkommen. Ihre jeweilige Evolutionsgeschichte korreliert stark mit pleistoz{\"a}nen Prozessen. Außerdem betonen meine Ergebnisse das enorme Ausmaß von verlorener genetischer Diversit{\"a}t dieser stark bedrohten Arten. Jede Art besitzt eine individuelle phylogeographische Geschichte. Ebenso fand ich aber auch allgemeing{\"u}ltige Muster von genetischer Differenzierung in allen Gruppen, welche direkt mit Ereignissen des Pleistoz{\"a}ns assoziiert werden k{\"o}nnen. Vergleicht man jedoch die einzelnen Ergebnisse der Arten, wird deutlich, dass die gleichen geologischen Prozesse nicht zwangsl{\"a}ufig in gleiche evolutive Ergebnisse resultieren. Einer der Gr{\"u}nde hierf{\"u}r k{\"o}nnte zum Beispiel die unterschiedliche Durchl{\"a}ssigkeit der entstandenen Landkorridore des Sundaschelfs sein. Die M{\"o}glichkeit diese neuen Habitate zu nutzen und somit auch zu passieren steht im direkten Bezug zu den spezifischen {\"o}kologischen Bed{\"u}rfnissen der Arten.Zusammenfassend leisten meine Erkenntnisse einen wichtigen Beitrag, die Evolution und geographische Aufteilung der genetischen Vielfalt in diesem Hotspot an Biodiversit{\"a}t zu verstehen. Obendrein k{\"o}nnen sie aber auch Auswirkungen auf die Erhaltung und systematische Klassifikation der untersuchten Arten haben.}, language = {en} } @phdthesis{Riedel2018, author = {Riedel, Marc}, title = {Photonic wiring of enzymatic reactions to photoactive entities for the construction of biohybrid electrodes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-417280}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 168}, year = {2018}, abstract = {In this work, different strategies for the construction of biohybrid photoelectrodes are investigated and have been evaluated according to their intrinsic catalytic activity for the oxidation of the cofactor NADH or for the connection with the enzymes PQQ glucose dehydrogenase (PQQ-GDH), FAD-dependent glucose dehydrogenase (FAD-GDH) and fructose dehydrogenase (FDH). The light-controlled oxidation of NADH has been analyzed with InGaN/GaN nanowire-modified electrodes. Upon illumination with visible light the InGaN/GaN nanowires generate an anodic photocurrent, which increases in a concentration-dependent manner in the presence of NADH, thus allowing determination of the cofactor. Furthermore, different approaches for the connection of enzymes to quantum dot (QD)-modified electrodes via small redox molecules or redox polymers have been analyzed and discussed. First, interaction studies with diffusible redox mediators such as hexacyanoferrate(II) and ferrocenecarboxylic acid have been performed with CdSe/ZnS QD-modified gold electrodes to build up photoelectrochemical signal chains between QDs and the enzymes FDH and PQQ-GDH. In the presence of substrate and under illumination of the electrode, electrons are transferred from the enzyme via the redox mediators to the QDs. The resulting photocurrent is dependent on the substrate concentration and allows a quantification of the fructose and glucose content in solution. A first attempt with immobilized redox mediator, i.e. ferrocenecarboxylic acid chemically coupled to PQQ-GDH and attached to QD-modified gold electrodes, reveal the potential to build up photoelectrochemical signal chains even without diffusible redox mediators in solution. However, this approach results in a significant deteriorated photocurrent response compared to the situation with diffusing mediators. In order to improve the photoelectrochemical performance of such redox mediator-based, light-switchable signal chains, an osmium complex-containing redox polymer has been evaluated as electron relay for the electronic linkage between QDs and enzymes. The redox polymer allows the stable immobilization of the enzyme and the efficient wiring with the QD-modified electrode. In addition, a 3D inverse opal TiO2 (IO-TiO2) electrode has been used for the integration of PbS QDs, redox polymer and FAD-GDH in order to increase the electrode surface. This results in a significantly improved photocurrent response, a quite low onset potential for the substrate oxidation and a broader glucose detection range as compared to the approach with ferrocenecarboxylic acid and PQQ-GDH immobilized on CdSe/ZnS QD-modified gold electrodes. Furthermore, IO-TiO2 electrodes are used to integrate sulfonated polyanilines (PMSA1) and PQQ-GDH, and to investigate the direct interaction between the polymer and the enzyme for the light-switchable detection of glucose. While PMSA1 provides visible light excitation and ensures the efficient connection between the IO-TiO2 electrode and the biocatalytic entity, PQQ-GDH enables the oxidation of glucose. Here, the IO-TiO2 electrodes with pores of approximately 650 nm provide a suitable interface and morphology, which is required for a stable and functional assembly of the polymer and enzyme. The successful integration of the polymer and the enzyme can be confirmed by the formation of a glucose-dependent anodic photocurrent. In conclusion, this work provides insights into the design of photoelectrodes and presents different strategies for the efficient coupling of redox enzymes to photoactive entities, which allows for light-directed sensing and provides the basis for the generation of power from sun light and energy-rich compounds.}, language = {en} } @phdthesis{Riedel2019, author = {Riedel, Simona}, title = {Characterization of Mitochondrial ABC Transporter Homologues in Rhodobacter capsulatus}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2019}, abstract = {ABC-Transporter (ABC abgeleitet von ATP-Binding Cassette) geh{\"o}ren zur Klasse der Transmembran-Proteine und kommen in allen drei Dom{\"a}nen des Lebens vor. Ihr struktureller Aufbau ist dabei stets {\"a}hnlich, wohingegen konservierte Proteinsequenzen selten vorkommen. Die Transporter sind aus zwei lipophilen, membran-durchspannenden Dom{\"a}nen, welche auch TMDs (abgeleitet von Transmembrane spanning Domains) genannt werden, und zwei hydrophilen Dom{\"a}nen, die auch NBDs (abgeleitet von Nucleotide Binding Domains) genannt werden, aufgebaut. Die Vielzahl der durch ABC-Transporter bef{\"o}rderten Molek{\"u}le erkl{\"a}rt dabei die enorme Anzahl diverser TMDs. In den Mitochondrien des Menschen findet man vier ABC-Transporter (ABCB6, ABCB7, ABCB8 und ABCB10) mit funktionellen Homologen in Hefen und Pflanzen. In Bakterien hingegen k{\"o}nnen, mit Ausnahme von Rickettsiae und verwandten Bakterien, keine Homologen zu mitochondrialen ABC-Transportern identifiziert werden. Die transportierten Molek{\"u}le sowie die damit verbundenen Funktionen sind im Einzelnen bislang weitgehend unbekannt. ABCB7 und die entsprechenden Homologen in Hefen (Atm1) und in Pflanzen (ATM3) konnten mit der cytosolischen Eisen-Schwefel-Cluster-Biosynthese in Zusammenhang gebracht werden. Eine schwefelhaltige Verbindung der mitochondrialen Matrix wird mit Hilfe dieses Transporters der cytosolischen Eisen-Schwefel-Cluster-Assemblierung zur Verf{\"u}gung gestellt. Die 2014 publizierten Kristallstrukturen von Atm1 (Hefe) und Atm1 aus Novosphingobium aromaticivorans offenbarten dabei eine hoch konservierte Glutathion-Bindetasche innerhalb der TMDs f{\"u}r ABCB7 Homologe. In der Modellpflanze Arabidopsis thaliana konnte ATM3 zus{\"a}tzlich mit der Biosynthese des Molybd{\"a}n-Cofaktors in Verbindung gebracht werden. In der vorliegenden Arbeit wurde das α-Proteobacterium Rhodobacter capsulatus als Modellorganismus genutzt, um mitochondriale ABC-Transporter Homologe zu untersuchen. Das Bakterium enth{\"a}lt zwei ABC-Transporter-Gene, rcc03139 und rcc02305, die mit den humanen mitochondrialen Transportern große Sequenz{\"u}bereinstimmungen aufweisen (rcc03139: 41 \% respektive 38 \% Identit{\"a}t mit ABCB8 und ABCB10, rcc02305: 47 \% identisch mit ABCB7 und ABCB6). Mit Hilfe erzeugter Interposon-Mutanten (Δrcc02305I und Δrcc03139I) konnte erstmals gezeigt werden, dass bakterielle Transporter funktionell sehr {\"a}hnliche Aufgaben wie die mitochondrialen ABC-Transporter {\"u}bernehmen. Beispielsweise akkumulierten beide Interposon-Mutanten reaktive Sauerstoff-Spezies (ROS) ohne gleichzeitige Akkumulation von Glutathion oder Eisen. Weiterhin konnten wir zeigen, dass, {\"a}hnlich wie bereits f{\"u}r ATM3 postuliert, die Biosynthese des Molybd{\"a}n-Cofaktors in Δrcc02305I ver{\"a}ndert ist. Mit Hilfe einer lebensf{\"a}higen Doppelmutante, in der beide ABC-Transporter-Gene gleichzeitig deletiert wurden, konnten wir ausschließen, dass die beiden bakteriellen ABC-Transporter grunds{\"a}tzlich redundante Funktionen haben. Durch die Analyse des Proteoms von Δrcc03139I im Vergleich zu der des Wildtyps, konnte eine extreme Beeinflussung der Tetrapyrrol Biosynthese sowie entsprechender Zielproteine identifiziert werden. Dies konnte zus{\"a}tzlich durch die Quantifizierung einzelner Zwischenprodukte der Biosynthese best{\"a}tigt werden. Im Gegensatz dazu konnte anhand der Analyse des Proteoms in Verbindung mit analytischen Methoden in Δrcc02305I ein Ungleichgewicht in der Schwefelverteilung identifiziert werden. Zusammen mit der Entdeckung einer Pyridoxalphosphat (PLP) Bindestelle in Rcc02305 und anderen ABCB7-artigen Transportern, welche direkt mit dem Walker-A-Motiv der NBD {\"u}berlappt, erm{\"o}glichte dies eine v{\"o}llig neue Theorie, wie die schwefelhaltige Verbindung transportiert werden kann. Wir gehen davon aus, dass an PLP zun{\"a}chst ein Persulfid produziert wird, welches unmittelbar mit dem Glutathion der transmembranen Bindetasche zu einem gemischten Polysulfid reagiert. Im Anschluss daran wird die ATP-Bindestelle frei und die Hydrolyse des ATPs l{\"o}st eine Konformations{\"a}nderung aus, welche das gemischte Polysulfid ins Periplasma bzw. in den intermembranen Raum freigibt.}, language = {en} } @phdthesis{Riedel2023, author = {Riedel, Soraya Lisanne}, title = {Development of electrochemical antibody-based and enzymatic assays for mycotoxin analysis in food}, doi = {10.25932/publishup-60747}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-607477}, school = {Universit{\"a}t Potsdam}, pages = {XV, 95}, year = {2023}, abstract = {Electrochemical methods are promising to meet the demand for easy-to-use devices monitoring key parameters in the food industry. Many companies run own lab procedures for mycotoxin analysis, but it is a major goal to simplify the analysis. The enzyme-linked immunosorbent assay using horseradish peroxidase as enzymatic label, together with 3,3',5,5' tetramethylbenzidine (TMB)/H2O2 as substrates allows sensitive mycotoxin detection with optical detection methods. For the miniaturization of the detection step, an electrochemical system for mycotoxin analysis was developed. To this end, the electrochemical detection of TMB was studied by cyclic voltammetry on different screen-printed electrodes (carbon and gold) and at different pH values (pH 1 and pH 4). A stable electrode reaction, which is the basis for the further construction of the electrochemical detection system, could be achieved at pH 1 on gold electrodes. An amperometric detection method for oxidized TMB, using a custom-made flow cell for screen-printed electrodes, was established and applied for a competitive magnetic bead-based immunoassay for the mycotoxin ochratoxin A. A limit of detection of 150 pM (60 ng/L) could be obtained and the results were verified with optical detection. The applicability of the magnetic bead-based immunoassay was tested in spiked beer using a handheld potentiostat connected via Bluetooth to a smartphone for amperometric detection allowing to quantify ochratoxin A down to 1.2 nM (0.5 µg/L). Based on the developed electrochemical detection system for TMB, the applicability of the approach was demonstrated with a magnetic bead-based immunoassay for the ergot alkaloid, ergometrine. Under optimized assay conditions a limit of detection of 3 nM (1 µg/L) was achieved and in spiked rye flour samples ergometrine levels in a range from 25 to 250 µg/kg could be quantified. All results were verified with optical detection. The developed electrochemical detection method for TMB gives great promise for the detection of TMB in many other HRP-based assays. A new sensing approach, based on an enzymatic electrochemical detection system for the mycotoxin fumonisin B1 was established using an Aspergillus niger fumonisin amine oxidase (AnFAO). AnFAO was produced recombinantly in E. coli as maltose-binding protein fusion protein and catalyzes the oxidative deamination of fumonisins, producing hydrogen peroxide. It was found that AnFAO has a high storage and temperature stability. The enzyme was coupled covalently to magnetic particles, and the enzymatically produced H2O2 in the reaction with fumonisin B1 was detected amperometrically in a flow injection system using Prussian blue/carbon electrodes and the custom-made wall-jet flow cell. Fumonisin B1 could be quantified down to 1.5 µM (≈ 1 mg/L). The developed system represents a new approach to detect mycotoxins using enzymes and electrochemical methods.}, language = {en} } @phdthesis{Riedelsberger2013, author = {Riedelsberger, Janin}, title = {Functional diversity of plant Shaker-like K+ channels and their regulation}, address = {Potsdam}, pages = {105 S.}, year = {2013}, language = {en} } @phdthesis{Rietsch2013, author = {Rietsch, Katrin}, title = {Body composition especially external skeletal robustness in association with physical activity and recreation in pre-pubertal children : a national and international investigation}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66913}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {In children the way of life, nutrition and recreation changed in recent years and as a consequence body composition shifted as well. It is established that overweight belongs to a global problem. In addition, German children exhibit a less robust skeleton than ten years ago. These developments may elevate the risk of cardiovascular diseases and skeletal modifications. Heredity and environmental factors as nutrition, socioeconomic status, physical activity and inactivity influence fat accumulation and the skeletal system. Based on these negative developments associations between type of body shape, skeletal measures and physical activity; relations between external skeletal robustness, physical activity and inactivity, BMI and body fat and also the progress of body composition especially external skeletal robustness in comparison in Russian and German children were investigated. In a cross-sectional study 691 German boys and girls aged 6 to 10 years were examined. Anthropometric measurements were taken and questionnaires about physical activity and inactivity were answered by parents. Additionally, pedometers were worn to determinate the physical activity in children. To compare the body composition in Russian and German children data from the years 2000 and 2010 were used. The study has shown that pyknomorphic individuals exhibit the highest external skeletal robustness and leptomorphic ones the lowest. Leptomorphic children may have a higher risk for bone diseases in adulthood. Pyknomorphic boys are more physically active by tendency. This is assessed as positive because pyknomorphic types display the highest BMI and body fat. Results showed that physical activity may reduce BMI and body fat. In contrast physical inactivity may lead to an increase of BMI and body fat and may rise with increasing age. Physical activity encourages additionally a robust skeleton. Furthermore external skeletal robustness is associated with BMI in order that BMI as a measure of overweight should be consider critically. The international 10-year comparison has shown an increase of BMI in Russian children and German boys. Currently, Russian children exhibit a higher external skeletal robustness than the Germans. However, in Russian boys skeleton is less robust than ten years ago. This trend should be observed in the future as well in other countries. All in all, several measures should be used to describe health situation in children and adults. Furthermore, in children it is essential to support physical activity in order to reduce the risk of obesity and to maintain a robust skeleton. In this way diseases are able to prevent in adulthood.}, language = {en} } @phdthesis{Riewe2008, author = {Riewe, David}, title = {The relevance of adenylate levels and adenylate converting enzymes on metabolism and development of potato (Solanum tuberosum L.) tubers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-27323}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Adenylates are metabolites with essential function in metabolism and signaling in all living organisms. As Cofactors, they enable thermodynamically unfavorable reactions to be catalyzed enzymatically within cells. Outside the cell, adenylates are involved in signalling processes in animals and emerging evidence suggests similar signaling mechanisms in the plants' apoplast. Presumably, apoplastic apyrases are involved in this signaling by hydrolyzing the signal mediating molecules ATP and ADP to AMP. This PhD thesis focused on the role of adenylates on metabolism and development of potato (Solanum tuberosum) by using reverse genetics and biochemical approaches. To study the short and long term effect of cellular ATP and the adenylate energy charge on potato tuber metabolism, an apyrase from Escherichia coli targeted into the amyloplast was expressed inducibly and constitutively. Both approaches led to the identification of adaptations to reduced ATP/energy charge levels on the molecular and developmental level. These comprised a reduction of metabolites and pathway fluxes that require significant amounts of ATP, like amino acid or starch synthesis, and an activation of processes that produce ATP, like respiration and an immense increase in the surface-to-volume ratio. To identify extracellular enzymes involved in adenylate conversion, green fluorescent protein and activity localization studies in potato tissue were carried out. It was found that extracellular ATP is imported into the cell by an apoplastic enzyme complement consisting of apyrase, unspecific phosphatase, adenosine nucleosidase and an adenine transport system. By changing the expression of a potato specific apyrase via transgenic approaches, it was found that this enzyme has strong impact on plant and particular tuber development in potato. Whereas metabolite levels were hardly altered, transcript profiling of tubers with reduced apyrase activity revealed a significant upregulation of genes coding for extensins, which are associated with polar growth. The results are discussed in context of adaptive responses of plants to changes in the adenylate levels and the proposed role of apyrase in apoplastic purinergic signaling and ATP salvaging. In summary, this thesis provides insight into adenylate regulated processes within and outside non-photosynthetic plant cells.}, language = {en} } @phdthesis{RobainaEstevez2017, author = {Robaina Estevez, Semidan}, title = {Context-specific metabolic predictions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401365}, school = {Universit{\"a}t Potsdam}, pages = {vi, 158}, year = {2017}, abstract = {All life-sustaining processes are ultimately driven by thousands of biochemical reactions occurring in the cells: the metabolism. These reactions form an intricate network which produces all required chemical compounds, i.e., metabolites, from a set of input molecules. Cells regulate the activity through metabolic reactions in a context-specific way; only reactions that are required in a cellular context, e.g., cell type, developmental stage or environmental condition, are usually active, while the rest remain inactive. The context-specificity of metabolism can be captured by several kinds of experimental data, such as by gene and protein expression or metabolite profiles. In addition, these context-specific data can be assimilated into computational models of metabolism, which then provide context-specific metabolic predictions. This thesis is composed of three individual studies focussing on context-specific experimental data integration into computational models of metabolism. The first study presents an optimization-based method to obtain context-specific metabolic predictions, and offers the advantage of being fully automated, i.e., free of user defined parameters. The second study explores the effects of alternative optimal solutions arising during the generation of context-specific metabolic predictions. These alternative optimal solutions are metabolic model predictions that represent equally well the integrated data, but that can markedly differ. This study proposes algorithms to analyze the space of alternative solutions, as well as some ways to cope with their impact in the predictions. Finally, the third study investigates the metabolic specialization of the guard cells of the plant Arabidopsis thaliana, and compares it with that of a different cell type, the mesophyll cells. To this end, the computational methods developed in this thesis are applied to obtain metabolic predictions specific to guard cell and mesophyll cells. These cell-specific predictions are then compared to explore the differences in metabolic activity between the two cell types. In addition, the effects of alternative optima are taken into consideration when comparing the two cell types. The computational results indicate a major reorganization of the primary metabolism in guard cells. These results are supported by an independent 13C labelling experiment.}, language = {en} } @phdthesis{Robalo2018, author = {Robalo, Jo{\~a}o Ramiro Alavedra Mendes}, title = {Investigating the role of fluorinated amino acids on protein structure and function using simulation}, school = {Universit{\"a}t Potsdam}, pages = {84}, year = {2018}, 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{RodriguezCubillos2018, author = {Rodriguez Cubillos, Andres Eduardo}, title = {Understanding the impact of heterozygosity on metabolism, growth and hybrid necrosis within a local Arabidopsis thaliana collection site}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416758}, school = {Universit{\"a}t Potsdam}, pages = {106}, year = {2018}, abstract = {Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization's impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around T{\"u}bingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size. In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed. This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation.}, language = {en} } @phdthesis{Roessner2001, author = {Roessner, Ute}, title = {Metabolic profiling of ransgenic potato tubers using GC-MS}, pages = {115 S.}, year = {2001}, language = {en} } @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{Rolo2023, author = {Rolo, David}, title = {Assembly of photosystem I in thylakoid membranes}, school = {Universit{\"a}t Potsdam}, pages = {177}, year = {2023}, abstract = {The light reactions of photosynthesis are carried out by a series of multiprotein complexes embedded in thylakoid membranes. Among them, photosystem I (PSI), acting as plastocyanin-ferderoxin oxidoreductase, catalyzes the final reaction. Together with light-harvesting antenna I, PSI forms a high-molecular-weight supercomplex of ~600 kDa, consisting of eighteen subunits and nearly two hundred co-factors. Assembly of the various components into a functional thylakoid membrane complex requires precise coordination, which is provided by the assembly machinery. Although this includes a small number of proteins (PSI assembly factors) that have been shown to play a role in the formation of PSI, the process as a whole, as well as the intricacy of its members, remains largely unexplored. In the present work, two approaches were used to find candidate PSI assembly factors. First, EnsembleNet was used to select proteins thought to be functionally related to known PSI assembly factors in Arabidopsis thaliana (approach I), and second, co-immunoprecipitation (Co-IP) of tagged PSI assembly factors in Nicotiana tabacum was performed (approach II). Here, the novel PSI assembly factors designated CO-EXPRESSED WITH PSI ASSEMBLY 1 (CEPA1) and Ycf4-INTERACTING PROTEIN 1 (Y4IP1) were identified. A. thaliana null mutants for CEPA1 and Y4IP1 showed a growth phenotype and pale leaves compared with the wild type. Biophysical experiments using pulse amplitude modulation (PAM) revealed insufficient electron transport on the PSII acceptor side. Biochemical analyses revealed that both CEPA1 and Y4IP1 are specifically involved in PSI accumulation in A. thaliana at the post-translational level but are not essential. Consistent with their roles as factors in the assembly of a thylakoid membrane protein complex, the two proteins localize to thylakoid membranes. Remarkably, cepa1 y4ip1 double mutants exhibited lethal phenotypes in early developmental stages under photoautotrophic growth. Finally, co-IP and native gel experiments supported a possible role for CEPA1 and Y4IP1 in mediating PSI assembly in conjunction with other PSI assembly factors (e.g., PPD1- and PSA3-CEPA1 and Ycf4-Y4IP1). The fact that CEPA1 and Y4IP1 are found exclusively in green algae and higher plants suggests eukaryote-specific functions. Although the specific mechanisms need further investigation, CEPA1 and Y4IP1 are two novel assembly factors that contribute to PSI formation.}, language = {en} } @phdthesis{RomeroMujalli2019, author = {Romero Mujalli, Daniel}, title = {Ecological modeling of adaptive evolutionary responses to rapid climate change}, doi = {10.25932/publishup-43062}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430627}, school = {Universit{\"a}t Potsdam}, pages = {167}, year = {2019}, abstract = {A contemporary challenge in Ecology and Evolutionary Biology is to anticipate the fate of populations of organisms in the context of a changing world. Climate change and landscape changes due to anthropic activities have been of major concern in the contemporary history. Organisms facing these threats are expected to respond by local adaptation (i.e., genetic changes or phenotypic plasticity) or by shifting their distributional range (migration). However, there are limits to their responses. For example, isolated populations will have more difficulties in developing adaptive innovations by means of genetic changes than interconnected metapopulations. Similarly, the topography of the environment can limit dispersal opportunities for crawling organisms as compared to those that rely on wind. Thus, populations of species with different life history strategy may differ in their ability to cope with changing environmental conditions. However, depending on the taxon, empirical studies investigating organisms' responses to environmental change may become too complex, long and expensive; plus, complications arising from dealing with endangered species. In consequence, eco-evolutionary modeling offers an opportunity to overcome these limitations and complement empirical studies, understand the action and limitations of underlying mechanisms, and project into possible future scenarios. In this work I take a modeling approach and investigate the effect and relative importance of evolutionary mechanisms (including phenotypic plasticity) on the ability for local adaptation of populations with different life strategy experiencing climate change scenarios. For this, I performed a review on the state of the art of eco-evolutionary Individual-Based Models (IBMs) and identify gaps for future research. Then, I used the results from the review to develop an eco-evolutionary individual-based modeling tool to study the role of genetic and plastic mechanisms in promoting local adaption of populations of organisms with different life strategies experiencing scenarios of climate change and environmental stochasticity. The environment was simulated through a climate variable (e.g., temperature) defining a phenotypic optimum moving at a given rate of change. The rate of change was changed to simulate different scenarios of climate change (no change, slow, medium, rapid climate change). Several scenarios of stochastic noise color resembling different climatic conditions were explored. Results show that populations of sexual species will rely mainly on standing genetic variation and phenotypic plasticity for local adaptation. Population of species with relatively slow growth rate (e.g., large mammals) - especially those of small size - are the most vulnerable, particularly if their plasticity is limited (i.e., specialist species). In addition, whenever organisms from these populations are capable of adaptive plasticity, they can buffer fitness losses in reddish climatic conditions. Likewise, whenever they can adjust their plastic response (e.g., bed-hedging strategy) they will cope with bluish environmental conditions as well. In contrast, life strategies of high fecundity can rely on non-adaptive plasticity for their local adaptation to novel environmental conditions, unless the rate of change is too rapid. A recommended management measure is to guarantee interconnection of isolated populations into metapopulations, such that the supply of useful genetic variation can be increased, and, at the same time, provide them with movement opportunities to follow their preferred niche, when local adaptation becomes problematic. This is particularly important for bluish and reddish climatic conditions, when the rate of change is slow, or for any climatic condition when the level of stress (rate of change) is relatively high.}, language = {en} } @phdthesis{RomeroPrada2023, author = {Romero Prada, Lorena Margarita}, title = {Crop improvement towards oxidative stress}, school = {Universit{\"a}t Potsdam}, pages = {155}, year = {2023}, language = {en} } @phdthesis{Roohi2009, author = {Roohi, Farnoosh}, title = {Synthesis and evaluation of thermo-responsive stationary phases for high performance liquid chromatography (HPLC)}, address = {Potsdam}, pages = {114 S.}, year = {2009}, language = {en} } @phdthesis{Rose2003, author = {Rose, Andreas}, title = {Analysis of phenolic compounds by dint of GDH-biosensors and immunoassays}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001048}, school = {Universit{\"a}t Potsdam}, year = {2003}, abstract = {In den letzten Jahren gerieten phenolische Substanzen, wie z.B. Chlor-, Nitrophenol oder Alkylphenolethoxylate aufgrund ihrer Toxizit{\"a}t sowie ihres kanzerogenen und endokrinen Potentials in das Interesse der {\"O}ffentlichkeit. Diese Substanzen gelangen in großen Mengen, z.B. aus industriellen Prozessen (Papier-, Kunststoff-, oder Lederindustrie) oder als Abbauprodukte von Pflanzenschutzmitteln in die Umwelt. Ziel dieser Arbeit war es, einfache biochemische Bestimmungsmethoden f{\"u}r verschiedene phenolische Umweltschadstoffe auf Basis biochemischer Erkennungselemente zu entwickeln. Diese sollten als Screeningmethoden in der Vor-Ort-Analytik einsetzbar sein. Die Anwendung sollte kosteng{\"u}nstig und einfach durchzuf{\"u}hren sein, so dass die Messung kein hochwissenschaftliches Personal erfordert. Daher stand im Hintergrund der Arbeit die Integration der Analysenmethode in ein kompaktes Handger{\"a}t. Zu diesem Zweck wurde ein Biosensor entwickelt der zur direkten Messung und in Kombination mit einem Immunoassay einsetzbar ist: 1.) Elektrochemischer Biosensor Ein elektrochemischer Biosensor stellt die Verbindung zwischen einer Elektrode und der biologischen Komponente dar. Als Messprinzip wurde die Amperometrie gew{\"a}hlt. Hierbei wird die Pr{\"a}senz des nachzuweisenden Stoffes durch die angelegte Spannung am Sensor visualisiert, da beim Vorhandensein ein Stromfluss gemessen wird. Um die Signalintensit{\"a}t zu erh{\"o}hen k{\"o}nnen Enzyme als Katalysatoren genutzt werden, die in der Lage sind die R{\"u}ckreaktion der Elektrodenreaktion zu realisieren. In diesem Fall wurde Glucose-Dehydrogenase (GDH) verwendet, die oxidierte phenolische Verbindungen reduzieren kann. Zusammen mit der Oxidation an der Sensoroberfl{\"a}che bildet sich ein Verst{\"a}rkungszyklus aus, der das urspr{\"u}ngliche Signal vielfach erh{\"o}ht. Wir waren in der Lage, GDH durch Einbetten in ein Polymerennetzwerk auf der Oberfl{\"a}che einer gedruckten Platin-Dickschicht-Elektrode zu immobilisieren. Als Resultat erhielten wir einen sehr empfindlichen und {\"a}ußerst stabilen Biosensor. Seine schnelle Ansprechzeit erm{\"o}glicht den Einsatz in automatisierten Fließsystemen zur Messung großer Probenzahlen. Der Einsatz in einem manuell betriebenen Handger{\"a}t konnte ebenfalls realisiert werden und brachte nur geringe Beeintr{\"a}chtigungen in bezug auf die Empfindlichkeit der Messung. Die erfolgreiche Implementierung des Biosensors in das Handger{\"a}t wurde in Rahmen eines internationalen Workshops in Barcelona, anhand der {\"U}berpr{\"u}fung der Reinigungsleistung von Kl{\"a}rwerken, gezeigt. 2.) Kombination mit Immunoassays Der Einsatzbereich der GDH-Biosensoren l{\"a}sst sich durch die Kombination mit anderen Techniken erweitern, wobei der Sensor zur Visualisierung der Nachweisreaktion dient. In diesem Fall kann der Sensor zur Bestimmung der Enzymaktivit{\"a}t von ß?Galactosidase (ßGal) verwendet werden. Der Nachweis geringster Enzymmengen wurde realisiert. Die ßGal wird zur Markierung eines Analytanalogen in Immunoassays verwendet, um die Bindung von Antik{\"o}rper und Analytmolek{\"u}l sichtbar zu machen. Im Immunoassay bildet sich ein Gleichgewicht zwischen Antik{\"o}rper, unmarkiertem Analyt und markiertem Analytanalog (Tracer) aus. {\"U}ber die Bestimmung der Enzymaktivit{\"a}t kann man die Analytkonzentration in der Probe errechnen. Wir haben unseren GDH-Biosensor erfolgreich mit zwei Techniken kombiniert. Zum Einen mit einem Assay zur Bestimmung von Nitrophenol, der in einem automatisiertem Fließsystem realisiert wurde. Hier wird die Mischung aus Antik{\"o}rpern, Analyt und Tracer {\"u}ber eine S{\"a}ule gegeben und gesp{\"u}lt. Die gebundenen Bestandteile werden durch den GDH-Biosensor quantifiziert. Zum Anderen wurde ein Kapillarimmunoassay entwickelt, der in das Handger{\"a}t integriert werden kann. Dabei wird der Antik{\"o}rper direkt an der Kapillare fixiert. Die Probe wird mit Tracer vermischt und in die Kapillare gegeben. Dort bildet sich das Gleichgewicht aus und weitere Probenbestandteile werden im Sp{\"u}lschritt eliminiert. Die Analytkonzentration wird durch die Bestimmung des gebunden Tracers (Aktivit{\"a}t der ßGal) mit Hilfe des GDH-Biosensors realisiert.}, language = {en} } @phdthesis{Rossmanith2005, author = {Rossmanith, Eva}, title = {Breeding biology, mating system and population dynamics of the Lesser Spotted Woodepcker (Picoides minor) : combining empirical and model investigations}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-5328}, school = {Universit{\"a}t Potsdam}, year = {2005}, abstract = {The protection of species is one major focus in conservation biology. The basis for any management concept is the knowledge of the species autecology. In my thesis, I studied the life-history traits and population dynamics of the endangered Lesser Spotted Woodpecker (Picoides minor) in Central Europe. Here, I combine a range of approaches, from empirical investigations of a Lesser Spotted Woodpecker population in the Taunus low mountain range in Germany, the analysis of empirical data and the development of an individual-based stochastic model simulating the population dynamics. In the field studies I collected basic demographic data of reproductive success and mortality. Moreover, breeding biology and behaviour were investigated in detail. My results showed a significant decrease of the reproductive success with later timing of breeding, caused by deterioration in food supply. Moreover, mate fidelity was of benefit, since pairs composed of individuals that bred together the previous year started earlier with egg laying and obtained a higher reproductive success. Both sexes were involved in parental care, but the care was only shared equally during incubation and the early nestling stage. In the late nestling stage, parental care strategies differed between sexes: Females considerably decreased feeding rate with number of nestlings and even completely deserted small broods. Males fed their nestlings irrespective of brood size and compensated for the females absence. The organisation of parental care in the Lesser Spotted Woodpecker is discussed to provide the possibility for females to mate with two males with separate nests and indeed, polyandry was confirmed. To investigate the influence of the observed flexibility in the social mating system on the population persistence, a stochastic individual-based model simulating the population dynamics of the Lesser Spotted Woodpecker was developed, based on empirical results. However, pre-breeding survival rates could not be obtained empirically and I present in this thesis a pattern-oriented modelling approach to estimate pre-breeding survival rates by comparing simulation results with empirical pattern of population structure and reproductive success on population level. Here, I estimated the pre-breeding survival for two Lesser Spotted Woodpecker populations on different latitudes to test the reliability of the results. Finally, I used the same simulation model to investigate the effect of flexibility in the mating system on the persistence of the population. With increasing rate of polyandry in the population, the persistence increased and even low rates of polyandry had a strong influence. Even when presuming only a low polyandry rate and costs of polyandry in terms of higher mortality and lower reproductive success for the secondary male, the positive effect of polyandry on the persistence of the population was still strong. This thesis greatly helped to increase the knowledge of the autecology of an endangered woodpecker species. Beyond the relevance for the species, I could demonstrate here that in general flexibility in mating systems are buffer mechanisms and reduce the impact of environmental and demographic noise.}, subject = {Modellierung}, language = {en} } @phdthesis{Rottstock2016, author = {Rottstock, Tanja}, title = {Effects of plant community diversity and composition on fungal pathogens in experimental grasslands}, school = {Universit{\"a}t Potsdam}, pages = {139}, year = {2016}, language = {en} } @phdthesis{Rudolf2008, author = {Rudolf, Lars}, title = {Population dynamics in theory and experiment : an investigation of species interactions on different scales of complexity}, pages = {109 S.}, year = {2008}, language = {en} } @phdthesis{RuizMartinez2016, author = {Ruiz-Martinez, Maria}, title = {Characterisation and engineering of lignocellulolytic enzymes from the soil bacterium Sorangium cellulosum}, school = {Universit{\"a}t Potsdam}, pages = {137}, year = {2016}, language = {en} } @phdthesis{Ruprecht2011, author = {Ruprecht, Colin}, title = {Characterization of genetic modules involved in cellulose synthesis in Arabidopsis thaliana}, address = {Potsdam}, pages = {109 S.}, year = {2011}, language = {en} } @phdthesis{Ruzicic2003, author = {Ruzicic, Slobodan}, title = {Isolation and Characterisation of Novel DOF Genese from Arabidopsis thaliana (L.) Heynh}, pages = {123 S.}, year = {2003}, language = {en} } @phdthesis{Ryngajllo2014, author = {Ryngajllo, Malgorzata}, title = {Harnessing gene expression informaton for prediction of protein subcellular localization and metabolite-coupled analysis of diurnal rythms in tomato leaves}, address = {Potsdam}, pages = {176 S.}, year = {2014}, language = {en} } @phdthesis{Roethlein2014, author = {R{\"o}thlein, Christoph}, title = {Investigation of polyglutamine fibril structure using a novel FRET-based approach}, school = {Universit{\"a}t Potsdam}, pages = {V, 119}, year = {2014}, language = {en} } @phdthesis{Sachse2014, author = {Sachse, Rita}, title = {Biological membranes in cell-free systems}, pages = {111, XIX}, year = {2014}, language = {en} } @phdthesis{Sakschewski2015, author = {Sakschewski, Boris}, title = {Impacts of major anthropogenic pressures on the terrestrial biosphere and its resilience to global change}, school = {Universit{\"a}t Potsdam}, pages = {159}, year = {2015}, language = {en} } @phdthesis{Samereier2011, author = {Samereier, Matthias}, title = {Functional analyses of microtubule and centrosome-associated proteins in Dictyostelium discoideum}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52835}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Understanding the role of microtubule-associated proteins is the key to understand the complex mechanisms regulating microtubule dynamics. This study employs the model system Dictyostelium discoideum to elucidate the role of the microtubule-associated protein TACC (Transforming acidic coiled-coil) in promoting microtubule growth and stability. Dictyostelium TACC was localized at the centrosome throughout the entire cell cycle. The protein was also detected at microtubule plus ends, however, unexpectedly only during interphase but not during mitosis. The same cell cycle-dependent localization pattern was observed for CP224, the Dictyostelium XMAP215 homologue. These ubiquitous MAPs have been found to interact with TACC proteins directly and are known to act as microtubule polymerases and nucleators. This work shows for the first time in vivo that both a TACC and XMAP215 family protein can differentially localize to microtubule plus ends during interphase and mitosis. RNAi knockdown mutants revealed that TACC promotes microtubule growth during interphase and is essential for proper formation of astral microtubules in mitosis. In many organisms, impaired microtubule stability upon TACC depletion was explained by the failure to efficiently recruit the TACC-binding XMAP215 protein to centrosomes or spindle poles. By contrast, fluorescence recovery after photobleaching (FRAP) analyses conducted in this study demonstrate that in Dictyostelium recruitment of CP224 to centrosomes or spindle poles is not perturbed in the absence of TACC. Instead, CP224 could no longer be detected at the tips of microtubules in TACC mutant cells. This finding demonstrates for the first time in vivo that a TACC protein is essential for the association of an XMAP215 protein with microtubule plus ends. The GFP-TACC strains generated in this work also turned out to be a valuable tool to study the unusual microtubule dynamics in Dictyostelium. Here, microtubules exhibit a high degree of lateral bending movements but, in contrast most other organisms, they do not obviously undergo any growth or shrinkage events during interphase. Despite of that they are affected by microtubuledepolymerizing drugs such as thiabendazole or nocodazol which are thought to act solely on dynamic microtubules. Employing 5D-fluorescence live cell microscopy and FRAP analyses this study suggests Dictyostelium microtubules to be dynamic only in the periphery, while they are stable at the centrosome. In the recent years, the identification of yet unknown components of the Dictyostelium centrosome has made tremendous progress. A proteomic approach previously conducted by our group disclosed several uncharacterized candidate proteins, which remained to be verified as genuine centrosomal components. The second part of this study focuses on the investigation of three such candidate proteins, Cenp68, CP103 and the putative spindle assembly checkpoint protein Mad1. While a GFP-CP103 fusion protein could clearly be localized to isolated centrosomes that are free of microtubules, Cenp68 and Mad1 were found to associate with the centromeres and kinetochores, respectively. The investigation of Cenp68 included the generation of a polyclonal anti-Cenp68 antibody, the screening for interacting proteins and the generation of knockout mutants which, however, did not display any obvious phenotype. Yet, Cenp68 has turned out as a very useful marker to study centromere dynamics during the entire cell cycle. During mitosis, GFP-Mad1 localization strongly resembled the behavior of other Mad1 proteins, suggesting the existence of a yet uncharacterized spindle assembly checkpoint in Dictyostelium.}, language = {en} } @phdthesis{Sammler2012, author = {Sammler, Svenja}, title = {Molecular evolution and conservation genetics in the two Philippine hornbill species Aceros waldeni and Penelopides panini}, address = {Potsdam}, pages = {105 S.}, year = {2012}, language = {en} } @phdthesis{SammlerKetmaierHavensteinetal.2012, author = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph}, title = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss}, doi = {10.1186/1471-2148-12-203}, year = {2012}, 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{Saplaoura2020, author = {Saplaoura, Eleftheria}, title = {Escaping the plant cell}, school = {Universit{\"a}t Potsdam}, pages = {156}, year = {2020}, 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{Sas2016, author = {Sas, Claudia}, title = {Evolution of the selfing syndrome in the genus capsella}, school = {Universit{\"a}t Potsdam}, pages = {94}, year = {2016}, 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{Schaarschmidt2021, author = {Schaarschmidt, Stephanie}, title = {Evaluation and application of omics approaches to characterize molecular responses to abiotic stresses in plants}, doi = {10.25932/publishup-50963}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-509630}, school = {Universit{\"a}t Potsdam}, pages = {viii, 117}, year = {2021}, abstract = {Aufgrund des globalen Klimawandels ist die Gew{\"a}hrleistung der Ern{\"a}hrungssicherheit f{\"u}r eine wachsende Weltbev{\"o}lkerung eine große Herausforderung. Insbesondere abiotische Stressoren wirken sich negativ auf Ernteertr{\"a}ge aus. Um klimaangepasste Nutzpflanzen zu entwickeln, ist ein umfassendes Verst{\"a}ndnis molekularer Ver{\"a}nderungen in der Reaktion auf unterschiedlich starke Umweltbelastungen erforderlich. Hochdurchsatz- oder "Omics"-Technologien k{\"o}nnen dazu beitragen, Schl{\"u}sselregulatoren und Wege abiotischer Stressreaktionen zu identifizieren. Zus{\"a}tzlich zur Gewinnung von Omics-Daten m{\"u}ssen auch Programme und statistische Analysen entwickelt und evaluiert werden, um zuverl{\"a}ssige biologische Ergebnisse zu erhalten. Ich habe diese Problemstellung in drei verschiedenen Studien behandelt und daf{\"u}r zwei Omics-Technologien benutzt. In der ersten Studie wurden Transkript-Daten von den beiden polymorphen Arabidopsis thaliana Akzessionen Col-0 und N14 verwendet, um sieben Programme hinsichtlich ihrer F{\"a}higkeit zur Positionierung und Quantifizierung von Illumina RNA Sequenz-Fragmenten („Reads") zu evaluieren. Zwischen 92\% und 99\% der Reads konnten an die Referenzsequenz positioniert werden und die ermittelten Verteilungen waren hoch korreliert f{\"u}r alle Programme. Bei der Durchf{\"u}hrung einer differentiellen Genexpressionsanalyse zwischen Pflanzen, die bei 20 °C oder 4 °C (K{\"a}lteakklimatisierung) exponiert wurden, ergab sich eine große paarweise {\"U}berlappung zwischen den Programmen. In der zweiten Studie habe ich die Transkriptome von zehn verschiedenen Oryza sativa (Reis) Kultivaren sequenziert. Daf{\"u}r wurde die PacBio Isoform Sequenzierungstechnologie benutzt. Die de novo Referenztranskriptome hatten zwischen 38.900 bis 54.500 hoch qualitative Isoformen pro Sorte. Die Isoformen wurden kollabiert, um die Sequenzredundanz zu verringern und danach evaluiert z.B. hinsichtlich des Vollst{\"a}ndigkeitsgrades (BUSCO), der Transkriptl{\"a}nge und der Anzahl einzigartiger Transkripte pro Genloci. F{\"u}r die hitze- und trockenheitstolerante Sorte N22 wurden ca. 650 einzigartige und neue Transkripte identifiziert, von denen 56 signifikant unterschiedlich in sich entwickelnden Samen unter kombiniertem Trocken- und Hitzestress exprimiert wurden. In der letzten Studie habe ich die Ver{\"a}nderungen in Metabolitprofilen von acht Reissorten gemessen und analysiert, die dem Stress hoher Nachttemperaturen (HNT) ausgesetzt waren und w{\"a}hrend der Trocken- und Regenzeit im Feld auf den Philippinen angebaut wurden. Es wurden jahreszeitlich bedingte Ver{\"a}nderungen im Metabolitspiegel sowie f{\"u}r agronomische Parameter identifiziert und m{\"o}gliche Stoffwechselwege, die einen Ertragsr{\"u}ckgang unter HNT-Bedingungen verursachen, vorgeschlagen. Zusammenfassend konnte ich zeigen, dass der Vergleich der RNA-seq Programme den Pflanzenwissenschaftler*innen helfen kann, sich f{\"u}r das richtige Werkzeug f{\"u}r ihre Daten zu entscheiden. Die de novo Transkriptom-Rekonstruktion von Reissorten ohne Genomsequenz bietet einen gezielten, kosteneffizienten Ansatz zur Identifizierung neuer Gene, die durch verschiedene Stressbedingungen reguliert werden unabh{\"a}ngig vom Organismus. Mit dem Metabolomik-Ansatz f{\"u}r HNT-Stress in Reis habe ich stress- und jahreszeitenspezifische Metabolite identifiziert, die in Zukunft als molekulare Marker f{\"u}r die Verbesserung von Nutzpflanzen verwendet werden k{\"o}nnten.}, language = {en} } @phdthesis{Schad2012, author = {Schad, Julia}, title = {Evolution of major histocompatibility complex genes in New World bats and their functional importance in parasite resistance and life-history decisions in the lesser bulldog bat (Noctilio albiventris)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63513}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {Immune genes of the major histocompatibility complex (MHC) constitute a central component of the adaptive immune system and play an essential role in parasite resistance and associated life-history strategies. In addition to pathogen-mediated selection also sexual selection mechanisms have been identified as the main drivers of the typically-observed high levels of polymorphism in functionally important parts of the MHC. The recognition of the individual MHC constitution is presumed to be mediated through olfactory cues. Indeed, MHC genes are in physical linkage with olfactory receptor genes and alter the individual body odour. Moreover, they are expressed on sperm and trophoplast cells. Thus, MHC-mediated sexual selection processes might not only act in direct mate choice decisions, but also through cryptic processes during reproduction. Bats (Chiroptera) represent the second largest mammalian order and have been identified as important vectors of newly emerging infectious diseases affecting humans and wildlife. In addition, they are interesting study subjects in evolutionary ecology in the context of olfactory communication, mate choice and associated fitness benefits. Thus, it is surprising that Chiroptera belong to the least studied mammalian taxa in terms of their MHC evolution. In my doctoral thesis I aimed to gain insights in the evolution and diversity pattern of functional MHC genes in some of the major New World bat families by establishing species-specific primers through genome-walking into unknown flanking parts of familiar sites. Further, I took a free-ranging population of the lesser bulldog bat (Noctilio albiventris) in Panama as an example to understand the functional importance of the individual MHC constitution in parasite resistance and reproduction as well as the possible underlying selective forces shaping the observed diversity. My studies indicated that the typical MHC characteristics observed in other mammalian orders, like evidence for balancing and positive selection as well as recombination and gene conversion events, are also present in bats shaping their MHC diversity. I found a wide range of copy number variation of expressed DRB loci in the investigated species. In Saccopteryx bilineata, a species with a highly developed olfactory communication system, I found an exceptionally high number of MHC loci duplications generating high levels of variability at the individual level, which has never been described for any other mammalian species so far. My studies included for the first time phylogenetic relationships of MHC genes in bats and I found signs for a family-specific independent mode of evolution of duplicated genes, regardless whether the highly variable exon 2 (coding for the antigen binding region of the molecule) or more conserved exons (3, 4; encoding protein stabilizing parts) were considered indicating a monophyletic origin of duplicated loci within families. This result questions the general assumed pattern of MHC evolution in mammals where duplicated genes of different families usually cluster together suggesting that duplication occurred before speciation took place, which implies a trans-species mode of evolution. However, I found a trans-species mode of evolution within genera (Noctilio, Myotis) based on exon 2 signified by an intermingled clustering of DRB alleles. The gained knowledge on MHC sequence evolution in major New World bat families will facilitate future MHC investigations in this order. In the N. albiventris study population, the single expressed MHC class II DRB gene showed high sequence polymorphism, moderate allelic variability and high levels of population-wide heterozygosity. Whereas demographic processes had minor relevance in shaping the diversity pattern, I found clear evidence for parasite-mediated selection. This was evident by historical positive Darwinian selection maintaining diversity in the functionally important antigen binding sites, and by specific MHC alleles which were associated with low and high ectoparasite burden according to predictions of the 'frequency dependent selection hypothesis'. Parasite resistance has been suggested to play an important role in mediating costly life history trade-offs leading to e.g. MHC- mediated benefits in sexual selection. The 'good genes model' predicts that males with a genetically well-adapted immune system in defending harmful parasites have the ability to allocate more resources to reproductive effort. I found support for this prediction since non-reproductive adult N. albiventris males carried more often an allele associated with high parasite loads, which differentiated them genetically from reproductively active males as well as from subadults, indicating a reduced transmission of this allele in subsequent generations. In addition, they suffered from increased ectoparasite burden which presumably reduced resources to invest in reproduction. Another sign for sexual selection was the observation of gender-specific difference in heterozygosity, with females showing lower levels of heterozygosity than males. This signifies that the sexes differ in their selection pressures, presumably through MHC-mediated molecular processes during reproduction resulting in a male specific heterozygosity advantage. My data make clear that parasite-mediated selection and sexual selection are interactive and operate together to form diversity at the MHC. Furthermore, my thesis is one of the rare studies contributing to fill the gap between MHC-mediated effects on co-evolutionary processes in parasite-host-interactions and on aspects of life-history evolution.}, language = {en} } @phdthesis{Schauer2006, author = {Schauer, Nicolas}, title = {Quantitative trait loci (QTL) for metabolite accumulation and metabolic regulation : metabolite profiling of interspecific crosses of tomato}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7643}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {The advent of large-scale and high-throughput technologies has recently caused a shift in focus in contemporary biology from decades of reductionism towards a more systemic view. Alongside the availability of genome sequences the exploration of organisms utilizing such approach should give rise to a more comprehensive understanding of complex systems. Domestication and intensive breeding of crop plants has led to a parallel narrowing of their genetic basis. The potential to improve crops by conventional breeding using elite cultivars is therefore rather limited and molecular technologies, such as marker assisted selection (MAS) are currently being exploited to re-introduce allelic variance from wild species. Molecular breeding strategies have mostly focused on the introduction of yield or resistance related traits to date. However given that medical research has highlighted the importance of crop compositional quality in the human diet this research field is rapidly becoming more important. Chemical composition of biological tissues can be efficiently assessed by metabolite profiling techniques, which allow the multivariate detection of metabolites of a given biological sample. Here, a GC/MS metabolite profiling approach has been applied to investigate natural variation of tomatoes with respect to the chemical composition of their fruits. The establishment of a mass spectral and retention index (MSRI) library was a prerequisite for this work in order to establish a framework for the identification of metabolites from a complex mixture. As mass spectral and retention index information is highly important for the metabolomics community this library was made publicly available. Metabolite profiling of tomato wild species revealed large differences in the chemical composition, especially of amino and organic acids, as well as on the sugar composition and secondary metabolites. Intriguingly, the analysis of a set of S. pennellii introgression lines (IL) identified 889 quantitative trait loci of compositional quality and 326 yield-associated traits. These traits are characterized by increases/decreases not only of single metabolites but also of entire metabolic pathways, thus highlighting the potential of this approach in uncovering novel aspects of metabolic regulation. Finally the biosynthetic pathway of the phenylalanine-derived fruit volatiles phenylethanol and phenylacetaldehyde was elucidated via a combination of metabolic profiling of natural variation, stable isotope tracer experiments and reverse genetic experimentation.}, subject = {Tomate}, language = {en} } @phdthesis{Schedina2017, author = {Schedina, Ina-Maria}, title = {Comparative genetic and transcriptomic analyses of the amazon molly, poecilia formosa and its parental species, poecilia mexicana and poecilia latipinna}, school = {Universit{\"a}t Potsdam}, pages = {124}, year = {2017}, language = {en} } @phdthesis{Scheich2004, author = {Scheich, Christoph}, title = {High-throughput evaluation of protein folding conditions and expression constructs for structural genomics}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001552}, school = {Universit{\"a}t Potsdam}, year = {2004}, abstract = {Das E. coli Expressionssystem ist das am h{\"a}ufigsten angewandte hinsichtlich der rekombinante Proteinexpression f{\"u}r strukturelle und funktionelle Analysen aufgrund der hohen erzielten Ausbeuten und der einfachen Handhabbarkeit. Allerdings ist insbesondere die Expression eukaryotischer Proteine in E. coli problematisch, z.B. wenn das Protein nicht korrekt gefaltet ist und in unl{\"o}slichen Inclusion Bodies anf{\"a}llt. In manchen F{\"a}llen ist die Analyse von Deletionskonstrukten oder einzelnen Proteindom{\"a}nen der Untersuchung des Voll{\"a}ngeproteins vorzuziehen. Dies umfasst die Herstellung eines Satzes von Expressionskonstrukten, welche charakterisiert werden m{\"u}ssen. In dieser Arbeit werden Methoden optimiert und evaluiert f{\"u}r die in vitro-Faltung von Inclusion Body-Proteinen sowie die Entwicklung einer Hochdurchsatz-Charakterisierung von Expressionskonstrukten. Die {\"U}berf{\"u}hrung von Inclusion Body-Proteinen in den nativen Zustand beinhaltet zwei Schritte: (a) Aufl{\"o}sen mit einen chaotropen Reagenz oder starkem ionischen Detergenz und (b) Faltung des Proteins durch Beseitigung des Chaotrops begleitet von dem Transfer in einen geeigneten Puffer. Die Ausbeute an nativ gefaltetem Protein ist oft stark eingeschr{\"a}nkt aufgrund von Aggregation und Fehlfaltung; sie kann allerdings durch die Zugabe bestimmter Additive zum Faltungspuffer erh{\"o}ht werden. Solche Additive m{\"u}ssen empirisch identifiziert werden. In dieser Arbeit wurde eine Testprozedur f{\"u}r Faltungsbedingungen entwickelt. Zur Reduzierung der m{\"o}glichen Kombinationen der getesteten Additive wurden sowohl empirische Beobachtungen aus der Literatur als auch bekannte Eigenschaften der Additive ber{\"u}cksichtigt. Zur Verminderung der eingesetzten Proteinmenge und des Arbeitsaufwandes wurde der Test automatisiert und miniaturisiert mittels eines Pipettierroboters. 20 Bedingungen zum schnellen Verd{\"u}nnen von denaturierten Proteinen werden hierbei getestet und zwei Bedingungen zur Faltung von Proteinen mit dem Detergenz/Cyclodextrin Protein-Faltungssystem von Rozema et al. (1996). 100 \&\#181;g Protein werden pro Bedingung eingesetzt. Zus{\"a}tzlich werden acht Bedingungen f{\"u}r die Faltung von His-Tag-Fusionsproteinen (ca. 200 \&\#181;g), welche an eine Metallchelat-Matrix immobilisiert sind, getestet. Die Testprozedur wurde erfolgreich angewendet zur Faltung eines humanen Proteins, der p22 Untereinheit von Dynactin, welche in E. coli in Inclusion Bodies exprimiert wird. So wie es sich bei vielen Proteinen darstellt, war auch f{\"u}r p22 Dynactin kein biologischer Nachweistest vorhanden, um den Erfolg des Faltungsexperimentes zu messen. Die L{\"o}slichkeit des Proteins kann nicht als eindeutiges Kriterium dienen, da neben nativ gefaltetem Protein, l{\"o}sliche fehlgefaltete Spezies und Mikroaggregate auftreten k{\"o}nnen. Diese Arbeit evaluiert Methoden zur Detektion kleiner Mengen nativen Proteins nach dem automatisierten Faltungstest. Bevor p22 Dynactin gefaltet wurde, wurden zwei Modellenzyme zur Evaluierung eingesetzt, bovine Carboanhydrase II (CAB) und Malat Dehydrogenase aus Schweineherz-Mitochondrien. Die wiedererlangte Aktivit{\"a}t nach der R{\"u}ckfaltung wurde korreliert mit verschiedenen biophysikalischen Methoden. Bindungsstudien mit 8-Anilino-1-Naphtalenesulfons{\"a}ure ergaben keine brauchbaren Informationen bei der R{\"u}ckfaltung von CAB aufgrund der zu geringen Sensitivit{\"a}t und da fehlgefaltete Proteine nicht eindeutig von nativem Protein unterschieden werden konnten. Tryptophan Fluoreszenzspektren der r{\"u}ckgefalteten CAB wurden zur Einsch{\"a}tzung des Erfolges der R{\"u}ckfaltung angewandt. Die Verschiebung des Intensit{\"a}tsmaximum zu einer niedrigeren Wellenl{\"a}nge im Vergleich zum denaturiert entfalteten Protein sowie die Fluoreszenzintensit{\"a}t korrelierten mit der wiedererlangten enzymatischen Aktivit{\"a}t. F{\"u}r beide Modellenzyme war analytische hydrophobe Interaktionschromatographie (HIC) brauchbar zur Identifizierung r{\"u}ckgefalteter Proben mit aktivem Enzym. Kompakt gefaltetes, aktives Enzym eluierte in einem distinkten Peak im abnehmenden Ammoniumsulfat-Gradienten. Das Detektionslimit f{\"u}r analytische HIC lag bei 5 \&\#181;g. Im Falle von CAB konnte gezeigt werden, dass Tryptophan-Fluoreszenz-Spektroskopie und analytische HIC in Kombination geeignet sind um Falsch-Positive oder Falsch-Negative, welche mit einem der Monitore erhalten wurden, auszuschließen. Diese beiden Methoden waren ebenfalls geeignet zur Identifizierung der Faltungsbedingungen von p22 Dynactin. Tryptophan-Fluoreszenz-Spektroskopie kann jedoch zu Falsch-Positiven f{\"u}hren, da in machen F{\"a}llen Spektren von l{\"o}slichen Mikroaggregaten kaum unterscheidbar sind von Spektren des nativ gefalteten Proteins. Dies zusammenfassend wurde eine schnelle und zuverl{\"a}ssige Testprozedur entwickelt, um Inclusion Body-Proteine einer strukturellen und funktionellen Analyse zug{\"a}nglich zu machen. In einem separaten Projekt wurden 88 verschiedene E. coli-Expressionskonstrukte f{\"u}r 17 humane Proteindom{\"a}nen, welche durch Sequenzanalyse identifiziert wurden, mit einer Hochdurchsatzreinigung und \–faltungsanalytik untersucht, um f{\"u}r die Strukturanalyse geeignete Kandidaten zu erhalten. Nach Expression in einem Milliliter im 96er Mikrotiterplattenformat und automatisierter Proteinreinigung wurden l{\"o}slich exprimierte Proteindom{\"a}nen direkt analysiert mittels 1D \&\#185;H-NMR Spektroskopie. Hierbei zeigte sich, dass insbesondere isolierte Methylgruppen-Signale unter 0.5 ppm sensitive und zuverl{\"a}ssige Sonden sind f{\"u}r gefaltetes Protein. Zus{\"a}tzlich zeigte sich, dass \– {\"a}hnlich zur Evaluierung des Faltungstests \– analytische HIC effizient eingesetzt werden kann zur Identifizierung von Konstrukten, welche kompakt gefaltetes Protein ergeben. Sechs Konstrukte, welche zwei Dom{\"a}nen repr{\"a}sentieren, konnten schnell als tauglich f{\"u}r die Strukturanalyse gefunden werden. Die Struktur einer dieser Dom{\"a}nen wurde k{\"u}rzlich von Mitarbeitern gel{\"o}st, die andere Struktur wurde im Laufe dieses Projektes von einer anderen Gruppe ver{\"o}ffentlicht.}, language = {en} } @phdthesis{Scherer2019, author = {Scherer, Philipp C{\´e}dric}, title = {Infection on the move}, school = {Universit{\"a}t Potsdam}, pages = {x, 107, XXXVIII}, year = {2019}, abstract = {Movement plays a major role in shaping population densities and contact rates among individuals, two factors that are particularly relevant for disease outbreaks. Although any differences in movement behaviour due to individual characteristics of the host and heterogeneity in landscape structure are likely to have considerable consequences for disease dynamics, these mechanisms are neglected in most epidemiological studies. Therefore, developing a general understanding how the interaction of movement behaviour and spatial heterogeneity shapes host densities, contact rates and ultimately pathogen spread is a key question in ecological and epidemiological research. In my thesis, I address this gap using both theoretical and empirical modelling approaches. In the theoretical part of my thesis, I investigated bottom-up effects of individual movement behaviour and landscape structure on host density, contact rates, and ultimately disease dynamics. I extended an established agent-based model that simulates ecological and epidemiological key processes to incorporate explicit movement of host individuals and landscape complexity. Neutral landscape models are a powerful basis for spatially-explicit modelling studies to imitate the complex characteristics of natural landscapes. In chapter 2, the first study of my thesis, I introduce two complementary R packages, NLMR and landscapetools, that I have co-developed to simplify the workflow of simulation and customization of such landscapes. To demonstrate the use of the packages I present a case study using the spatially explicit eco-epidemiological model and show that landscape complexity per se increases the probability of disease persistence. By using simple rules to simulate explicit host movement, I highlight in chapter 3 how disease dynamics are affected by population-level properties emerging from different movement rules leading to differences in the realized movement distance, spatiotemporal host density, and heterogeneity in transmission rates. As a consequence, mechanistic movement decisions based on the underlying landscape or conspecific competition led to considerably higher probabilities than phenomenological random walk approaches due directed movement leading to spatiotemporal differences in host densities. The results of these two chapters highlight the need to explicitly consider spatial heterogeneity and host movement behaviour when theoretical approaches are used to assess control measures to prevent outbreaks or eradicate diseases. In the empirical part of my thesis (chapter 4), I focus on the spatiotemporal dynamics of Classical Swine Fever in a wild boar population by analysing epidemiological data that was collected during an outbreak in Northern Germany persisting for eight years. I show that infection risk exhibits different seasonal patterns on the individual and the regional level. These patterns on the one hand show a higher infection risk in autumn and winter that may arise due to onset of mating behaviour and hunting intensity, which result in increased movement ranges. On the other hand, the increased infection risk of piglets, especially during the birth season, indicates the importance of new susceptible host individuals for local pathogen spread. The findings of this chapter underline the importance of different spatial and temporal scales to understand different components of pathogen spread that can have important implications for disease management. Taken together, the complementary use of theoretical and empirical modelling in my thesis highlights that our inferences about disease dynamics depend heavily on the spatial and temporal resolution used and how the inclusion of explicit mechanisms underlying hosts movement are modelled. My findings are an important step towards the incorporation of spatial heterogeneity and a mechanism-based perspective in eco-epidemiological approaches. This will ultimately lead to an enhanced understanding of the feedbacks of contact rates on pathogen spread and disease persistence that are of paramount importance to improve predictive models at the interface of ecology and epidemiology.}, language = {en} } @phdthesis{Schiffers2008, author = {Schiffers, Katja}, title = {Plant community response to small-scale disturbances lessons from a molehill meadow}, address = {Potsdam}, pages = {IV, 2, 106 S. : graph. Darst.}, year = {2008}, language = {en} } @phdthesis{Schirmack2015, author = {Schirmack, Janosch}, title = {Activity of methanogenic archaea under simulated Mars analog conditions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73010}, school = {Universit{\"a}t Potsdam}, pages = {VI, 108}, year = {2015}, abstract = {Assumed comparable environmental conditions of early Mars and early Earth in 3.7 Ga ago - at a time when first fossil records of life on Earth could be found - suggest the possibility of life emerging on both planets in parallel. As conditions changed, the hypothetical life on Mars either became extinct or was able to adapt and might still exist in biological niches. The controversial discussed detection of methane on Mars led to the assumption, that it must have a recent origin - either abiotic through active volcanism or chemical processes, or through biogenic production. Spatial and seasonal variations in the detected methane concentrations and correlations between the presence of water vapor and geological features such as subsurface hydrogen, which are occurring together with locally increased detected concentrations of methane, gave fuel to the hypothesis of a possible biological source of the methane on Mars. Therefore the phylogenetically old methanogenic archaea, which have evolved under early Earth conditions, are often used as model-organisms in astrobiological studies to investigate the potential of life to exist in possible extraterrestrial habitats on our neighboring planet. In this thesis methanogenic archaea originating from two extreme environments on Earth were investigated to test their ability to be active under simulated Mars analog conditions. These extreme environments - the Siberian permafrost-affected soil and the chemoautotrophically based terrestrial ecosystem of Movile cave, Romania - are regarded as analogs for possible Martian (subsurface) habitats. Two novel species of methanogenic archaea isolated from these environments were described within the frame of this thesis. It could be shown that concentrations up to 1 wt\% of Mars regolith analogs added to the growth media had a positive influence on the methane production rates of the tested methanogenic archaea, whereas higher concentrations resulted in decreasing rates. Nevertheless it was possible for the organisms to metabolize when incubated on water-saturated soil matrixes made of Mars regolith analogs without any additional nutrients. Long-term desiccation resistance of more than 400 days was proven with reincubation and indirect counting of viable cells through a combined treatment with propidium monoazide (to inactivate DNA of destroyed cells) and quantitative PCR. Phyllosilicate rich regolith analogs seem to be the best soil mixtures for the tested methanogenic archaea to be active under Mars analog conditions. Furthermore, in a simulation chamber experiment the activity of the permafrost methanogen strain Methanosarcina soligelidi SMA-21 under Mars subsurface analog conditions could be proven. Through real-time wavelength modulation spectroscopy measurements the increase in the methane concentration at temperatures down to -5 °C could be detected. The results presented in this thesis contribute to the understanding of the activity potential of methanogenic archaea under Mars analog conditions and therefore provide insights to the possible habitability of present-day Mars (near) subsurface environments. Thus, it contributes also to the data interpretation of future life detection missions on that planet. For example the ExoMars mission of the European Space Agency (ESA) and Roscosmos which is planned to be launched in 2018 and is aiming to drill in the Martian subsurface.}, language = {en} } @phdthesis{Schirmer2019, author = {Schirmer, Annika}, title = {Consistent individual differences in movement-related behaviour as equalising and/or stabilising mechanisms for species coexistence}, school = {Universit{\"a}t Potsdam}, pages = {154}, year = {2019}, abstract = {The facilitation of species coexistence has been a central theme in ecological research for years, highlighting two key aspects: ecological niches and competition between species. According to the competitive exclusion principle, the overlap of species niches predicts the amount of shared resources and therefore competition between species, determining their ability to coexist. Only if niches of two species are sufficiently different, thus niche overlap is low, competition within species is higher than competition between species and stable coexistence is possible. Thereby, differences in species mean traits are focused on and conspecific individuals are assumed to be interchangeable. This approach might be outdated since behaviour, as a key aspect mediating niche differentiation between species, is individual based. Individuals from one species consistently differ across time and situations in their behavioural traits. Causes and consequences of consistent behavioural differences have been thoroughly investigated stimulating their recent incorporation into ecological interactions and niche theory. Spatial components have so far been largely overlooked, although animal movement is strongly connected to several aspects of ecological niches and interactions between individuals. Furthermore, numerous movement aspects haven been proven to be crucially influenced by consistent individual differences. Considering spatial parameters could therefore crucially broaden our understanding of how individual niches are formed and ecological interactions are shaped. Furthermore, extending established concepts on species interactions by an individual component could provide new insights into how species coexistence is facilitated and local biodiversity is maintained. The main aim of this thesis was to test whether consistent inter-individual differences can facilitate the coexistence of ecological similar species. Therefore, the effects of consistent inter-individual differences on the spatial behaviour of two rodent species, the bank vole (Myodes glareolus) and the striped field mouse (Apodemus agrarius), were investigated and put in the context of: (i) individual spatial niches, (ii) interactions between species, and (iii) the importance of different levels of behavioural variation within species for their interactions. Consistent differences of study animals in boldness and exploration were quantified with the same tests in all presented studies and always combined with observations of movement and space use via automated VHF radio telemetry. Consequently, results are comparable throughout the thesis and the methods provide a common denominator for all chapters. The first two chapters are based on observations of free-ranging rodents in natural populations, while chapter III represents an experimental approach under semi-natural conditions. Chapter I focusses on the effect of consistent differences in boldness and exploration on movement and space use of bank voles and their contribution to individual spatial niche separation. Results show boldness to be the dominating predictor for spatial parameters in bank voles. Irrespective of sex, bolder individuals had larger home ranges, moved longer distances, had less spatial interactions with conspecifics and occupied different microhabitats compared to shy individuals. The same boldness-dependent spatial patterns could be observed in striped field mice which is reported in chapter II. Therefore, both study species showed individual spatial niche occupation. Chapter II builds on findings from the first chapter, investigating the effect of boldness driven individual spatial niche occupation on the interactions between species. Irrespective of species and sex, bolder individuals had more interspecific spatial interactions, but less intraspecific interactions, compared to shy individuals. Due to individual niches occupation the competitive environment individuals experience is not random. Interactions are restricted to individuals of similar behavioural type with presumably similar competitive ability, which could balance differences on the species level and support coexistence. In chapter III the experimental populations were either comprised of only shy or only bold bank voles, while striped field mice varied, creating either a shy- or bold-biased competitive community. Irrespective of behavioural type, striped field mice had more intraspecific interactions in bold-biased competitive communities. Only in a shy-biased competitive community, bolder striped field mice had less interspecific interactions compared to shy individuals. Bank voles showed no difference in intra- or interspecific interactions between populations. Chapter III highlights, that not only consistent inter-individual differences per se are important for interactions within and between species, but also the amount of behavioural variation within coexisting species. Overall, this thesis highlights the importance of considering consistent inter-individual differences in a spatial context and their connection to individual spatial niche occupation, as well as the resulting effects on interactions within and between species. Individual differences are discussed in the context of similarity of individuals, individual and species niche width, and individual and species niche overlap. Thereby, this thesis makes one step further from the existing research on individual niches towards integrating consistent inter-individual differences into the larger framework of species coexistence.}, language = {en} } @phdthesis{Schiro2019, author = {Schiro, Gabriele}, title = {Spatial distribution of phyllosphere fungi in topographically heterogeneous wheat fields}, school = {Universit{\"a}t Potsdam}, pages = {105}, year = {2019}, language = {en} } @phdthesis{Schlossarek2023, author = {Schlossarek, Dennis}, title = {Identification of dynamic protein-metabolite complexes in saccharomyces cerevisiae using co-fractionation mass spectrometry}, doi = {10.25932/publishup-58282}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582826}, school = {Universit{\"a}t Potsdam}, pages = {123}, year = {2023}, abstract = {Cells are built from a variety of macromolecules and metabolites. Both, the proteome and the metabolome are highly dynamic and responsive to environmental cues and developmental processes. But it is not their bare numbers, but their interactions that enable life. The protein-protein (PPI) and protein-metabolite interactions (PMI) facilitate and regulate all aspects of cell biology, from metabolism to mitosis. Therefore, the study of PPIs and PMIs and their dynamics in a cell-wide context is of great scientific interest. In this dissertation, I aim to chart a map of the dynamic PPIs and PMIs across metabolic and cellular transitions. As a model system, I study the shift from the fermentative to the respiratory growth, known as the diauxic shift, in the budding yeast Saccharomyces cerevisiae. To do so, I am applying a co-fractionation mass spectrometry (CF-MS) based method, dubbed protein metabolite interactions using size separation (PROMIS). PROMIS, as well as comparable methods, will be discussed in detail in chapter 1. Since PROMIS was developed originally for Arabidopsis thaliana, in chapter 2, I will describe the adaptation of PROMIS to S. cerevisiae. Here, the obtained results demonstrated a wealth of protein-metabolite interactions, and experimentally validated 225 previously predicted PMIs. Applying orthogonal, targeted approaches to validate the interactions of a proteogenic dipeptide, Ser-Leu, five novel protein-interactors were found. One of those proteins, phosphoglycerate kinase, is inhibited by Ser-Leu, placing the dipeptide at the regulation of glycolysis. In chapter 3, I am presenting PROMISed, a novel web-tool designed for the analysis of PROMIS- and other CF-MS-datasets. Starting with raw fractionation profiles, PROMISed enables data pre-processing, profile deconvolution, scores differences in fractionation profiles between experimental conditions, and ultimately charts interaction networks. PROMISed comes with a user-friendly graphic interface, and thus enables the routine analysis of CF-MS data by non-computational biologists. Finally, in chapter 4, I applied PROMIS in combination with the isothermal shift assay to the diauxic shift in S. cerevisiae to study changes in the PPI and PMI landscape across this metabolic transition. I found a major rewiring of protein-protein-metabolite complexes, exemplified by the disassembly of the proteasome in the respiratory phase, the loss of interaction of an enzyme involved in amino acid biosynthesis and its cofactor, as well as phase and structure specific interactions between dipeptides and enzymes of central carbon metabolism. In chapter 5, I am summarizing the presented results, and discuss a strategy to unravel the potential patterns of dipeptide accumulation and binding specificities. Lastly, I recapitulate recently postulated guidelines for CF-MS experiments, and give an outlook of protein interaction studies in the near future.}, language = {en} } @phdthesis{Schmidt2002, author = {Schmidt, Ulrike}, title = {Characterisation of the guard cell-specific phosphoenolpyruvate carboxylase and PEPC kinases from Solanum tuberosum}, pages = {108 S.}, year = {2002}, language = {en} } @phdthesis{Schmidtke2009, author = {Schmidtke, Andrea}, title = {Biodiversity effects on the performance of terrestrial plant and phytoplankton communities}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-38936}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Die {\"O}kosysteme unserer Erde sind durch das rasante Artensterben infolge von Umweltver{\"a}nderungen durch den Menschen und des globalen Klimawandels stark betroffen. Mit den Auswirkungen dieses Artenverlustes und der damit einhergehenden Ver{\"a}nderung der Diversit{\"a}t besch{\"a}ftigt sich die heutige Biodiversit{\"a}tsforschung. Spezieller wird der Effekt der Diversit{\"a}t auf {\"O}kosystemprozesse wie beispielsweise den Biomasseaufbau von Prim{\"a}rproduzenten oder der Resistenz einer Gemeinschaft gegen die Einwanderung neuer Arten untersucht. Die Quantifizierung des Einflusses der Diversit{\"a}t auf die Prim{\"a}rproduktion und das Verst{\"a}ndnis der zugrunde liegenden Mechanismen ist von besonderer Wichtigkeit. In terrestrischen Pflanzengemeinschaften wurde bereits ein positiver Diversit{\"a}tseffekt auf die Gemeinschaftsbiomasse beobachtet. Dies wird haupts{\"a}chlich durch den Komplementarit{\"a}ts- und/oder den Dominanzeffekt erkl{\"a}rt. Die Komplementarit{\"a}t zwischen Arten ist beispielsweise bei Unterschieden in der Ressourcenausnutzung gegeben (z.B. unterschiedliche Wurzeltiefen). Diese kann zu einer besseren N{\"a}hrstoffausnutzung in diverseren Gemeinschaften f{\"u}hren, die letztlich deren h{\"o}here Biomassen erkl{\"a}rt. Der Dominanzeffekt hingegen beruht auf der in diverseren Gemeinschaften h{\"o}heren Wahrscheinlichkeit, eine hochproduktive Art anzutreffen, was letztlich die h{\"o}here Biomasse der Gemeinschaft verursacht. Diversit{\"a}tseffekte auf {\"O}kosystemprozesse wurden bisher haupts{\"a}chlich auf der Gemeinschaftsebene untersucht. Analysen {\"u}ber die Reaktionen, die alle Arten einer Gemeinschaft einschließen, fehlen bisher. Daher wurde der Einfluss der Diversit{\"a}t auf die individuelle Performance von Pflanzenarten innerhalb des Biodiversit{\"a}tsprojektes „Das Jena Experiment" untersucht. Dieses Experiment umfasst 60 Arten, die charakteristisch f{\"u}r Mitteleurop{\"a}ische Graslandschaften sind. Die Arten wurden in die 4 funktionellen Gruppen Gr{\"a}ser, kleine Kr{\"a}uter, große Kr{\"a}uter und Leguminosen eingeteilt. Im Freilandversuch zeigte sich, dass mit steigender Artenzahl die individuelle Pflanzenh{\"o}he zunahm, w{\"a}hrend die individuelle oberirdische Biomasse sank. Der positive Diversit{\"a}tseffekt auf die pflanzliche Gemeinschaftsbiomasse kann folglich nicht auf der individuellen oberirdischen Biomassezunahme beruhen. {\"U}berdies reagierten die einzelnen funktionellen Gruppen und sogar die einzelnen Arten innerhalb einer funktionellen Gruppe unterschiedlich auf Diversit{\"a}tsver{\"a}nderungen. Folglich ist zu vermuten, dass einige {\"O}kosystemprozesse auf Gemeinschaftsebene durch die Reaktionen von bestimmten funktionellen Gruppen bzw. Arten hervorgerufen werden. Diversit{\"a}tseffekte auf Gemeinschaftsbiomassen wurden bislang haupts{\"a}chlich mit terrestrischen Pflanzen und weniger mit frei-schwebenden Algenarten (Phytoplankton) erforscht. Demzufolge wurde der Einfluss der Diversit{\"a}t auf die Biomasse von Phytoplankton-Gemeinschaften experimentell untersucht, wobei es sowohl zu negativen als auch positiven Diversit{\"a}tseffekten kam. Eine negative Beziehung zwischen Diversit{\"a}t und Gemeinschaftsbiomasse zeigte sich, wenn schnell-w{\"u}chsige Algenarten nur geringe Biomassen in Mono- und Mischkultur aufbauten. Die vorhandenen N{\"a}hrstoffe in der Mischkultur wurden von den schnell-w{\"u}chsigen Arten monopolisiert und folglich standen sie den langsam-w{\"u}chsigen Algenarten, welche viel Biomasse in Monokultur aufbauten, nicht mehr zur Verf{\"u}gung. Zu einem positiven Diversit{\"a}tseffekt auf die Gemeinschaftsbiomasse kam es, wenn die Artengemeinschaft eine positive Beziehung zwischen Wachstumsrate und Biomasse in Monokultur zeigte, sodass die schnell-w{\"u}chsige Algenarten viel Biomasse aufbauten. Da diese schnell-w{\"u}chsigen Algen in der Mischkultur dominant wurden, bestand die Gemeinschaft letztlich aus hoch-produktiven Algenarten, was zu einer erh{\"o}hten Gesamtbiomasse f{\"u}hrte. Diese beiden Versuchsans{\"a}tze verdeutlichen Mechanismen f{\"u}r die unterschiedlichen Reaktionen der Gemeinschaften auf Diversit{\"a}tsver{\"a}nderungen, welche auch f{\"u}r terrestrische Pflanzengemeinschaften gefunden wurden. Ein anderer wichtiger {\"O}kosystemprozess, der von der Diversit{\"a}t beeinflusst wird, ist die Anf{\"a}lligkeit von Gemeinschaften gegen{\"u}ber invasiven Arten (Invasibilit{\"a}t). Die Invasibilit{\"a}t wird von einer Vielzahl von Faktoren beeinflusst und demzufolge wurde der Effekt der Diversit{\"a}t und der Produktivit{\"a}t (N{\"a}hrstoffgehalt) auf die Invasibilit{\"a}t von Phytoplankton-Gemeinschaften in An- und Abwesenheit eines Herbivoren untersucht. Die zwei funktionell unterschiedlichen invasiven Arten waren die Blaualge Cylindrospermopsis raciborskii (schlecht fressbar) und der Phytoflagellat Cryptomonas sp. (gut fressbar). Es zeigte sich, dass der Fraßdruck, welcher selber durch die Produktivit{\"a}t beeinflusst wurde, einen bedeutenden Effekt auf die Invasibilit{\"a}t von Phytoplankton-Gemeinschaften hat. Die funktionellen Eigenschaften der invasiven und residenten Arten waren zudem bedeutender als die Artenzahl.}, language = {en} } @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} } @phdthesis{Schuette2011, author = {Sch{\"u}tte, Moritz}, title = {Evolutionary fingerprints in genome-scale networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57483}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus reproduce a recent finding or rebuild an evolutionary process in order to learn about its mechanism. The quest for evolutionary fingerprints in metabolic and gene-coexpression networks is the central topic of this cumulative thesis based on four published articles. An understanding of the actual origin of life will probably remain an insoluble problem. However, one can argue that after a first simple metabolism has evolved, the further evolution of metabolism occurred in parallel with the evolution of the sequences of the catalyzing enzymes. Indications of such a coevolution can be found when correlating the change in sequence between two enzymes with their distance on the metabolic network which is obtained from the KEGG database. We observe that there exists a small but significant correlation primarily on nearest neighbors. This indicates that enzymes catalyzing subsequent reactions tend to be descended from the same precursor. Since this correlation is relatively small one can at least assume that, if new enzymes are no "genetic children" of the previous enzymes, they certainly be descended from any of the already existing ones. Following this hypothesis, we introduce a model of enzyme-pathway coevolution. By iteratively adding enzymes, this model explores the metabolic network in a manner similar to diffusion. With implementation of an Gillespie-like algorithm we are able to introduce a tunable parameter that controls the weight of sequence similarity when choosing a new enzyme. Furthermore, this method also defines a time difference between successive evolutionary innovations in terms of a new enzyme. Overall, these simulations generate putative time-courses of the evolutionary walk on the metabolic network. By a time-series analysis, we find that the acquisition of new enzymes appears in bursts which are pronounced when the influence of the sequence similarity is higher. This behavior strongly resembles punctuated equilibrium which denotes the observation that new species tend to appear in bursts as well rather than in a gradual manner. Thus, our model helps to establish a better understanding of punctuated equilibrium giving a potential description at molecular level. From the time-courses we also extract a tentative order of new enzymes, metabolites, and even organisms. The consistence of this order with previous findings provides evidence for the validity of our approach. While the sequence of a gene is actually subject to mutations, its expression profile might also indirectly change through the evolutionary events in the cellular interplay. Gene coexpression data is simply accessible by microarray experiments and commonly illustrated using coexpression networks where genes are nodes and get linked once they show a significant coexpression. Since the large number of genes makes an illustration of the entire coexpression network difficult, clustering helps to show the network on a metalevel. Various clustering techniques already exist. However, we introduce a novel one which maintains control of the cluster sizes and thus assures proper visual inspection. An application of the method on Arabidopsis thaliana reveals that genes causing a severe phenotype often show a functional uniqueness in their network vicinity. This leads to 20 genes of so far unknown phenotype which are however suggested to be essential for plant growth. Of these, six indeed provoke such a severe phenotype, shown by mutant analysis. By an inspection of the degree distribution of the A.thaliana coexpression network, we identified two characteristics. The distribution deviates from the frequently observed power-law by a sharp truncation which follows after an over-representation of highly connected nodes. For a better understanding, we developed an evolutionary model which mimics the growth of a coexpression network by gene duplication which underlies a strong selection criterion, and slight mutational changes in the expression profile. Despite the simplicity of our assumption, we can reproduce the observed properties in A.thaliana as well as in E.coli and S.cerevisiae. The over-representation of high-degree nodes could be identified with mutually well connected genes of similar functional families: zinc fingers (PF00096), flagella, and ribosomes respectively. In conclusion, these four manuscripts demonstrate the usefulness of mathematical models and statistical tools as a source of new biological insight. While the clustering approach of gene coexpression data leads to the phenotypic characterization of so far unknown genes and thus supports genome annotation, our model approaches offer explanations for observed properties of the coexpression network and furthermore substantiate punctuated equilibrium as an evolutionary process by a deeper understanding of an underlying molecular mechanism.}, 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{Seerangan2023, author = {Seerangan, Kumar}, title = {Actin-based regulation of cell and tissue scale morphogenesis in developing leaves}, school = {Universit{\"a}t Potsdam}, pages = {120}, year = {2023}, abstract = {Leaves exhibit cells with varying degrees of shape complexity along the proximodistal axis. Heterogeneities in growth directions within individual cells bring about such complexity in cell shape. Highly complex and interconnected gene regulatory networks and signaling pathways have been identified to govern these processes. In addition, the organization of cytoskeletal networks and cell wall mechanical properties greatly influences the regulation of cell shape. Research has shown that microtubules are involved in regulating cellulose deposition and direc-tion of cell growth. However, comprehensive analysis of the regulation of the actin cytoskele-ton in cell shape regulation has not been well studied. This thesis provides evidence that actin regulates aspects of cell growth, division, and direction-al expansion that impacts morphogenesis of developing leaves. The jigsaw puzzle piece mor-phology of epidermal pavement cells further serves as an ideal system to investigate the com-plex process of morphogenetic processes occurring at the cellular level. Here we have em-ployed live cell based imaging studies to track the development of pavement cells in actin com-promised conditions. Genetic perturbation of two predominantly expressed vegetative actin genes ACTIN2 and ACTIN7 results in delayed emergence of the cellular protrusions in pave-ment cells. Perturbation of actin also impacted the organization of microtubule in these cells that is known to promote emergence of cellular protrusions. Further, live-cell imaging of actin or-ganization revealed a correlation with cell shape, suggesting that actin plays a role in influencing pavement cell morphogenesis. In addition, disruption of actin leads to an increase in cell size along the leaf midrib, with cells being highly anisotropic due to reduced cell division. The reduction of cell division further im-pacted the morphology of the entire leaf, with the mutant leaves being more curved. These re-sults suggests that actin plays a pivotal role in regulating morphogenesis at the cellular and tis-sue scales thereby providing valuable insights into the role of the actin cytoskeleton in plant morphogenesis.}, language = {en} } @phdthesis{Seibert, author = {Seibert, Tanja Stefanie}, title = {The T6P pathway in Solanum tuberosum}, pages = {212}, language = {en} } @phdthesis{Serrano2014, author = {Serrano, Paloma}, title = {Methanogens from Siberian permafrost as models for life on Mars : response to simulated martian conditions and biosignature characterization}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72299}, school = {Universit{\"a}t Potsdam}, year = {2014}, abstract = {Mars is one of the best candidates among planetary bodies for supporting life. The presence of water in the form of ice and atmospheric vapour together with the availability of biogenic elements and energy are indicators of the possibility of hosting life as we know it. The occurrence of permanently frozen ground - permafrost, is a common phenomenon on Mars and it shows multiple morphological analogies with terrestrial permafrost. Despite the extreme inhospitable conditions, highly diverse microbial communities inhabit terrestrial permafrost in large numbers. Among these are methanogenic archaea, which are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. Moreover, methanogens from Siberian permafrost are extremely resistant against different types of physiological stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. The main aims of this investigation are to assess the survival of methanogenic archaea under Mars conditions, focusing on methanogens from Siberian permafrost, and to characterize their biosignatures by means of Raman spectroscopy, a powerful technology for microbial identification that will be used in the ExoMars mission. For this purpose, methanogens from Siberian permafrost and non-permafrost habitats were subjected to simulated martian desiccation by exposure to an ultra-low subfreezing temperature (-80ºC) and to Mars regolith (S-MRS and P-MRS) and atmospheric analogues. They were also exposed to different concentrations of perchlorate, a strong oxidant found in martian soils. Moreover, the biosignatures of methanogens were characterized at the single-cell level using confocal Raman microspectroscopy (CRM). The results showed survival and methane production in all methanogenic strains under simulated martian desiccation. After exposure to subfreezing temperatures, Siberian permafrost strains had a faster metabolic recovery, whereas the membranes of non-permafrost methanogens remained intact to a greater extent. The strain Methanosarcina soligelidi SMA-21 from Siberian permafrost showed significantly higher methane production rates than all other strains after the exposure to martian soil and atmospheric analogues, and all strains survived the presence of perchlorate at the concentration on Mars. Furthermore, CRM analyses revealed remarkable differences in the overall chemical composition of permafrost and non-permafrost strains of methanogens, regardless of their phylogenetic relationship. The convergence of the chemical composition in non-sister permafrost strains may be the consequence of adaptations to the environment, and could explain their greater resistance compared to the non-permafrost strains. As part of this study, Raman spectroscopy was evaluated as an analytical technique for remote detection of methanogens embedded in a mineral matrix. This thesis contributes to the understanding of the survival limits of methanogenic archaea under simulated martian conditions to further assess the hypothetical existence of life similar to methanogens on the martian subsurface. In addition, the overall chemical composition of methanogens was characterized for the first time by means of confocal Raman microspectroscopy, with potential implications for astrobiological research.}, 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{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{Sharma2008, author = {Sharma, Reeta}, title = {Molecular genetic analysis of Bengal tiger (Panthera tigris tigres) population and its implication in conservation and wildlife forensics}, address = {Potsdam}, pages = {101 Bl. : gtaph. Darst. Kt.}, year = {2008}, language = {en} } @phdthesis{Sharma2011, author = {Sharma, Tripti}, title = {Regulation of potassium channels in plants : biophysical mechanisms and physiological implacations}, address = {Potsdam}, pages = {104 S.}, year = {2011}, language = {en} } @phdthesis{Shen2022, author = {Shen, Yawen}, title = {Functional characterization of the gene regulatory network of C2H2-type zine finger protein ZAT8 in Arabidopsis thaliana}, pages = {124}, year = {2022}, language = {en} }