@phdthesis{Wasiolka2007,
  author    = {Wasiolka, Bernd},
  title     = {The impact of overgrazing on reptile diversity and population dynamics of Pedioplanis l. lineoocellata in the southern Kalahari},
  publisher = {Univ.-Verl.},
  address   = {Potsdam},
  pages     = {v, 101 BL. : Ill., graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Wasiolka2007,
  author    = {Wasiolka, Bernd},
  title     = {The impact of overgrazing on reptile diversity and population dynamics of Pedioplanis l. lineoocellata in the southern Kalahari},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16611},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Die Vegetationskomposition und -struktur, beispielsweise die unterschiedliche Architektur von B{\"a}umen, Str{\"a}uchern, Gr{\"a}sern und Kr{\"a}utern, bietet ein großes Spektrum an Habitaten und Nischen, die wiederum eine hohe Tierdiversit{\"a}t in den Savannensystemen des s{\"u}dlichen Afrikas erm{\"o}glichen. Dieses {\"O}kosystem wurde jedoch {\"u}ber Jahrzehnte weltweit durch intensive anthropogene Landnutzung (z.B. Viehwirtschaft) nachhaltig ver{\"a}ndert. Dabei wurden die Zusammensetzung, Diversit{\"a}t und Struktur der Vegetation stark ver{\"a}ndert. {\"U}berweidung in Savannensystemen f{\"u}hrt zu einer Degradation des Habitates einhergehend mit dem Verlust von perennierenden Gr{\"a}sern und krautiger Vegetation. Dies f{\"u}hrt zu einem Anstieg an vegetationsfreien Bodenfl{\"a}chen. Beides, sowohl der Verlust an perennierenden Gr{\"a}sern und krautiger Vegetation sowie der Anstieg an vegetationsfreien Fl{\"a}chen f{\"u}hrt zu verbesserten Etablierungsbedingungen f{\"u}r Str{\"a}ucher (z.B. Rhigozum trichotomum, Acacia mellifera) und auf lange Sicht zu stark verbuschten Fl{\"a}chen. Die Tierdiversit{\"a}t in Savannen ist hiervon entscheidend beeinflusst. Mit sinkender struktureller Diversit{\"a}t verringert sich auch die Tierdiversit{\"a}t. W{\"a}hrend der Einfluss von {\"U}berweidung auf die Vegetation relativ gut untersucht ist sind Informationen {\"u}ber den Einfluss von {\"U}berweidung auf die Tierdiversit{\"a}t, speziell f{\"u}r Reptilien, eher sp{\"a}rlich vorhanden. Zus{\"a}tzlich ist sehr wenig bekannt zum Einfluss auf die Populationsdynamik (z.B. Verhaltensanpassungen, Raumnutzung, {\"U}berlebensrate, Sterberate) einzelner Reptilienarten. Ziel meiner Doktorarbeit ist es den Einfluss von {\"U}berweidung durch kommerzielle Farmnutzung auf die Reptiliengemeinschaft und auf verschiedene Aspekte der Populationsdynamik der Echse Pedioplanis lineoocellata lineoocellata zu untersuchen. Hinsichtlich bestimmter Naturschutzmaßnahmen ist es einerseits wichtig zu verstehen welchen Auswirkungen {\"U}berweidung auf die gesamte Reptiliengemeinschaft hat. Und zum anderen wie entscheidende Faktoren der Populationsdynamik beeinflusst werden. Beides f{\"u}hrt zu einem besseren Verst{\"a}ndnis der Reaktion von Reptilien auf Habitatdegradation zu erlangen. Die Ergebnisse meiner Doktorarbeit zeigen eindeutig einen negativen Einfluss der {\"U}berweidung und der daraus resultierende Habitatdegradation auf (1) die gesamte Reptiliengemeinschaft und (2) auf einzelne Aspekte der Populationsdynamik von P. lineoocellata. Im Teil 1 wird die signifikante Reduzierung der Reptiliendiversit{\"a}t und Abundanz in degradierten Habitaten beschrieben. Im zweiten Teil wird gezeigt, dass P. lineoocellata das Verhalten an die verschlechterten Lebensbedingungen anpassen kann. Die Art bewegt sich sowohl h{\"a}ufiger als auch {\"u}ber einen l{\"a}ngeren Zeitraum und legt dabei gr{\"o}ßere Distanzen zur{\"u}ck. Zus{\"a}tzlich vergr{\"o}ßerte die Art ihr Revier (home range) (Teil 3). Im abschließenden Teil wird der negative Einfluss von {\"U}berweidung auf die Populationsdynamik von P. lineoocellata beschrieben: In degradierten Habitaten nimmt die Populationsgr{\"o}ße von adulten und juvenilen Echsen ab, die {\"U}berlebens- und Geburtenrate sinken, w{\"a}hren zus{\"a}tzlich das Pr{\"a}dationsrisiko ansteigt. Verantwortlich hierf{\"u}r ist zum einen die ebenfalls reduzierte Nahrungsverf{\"u}gbarkeit (Arthropoden) auf degradierten Fl{\"a}chen. Dies hat zur Folge, dass die Populationsgr{\"o}ße abnimmt und die Fitness der Individuen verringert wird, welches sich durch eine Reduzierung der {\"U}berlebens- und Geburtenrate bemerkbar macht. Und zum anderen ist es die Reduzierung der Vegetationsbedeckung und der R{\"u}ckgang an perennierenden Gr{\"a}sern welche sich negativ auswirken. Als Konsequenz hiervon gehen Nischen und Mikrohabitate verloren und die M{\"o}glichkeiten der Reptilien zur Thermoregulation sind verringert. Des Weiteren hat dieser Verlust an perennierender Grasbedeckung auch ein erh{\"o}htes Pr{\"a}dationsrisikos zur Folge. Zusammenfassend l{\"a}sst sich sagen, dass nicht nur B{\"a}ume und Str{\"a}ucher, wie in anderen Studien gezeigt, eine bedeutende Rolle f{\"u}r die Diversit{\"a}t spielen, sondern auch das perennierende Gras eine wichtige Rolle f{\"u}r die Faunendiversit{\"a}t spielt. Weiterhin zeigte sich, dass Habitatdegradation nicht nur die Population als gesamtes beeinflusst, sondern auch das Verhalten und Populationsparameter einzelner Arten. Des Weiteren ist es Reptilien m{\"o}glich durch Verhaltensflexibilit{\"a}t auf verschlechterte Umweltbedingen zu reagieren.},
  language  = {en}
}
@phdthesis{Weckwerth2006,
  author    = {Weckwerth, Wolfram},
  title     = {Development and applications of mass spectrometric techniques in plant physiology, biochemistry and systems biology : quantifying the molecular phenotype},
  address   = {Potsdam},
  pages     = {75, 50 S. : graph. Darst.},
  year      = {2006},
  language  = {en}
}
@phdthesis{Wegerich2010,
  author    = {Wegerich, Franziska},
  title     = {Engineered human cytochrome c : investigation of superoxide and protein-protein interaction and application in bioelectronic systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-50782},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {The aim of this thesis is the design, expression and purification of human cytochrome c mutants and their characterization with regard to electrochemical and structural properties as well as with respect to the reaction with the superoxide radical and the selected proteins sulfite oxidase from human and fungi bilirubin oxidase. All three interaction partners are studied here for the first time with human cyt c and with mutant forms of cyt c. A further aim is the incorporation of the different cyt c forms in two bioelectronic systems: an electrochemical superoxide biosensor with an enhanced sensitivity and a protein multilayer assembly with and without bilirubin oxidase on electrodes. The first part of the thesis is dedicated to the design, expression and characterization of the mutants. A focus is here the electrochemical characterization of the protein in solution and immobilized on electrodes. Further the reaction of these mutants with superoxide was investigated and the possible reaction mechanisms are discussed. In the second part of the work an amperometric superoxide biosensor with selected human cytochrome c mutants was constructed and the performance of the sensor electrodes was studied. The human wild-type and four of the five mutant electrodes could be applied successfully for the detection of the superoxide radical. In the third part of the thesis the reaction of horse heart cyt c, the human wild-type and seven human cyt c mutants with the two proteins sulfite oxidase and bilirubin oxidase was studied electrochemically and the influence of the mutations on the electron transfer reactions was discussed. Finally protein multilayer electrodes with different cyt form including the mutant forms G77K and N70K which exhibit different reaction rates towards BOD were investigated and BOD together with the wild-type and engineered cyt c was embedded in the multilayer assembly. The relevant electron transfer steps and the kinetic behavior of the multilayer electrodes are investigated since the functionality of electroactive multilayer assemblies with incorporated redox proteins is often limited by the electron transfer abilities of the proteins within the multilayer. The formation via the layer-by-layer technique and the kinetic behavior of the mono and bi-protein multilayer system are studied by SPR and cyclic voltammetry. In conclusion this thesis shows that protein engineering is a helpful instrument to study protein reactions as well as electron transfer mechanisms of complex bioelectronic systems (such as bi-protein multilayers). Furthermore, the possibility to design tailored recognition elements for the construction of biosensors with an improved performance is demonstrated.},
  language  = {en}
}
@phdthesis{Weits2015,
  author    = {Weits, Daniel},
  title     = {Regulation of the molecular response to low oxygen in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {113},
  year      = {2015},
  language  = {en}
}
@phdthesis{Weiss2011,
  author    = {Weiß, Julia},
  title     = {Computer assisted proteomics in a systems biology context},
  address   = {Potsdam},
  pages     = {VIII, 138, XVII S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{Weiss2017,
  author    = {Weiß, Lina},
  title     = {Understanding the emergence and maintenance of biodiversity in grasslands},
  school      = {Universit{\"a}t Potsdam},
  pages     = {153},
  year      = {2017},
  language  = {en}
}
@phdthesis{Welsch2022,
  author    = {Welsch, Maryna},
  title     = {Investigation of the stress tolerance regulatory network integration of the NAC transcription factor JUNGBRUNNEN1 (JUB1)},
  doi       = {10.25932/publishup-54731},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-547310},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIII, 116},
  year      = {2022},
  abstract  = {The NAC transcription factor (TF) JUNGBRUNNEN1 (JUB1) is an important negative regulator of plant senescence, as well as of gibberellic acid (GA) and brassinosteroid (BR) biosynthesis in Arabidopsis thaliana. Overexpression of JUB1 promotes longevity and enhances tolerance to drought and other abiotic stresses. A similar role of JUB1 has been observed in other plant species, including tomato and banana. Our data show that JUB1 overexpressors (JUB1-OXs) accumulate higher levels of proline than WT plants under control conditions, during the onset of drought stress, and thereafter. We identified that overexpression of JUB1 induces key proline biosynthesis and suppresses key proline degradation genes. Furthermore, bZIP63, the transcription factor involved in proline metabolism, was identified as a novel downstream target of JUB1 by Yeast One-Hybrid (Y1H) analysis and Chromatin immunoprecipitation (ChIP). However, based on Electrophoretic Mobility Shift Assay (EMSA), direct binding of JUB1 to bZIP63 could not be confirmed. Our data indicate that JUB1-OX plants exhibit reduced stomatal conductance under control conditions. However, selective overexpression of JUB1 in guard cells did not improve drought stress tolerance in Arabidopsis. Moreover, the drought-tolerant phenotype of JUB1 overexpressors does not solely depend on the transcriptional control of the DREB2A gene. Thus, our data suggest that JUB1 confers tolerance to drought stress by regulating multiple components. Until today, none of the previous studies on JUB1´s regulatory network focused on identifying protein-protein interactions. We, therefore, performed a yeast two-hybrid screen (Y2H) which identified several protein interactors of JUB1, two of which are the calcium-binding proteins CaM1 and CaM4. Both proteins interact with JUB1 in the nucleus of Arabidopsis protoplasts. Moreover, JUB1 is expressed with CaM1 and CaM4 under the same conditions. Since CaM1.1 and CaM4.1 encode proteins with identical amino acid sequences, all further experiments were performed with constructs involving the CaM4 coding sequence. Our data show that JUB1 harbors multiple CaM-binding sites, which are localized in both the N-terminal and C-terminal regions of the protein. One of the CaM-binding sites, localized in the DNA-binding domain of JUB1, was identified as a functional CaM-binding site since its mutation strongly reduced the binding of CaM4 to JUB1. Furthermore, JUB1 transactivates expression of the stress-related gene DREB2A in mesophyll cells; this effect is significantly reduced when the calcium-binding protein CaM4 is expressed as well. Overexpression of both genes in Arabidopsis results in early senescence observed through lower chlorophyll content and an enhanced expression of senescence-associated genes (SAGs) when compared with single JUB1 overexpressors. Our data also show that JUB1 and CaM4 proteins interact in senescent leaves, which have increased Ca2+ levels when compared to young leaves. Collectively, our data indicate that JUB1 activity towards its downstream targets is fine-tuned by calcium-binding proteins during leaf senescence.},
  language  = {en}
}
@phdthesis{Wen2020,
  author    = {Wen, Xi},
  title     = {Distribution patterns and environmental drivers of methane-cycling microorganisms in natural environments and restored wetlands},
  doi       = {10.25932/publishup-47177},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-471770},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, iii, 152},
  year      = {2020},
  abstract  = {Methane is an important greenhouse gas contributing to global climate change. Natural environments and restored wetlands contribute a large proportion to the global methane budget. Methanogenic archaea (methanogens) and methane oxidizing bacteria (methanotrophs), the biogenic producers and consumers of methane, play key roles in the methane cycle in those environments. A large number of studies revealed the distribution, diversity and composition of these microorganisms in individual habitats. However, uncertainties exist in predicting the response and feedback of methane-cycling microorganisms to future climate changes and related environmental changes due to the limited spatial scales considered so far, and due to a poor recognition of the biogeography of these important microorganisms combining global and local scales. With the aim of improving our understanding about whether and how methane-cycling microbial communities will be affected by a series of dynamic environmental factors in response to climate change, this PhD thesis investigates the biogeographic patterns of methane-cycling communities, and the driving factors which define these patterns at different spatial scales. At the global scale, a meta-analysis was performed by implementing 94 globally distributed public datasets together with environmental data from various natural environments including soils, lake sediments, estuaries, marine sediments, hydrothermal sediments and mud volcanos. In combination with a global biogeographic map of methanogenic archaea from multiple natural environments, this thesis revealed that biogeographic patterns of methanogens exist. The terrestrial habitats showed higher alpha diversities than marine environments. Methanoculleus and Methanosaeta (Methanothrix) are the most frequently detected taxa in marine habitats, while Methanoregula prevails in terrestrial habitats. Estuary ecosystems, the transition zones between marine and terrestrial/limnic ecosystems, have the highest methanogenic richness but comparably low methane emission rates. At the local scale, this study compared two rewetted fens with known high methane emissions in northeastern Germany, a coastal brackish fen (H{\"u}telmoor) and a freshwater riparian fen (Polder Zarnekow). Consistent with different geochemical conditions and land-use history, the two rewetted fens exhibit dissimilar methanogenic and, especially, methanotrophic community compositions. The methanotrophic community was generally under-represented among the prokaryotic communities and both fens show similarly low ratios of methanotrophic to methanogenic abundances. Since few studies have characterized methane-cycling microorganisms in rewetted fens, this study provides first evidence that the rapid and well re-established methanogenic community in combination with the low and incomplete re-establishment of the methanotrophic community after rewetting contributes to elevated sustained methane fluxes following rewetting. Finally, this thesis demonstrates that dispersal limitation only slightly regulates the biogeographic distribution patterns of methanogenic microorganisms in natural environments and restored wetlands. Instead, their existence, adaption and establishment are more associated with the selective pressures under different environmental conditions. Salinity, pH and temperature are identified as the most important factors in shaping microbial community structure at different spatial scales (global versus terrestrial environments). Predicted changes in climate, such as increasing temperature, changes in precipitation patterns and increasing frequency of flooding events, are likely to induce a series of environmental alterations, which will either directly or indirectly affect the driving environmental forces of methanogenic communities, leading to changes in their community composition and thus potentially also in methane emission patterns in the future.},
  language  = {en}
}
@phdthesis{Wenk2020,
  author    = {Wenk, Sebastian},
  title     = {Engineering formatotrophic growth in Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {V, 107},
  year      = {2020},
  abstract  = {To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli - which cannot naturally grow on formate - via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli.   In the third chapter, I present the establishment of the serine threonine cycle (STC) - a synthetic formate assimilation pathway - in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) - a short, linear formate assimilation route - in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source.},
  language  = {en}
}
@phdthesis{Westbury2018,
  author    = {Westbury, Michael V.},
  title     = {Unraveling evolution through Next Generation Sequencing},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409981},
  school      = {Universit{\"a}t Potsdam},
  pages     = {129},
  year      = {2018},
  abstract  = {The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the biological sciences, one of which being the field of evolutionary biology. Researchers have begun to move away from the study of laboratory model organisms to wild, natural populations and species which has greatly expanded our knowledge of evolution. NGS boasts a number of benefits over more traditional sequencing approaches. The main benefit comes from the capability to generate information for drastically more loci for a fraction of the cost. This is hugely beneficial to the study of wild animals as, even when large numbers of individuals are unobtainable, the amount of data produced still allows for accurate, reliable population and species level results from a small selection of individuals. The use of NGS to study species for which little to no previous research has been carried out on and the production of novel evolutionary information and reference datasets for the greater scientific community were the focuses of this thesis. Two studies in this thesis focused on producing novel mitochondrial genomes from shotgun sequencing data through iterative mapping, bypassing the need for a close relative to serve as a reference sequence. These mitochondrial genomes were then used to infer species level relationships through phylogenetic analyses. The first of these studies involved reconstructing a complete mitochondrial genome of the bat eared fox (Otocyon megalotis). Phylogenetic analyses of the mitochondrial genome confidently placed the bat eared fox as sister to the clade consisting of the raccoon dog and true foxes within the canidae family. The next study also involved reconstructing a mitochondrial genome but in this case from the extinct Macrauchenia of South America. As this study utilised ancient DNA, it involved a lot of parameter testing, quality controls and strict thresholds to obtain a near complete mitochondrial genome devoid of contamination known to plague ancient DNA studies. Phylogenetic analyses confidently placed Macrauchenia as sister to all living representatives of Perissodactyla with a divergence time of ~66 million years ago. The third and final study of this thesis involved de novo assemblies of both nuclear and mitochondrial genomes from brown and striped hyena and focussed on demographic, genetic diversity and population genomic analyses within the brown hyena. Previous studies of the brown hyena hinted at very low levels of genomic diversity and, perhaps due to this, were unable to find any notable population structure across its range. By incorporating a large number of genetic loci, in the form of complete nuclear genomes, population structure within the brown hyena was uncovered. On top of this, genomic diversity levels were compared to a number of other species. Results showed the brown hyena to have the lowest genomic diversity out of all species included in the study which was perhaps caused by a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. The studies within this thesis show the power NGS sequencing has and its utility within evolutionary biology. The most notable capabilities outlined in this thesis involve the study of species for which no reference data is available and in the production of large amounts of data, providing evolutionary answers at the species and population level that data produced using more traditional techniques simply could not.},
  language  = {en}
}
@phdthesis{Westphal2010,
  author    = {Westphal, Kera},
  title     = {Analysis of the proteasome inhibitor-induced induction of antioxidative enzymes},
  address   = {Potsdam},
  pages     = {V, 103 Bl. : graph. Darst.},
  year      = {2010},
  language  = {en}
}
@phdthesis{Wettstein2015,
  author    = {Wettstein, Christoph},
  title     = {Cytochrome c-DNA and cytochrome c-enzyme interactions for the construction of analytical signal chains},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-78367},
  school      = {Universit{\"a}t Potsdam},
  pages     = {120},
  year      = {2015},
  abstract  = {Electron transfer (ET) reactions play a crucial role in the metabolic pathways of all organisms. In biotechnological approaches, the redox properties of the protein cytochrome c (cyt c), which acts as an electron shuttle in the respiratory chain, was utilized to engineer ET chains on electrode surfaces. With the help of the biopolymer DNA, the redox protein assembles into electro active multilayer (ML) systems, providing a biocompatible matrix for the entrapment of proteins. In this study the characteristics of the cyt c and DNA interaction were defined on the molecular level for the first time and the binding sites of DNA on cyt c were identified. Persistent cyt c/DNA complexes were formed in solution under the assembly conditions of ML architectures, i.e. pH 5.0 and low ionic strength. At pH 7.0, no agglomerates were formed, permitting the characterization of the NMR spectroscopy. Using transverse relaxation-optimized spectroscopy (TROSY)-heteronuclear single quantum coherence (HSQC) experiments, DNAs' binding sites on the protein were identified. In particular, negatively charged AA residues, which are known interaction sites in cyt c/protein binding were identified as the main contact points of cyt c and DNA. Moreover, the sophisticated task of arranging proteins on electrode surfaces to create functional ET chains was addressed. Therefore, two different enzyme types, the flavin dependent fructose dehydrogenase (FDH) and the pyrroloquinoline quinone dependent glucose dehydrogenase (PQQ-GDH), were tested as reaction partners of freely diffusing cyt c and cyt c immobilized on electrodes in mono- and MLs. The characterisation of the ET processes was performed by means of electrochemistry and the protein deposition was monitored by microgravimetric measurements. FDH and PQQ-GDH were found to be generally suitable for combination with the cyt c/DNA ML system, since both enzymes interact with cyt c in solution and in the immobilized state. The immobilization of FDH and cyt c was achieved with the enzyme on top of a cyt c monolayer electrode without the help of a polyelectrolyte. Combining FDH with the cyt c/DNA ML system did not succeed, yet. However, the basic conditions for this protein-protein interaction were defined. PQQ-GDH was successfully coupled with the ML system, demonstrating that that the cyt c/DNA ML system provides a suitable interface for enzymes and that the creation of signal chains, based on the idea of co-immobilized proteins is feasible. Future work may be directed to the investigation of cyt c/DNA interaction under the precise conditions of ML assembly. Therefore, solid state NMR or X-ray crystallography may be required. Based on the results of this study, the combination of FDH with the ML system should be addressed. Moreover, alternative types of enzymes may be tested as catalytic component of the ML assembly, aiming on the development of innovative biosensor applications.},
  language  = {en}
}
@phdthesis{Wiemann2009,
  author    = {Wiemann, Annika},
  title     = {Population genetics and social dynamics in harbour porpoises and bottlenose dolphins (Cetacea) : posibble implications for nature conservation},
  address   = {Potsdam},
  pages     = {173 S.},
  year      = {2009},
  language  = {en}
}
@phdthesis{WijesinghaAhchige2022,
  author    = {Wijesingha Ahchige, Micha},
  title     = {Canalization of plant metabolism and yield},
  doi       = {10.25932/publishup-54884},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-548844},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, 160},
  year      = {2022},
  abstract  = {Plant metabolism is the main process of converting assimilated carbon to different crucial compounds for plant growth and therefore crop yield, which makes it an important research topic. Although major advances in understanding genetic principles contributing to metabolism and yield have been made, little is known about the genetics responsible for trait variation or canalization although the concepts have been known for a long time. In light of a growing global population and progressing climate change, understanding canalization of metabolism and yield seems ever-more important to ensure food security. Our group has recently found canalization metabolite quantitative trait loci (cmQTL) for tomato fruit metabolism, showing that the concept of canalization applies on metabolism. In this work two approaches to investigate plant metabolic canalization and one approach to investigate yield canalization are presented. In the first project, primary and secondary metabolic data from Arabidopsis thaliana and Phaseolus vulgaris leaf material, obtained from plants grown under different conditions was used to calculate cross-environment coefficient of variations or fold-changes of metabolite levels per genotype and used as input for genome wide association studies. While primary metabolites have lower CV across conditions and show few and mostly weak associations to genomic regions, secondary metabolites have higher CV and show more, strong metabolite to genome associations. As candidate genes, both potential regulatory genes as well as metabolic genes, can be found, albeit most metabolic genes are rarely directly related to the target metabolites, suggesting a role for both potential regulatory mechanisms as well as metabolic network structure for canalization of metabolism. In the second project, candidate genes of the Solanum lycopersicum cmQTL mapping are selected and CRISPR/Cas9-mediated gene-edited tomato lines are created, to validate the genes role in canalization of metabolism. Obtained mutants appeared to either have strong aberrant developmental phenotypes or appear wild type-like. One phenotypically inconspicuous mutant of a pantothenate kinase, selected as candidate for malic acid canalization shows a significant increase of CV across different watering conditions. Another such mutant of a protein putatively involved in amino acid transport, selected as candidate for phenylalanine canalization shows a similar tendency to increased CV without statistical significance. This potential role of two genes involved in metabolism supports the hypothesis of structural relevance of metabolism for its own stability. In the third project, a mutant for a putative disulfide isomerase, important for thylakoid biogenesis, is characterized by a multi-omics approach. The mutant was characterized previously in a yield stability screening and showed a variegated leaf phenotype, ranging from green leaves with wild type levels of chlorophyll over differently patterned variegated to completely white leaves almost completely devoid of photosynthetic pigments. White mutant leaves show wild type transcript levels of photosystem assembly factors, with the exception of ELIP and DEG orthologs indicating a stagnation at an etioplast to chloroplast transition state. Green mutant leaves show an upregulation of these assembly factors, possibly acting as overcompensation for partially defective disulfide isomerase, which seems sufficient for proper chloroplast development as confirmed by a wild type-like proteome. Likely as a result of this phenotype, a general stress response, a shift to a sink-like tissue and abnormal thylakoid membranes, strongly alter the metabolic profile of white mutant leaves. As the severity and pattern of variegation varies from plant to plant and may be effected by external factors, the effect on yield instability, may be a cause of a decanalized ability to fully exploit the whole leaf surface area for photosynthetic activity.},
  language  = {en}
}
@phdthesis{Wilczek2005,
  author    = {Wilczek, Sabine},
  title     = {Spatial and seasonal distribution of extracellular enzyme activities in the River Elbe and their regulation by envirommental variables},
  pages     = {114 S. : Ill., graph. Darst.},
  year      = {2005},
  language  = {en}
}
@phdthesis{Wilhelm2007,
  author    = {Wilhelm, Susann},
  title     = {Climate induced impacts on lake functioning in summer},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14599},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Es gibt bereits viele Hinweise daf{\"u}r, dass Seen sehr sensibel auf die anthropogen verursachte Klimaerw{\"a}rmung reagiert haben. Bis jetzt haben sich die Studien der Klimafolgenforschung haupts{\"a}chlichst auf die Auswirkungen der Erw{\"a}rmung im Winter und Fr{\"u}hling konzentriert. {\"U}ber den Einfluss der Klimaerw{\"a}rmung auf Seen in den gem{\"a}ßigten Breiten im Sommer ist weniger bekannt. In der vorliegenden Doktorarbeit habe ich einige Faktoren, welche die Reaktion von Seen auf die Erw{\"a}rmung im Sommer vermutlich stark mitbestimmt haben, untersucht. Der Schwerpunkt lag dabei auf klimatisch induzierten Auswirkungen auf die thermische Charakteristik und die Ph{\"a}nologie und Abundanz des Planktons eines flachen und polymiktischen Sees (M{\"u}ggelsee, Berlin). Zuerst wurde der Einfluss der Klimaerw{\"a}rmung auf die Ph{\"a}nologie und Abundanz des Planktons in verschiedenen Jahreszeiten untersucht. Das schnellwachsende Phyto- und Zooplankton (Daphnia) im Fr{\"u}hjahr hat sich vorwiegend synchron vorverschoben, wohingegen Ver{\"a}nderungen des Sommerzooplanktons deutlich artspezifisch und nicht synchron waren. Die Ph{\"a}nologie oder Abundanz einiger Sommercopepoden hat sich entsprechend der individuellen thermischen Anforderungen innerhalb bestimmter Entwicklungsstufen, wie zum Beispiel der Emergenz von der Diapause im Fr{\"u}hling, ver{\"a}ndert. Die Studie unterstreicht, dass nicht nur der Grad der Erw{\"a}rmung, sondern auch dessen Zeitpunkt innerhalb des Jahres von großer {\"o}kologischer Bedeutung ist. Um die Auswirkungen des Klimawandels auf die thermischen Eigenschaften des Sees zu erforschen, habe ich die Langzeitentwicklung der t{\"a}glichen epilimnischen Temperaturextrema w{\"a}hrend des Sommers untersucht. Durch diese Studie wurde zum ersten Mal f{\"u}r Seen gezeigt, dass die t{\"a}glichen epilimnischen Minima (Nacht) st{\"a}rker angestiegen sind als die Maxima (Tag), wodurch sich der t{\"a}gliche epilimnische Temperaturbereich deutlich verringert hat. Diese Tag-Nacht-Asymmetrie in der epilimnischen Temperatur wurde durch eine erh{\"o}hte Emission von Langwellenstrahlung aus der Atmosph{\"a}re w{\"a}hrend der Nacht verursacht. Dies unterstreicht, dass nicht nur Erh{\"o}hungen der Lufttemperatur, sondern auch {\"A}nderungen anderer meteorologischer Variablen wie der Windgeschwindigkeit, der Luftfeuchte und der Bew{\"o}lkung eine wichtige Rolle bei der Bestimmung der Seetemperatur im Hinblick auf weitere Klimaver{\"a}nderungen spielen werden. Zudem wurde eine Kurzzeitanalyse zum Schichtungsverhalten des polymiktischen Sees durchgef{\"u}hrt, um die H{\"a}ufigkeit und Dauer von Schichtungsereignissen und deren Einfluss auf den gel{\"o}sten Sauerstoff, die gel{\"o}sten N{\"a}hrstoffe und das Phytoplankton zu untersuchen. Selbst w{\"a}hrend der l{\"a}ngsten Schichtungsereignisse (Hitzewellen 2003 und 2006) unterschieden sich die Auswirkungen auf den See von denen, welche in flachen dimiktischen Seen w{\"a}hrend der kontinuierlichen Sommerschichtung auftreten. Die hypolimnische Temperatur war h{\"o}her, was die Sauerstoffzehrung und die Akkumulation von gel{\"o}sten N{\"a}hrstoffen beg{\"u}nstigt hat. Die thermische Schichtung wird in Zukunft sehr wahrscheinlich zunehmen. Dies l{\"a}sst darauf schließen, dass polymiktische Seen sehr anf{\"a}llig gegen{\"u}ber {\"A}nderungen im Hinblick auf projizierte Klimaver{\"a}nderungen sein werden. Abschließend wurde eine Studie {\"u}ber Lang- und Kurzzeitver{\"a}nderungen in der Entwicklung der planktischen Larven der Muschel Dreissena polymorpha durchgef{\"u}hrt, um den Einfluss der Ver{\"a}nderungen im thermischen und trophischen Regime des Sees zu analysieren. Die Klimaerw{\"a}rmung und die Verringerung in der externen N{\"a}hrstofffracht haben die Abundanz der Larven stark beeinflusst indem sie jeweils auf bestimmte Entwicklungsphasen dieser Art w{\"a}hrend der warmen Jahreszeiten gewirkt haben. Der Anstieg in der Abundanz und der L{\"a}nge der Larven stand im Zusammenhang mit dem R{\"u}ckgang der N{\"a}hrstofffracht und der Ver{\"a}nderung der Phytoplanktonzusammensetzung. Die Hitzewellen in den Jahren 2003 und 2006 haben diesen positiven Effekt auf die Larvenabundanz jedoch durch ung{\"u}nstige Sauerstoffkonzentrationen w{\"a}hrend der sehr langen Schichtung aufgehoben. Die Klimaerw{\"a}rmung kann demzufolge entgegenwirkende Effekte in produktiven flachen Seen, in welchen die externe N{\"a}hrstofffracht reduziert wurde, ausl{\"o}sen. Aus diesen Ergebnissen schließe ich, dass nicht nur die Art des Klimawandels und damit der Zeitpunkt der Erw{\"a}rmung und das Auftreten von Extremen wie Hitzewellen, sondern auch standortspezifische Bedingungen wie Schichtungsverhalten und Trophiegrad entscheidende Faktoren sind, welche die Auswirkungen der Klimaerw{\"a}rmung auf interne Seeprozesse im Sommer bestimmen. Somit sollte sich die weiterf{\"u}hrende Klimafolgenforschung f{\"u}r Seen darauf konzentrieren, wie verschiedene Seetypen auf die komplexen Umweltver{\"a}nderungen im Sommer reagieren, damit ein umfassenderes Verst{\"a}ndnis {\"u}ber den Einfluss von anthropogen verursachten Ver{\"a}nderungen auf Seen der gem{\"a}ßigten Breiten erreicht wird.},
  language  = {en}
}
@phdthesis{Winck2011,
  author    = {Winck, Flavia Vischi},
  title     = {Nuclear proteomics and transcription factor profiling in Chlamydomonas reinhardtii},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53909},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {The transcriptional regulation of the cellular mechanisms involves many different components and different levels of control which together contribute to fine tune the response of cells to different environmental stimuli. In some responses, diverse signaling pathways can be controlled simultaneously. One of the most important cellular processes that seem to possess multiple levels of regulation is photosynthesis. A model organism for studying photosynthesis-related processes is the unicellular green algae Chlamydomonas reinhardtii, due to advantages related to culturing, genetic manipulation and availability of genome sequence. In the present study, we were interested in understanding the regulatory mechanisms underlying photosynthesis-related processes. To achieve this goal different molecular approaches were followed. In order to indentify protein transcriptional regulators we optimized a method for isolation of nuclei and performed nuclear proteome analysis using shotgun proteomics. This analysis permitted us to improve the genome annotation previously published and to discover conserved and enriched protein motifs among the nuclear proteins. In another approach, a quantitative RT-PCR platform was established for the analysis of gene expression of predicted transcription factor (TF) and other transcriptional regulator (TR) coding genes by transcript profiling. The gene expression profiles for more than one hundred genes were monitored in time series experiments under conditions of changes in light intensity (200 µE m-2 s-1 to 700 µE m-2 s-1), and changes in concentration of carbon dioxide (5\% CO2 to 0.04\% CO2). The results indicate that many TF and TR genes are regulated in both environmental conditions and groups of co-regulated genes were found. Our findings also suggest that some genes can be common intermediates of light and carbon responsive regulatory pathways. These approaches together gave us new insights about the regulation of photosynthesis and revealed new candidate regulatory genes, helping to decipher the gene regulatory networks in Chlamydomonas. Further experimental studies are necessary to clarify the function of the candidate regulatory genes and to elucidate how cells coordinately regulate the assimilation of carbon and light responses.},
  language  = {en}
}
@phdthesis{Wojciechowska2022,
  author    = {Wojciechowska, Izabela},
  title     = {The journey towards the discovery of new protein-metabolite interactions in Arabidopsis thaliana and further functional characterization of selected binding events},
  school      = {Universit{\"a}t Potsdam},
  pages     = {150},
  year      = {2022},
  language  = {en}
}
@phdthesis{Wojcik2024,
  author    = {Wojcik, Laurie Anne Myriam},
  title     = {Beyond a single diversity facet: implications for the links between biodiversity, environmental changes and ecosystem functioning},
  doi       = {10.25932/publishup-64692},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-646925},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vi, 189},
  year      = {2024},
  abstract  = {Human activities modify nature worldwide via changes in the environment, biodiversity and the functioning of ecosystems, which in turn disrupt ecosystem services and feed back negatively on humans. A pressing challenge is thus to limit our impact on nature, and this requires detailed understanding of the interconnections between the environment, biodiversity and ecosystem functioning. These three components of ecosystems each include multiple dimensions, which interact with each other in different ways, but we lack a comprehensive picture of their interconnections and underlying mechanisms. Notably, diversity is often viewed as a single facet, namely species diversity, while many more facets exist at different levels of biological organisation (e.g. genetic, phenotypic, functional, multitrophic diversity), and multiple diversity facets together constitute the raw material for adaptation to environmental changes and shape ecosystem functioning. Consequently, investigating the multidimensionality of ecosystems, and in particular the links between multifaceted diversity, environmental changes and ecosystem functions, is crucial for ecological research, management and conservation. This thesis aims to explore several aspects of this question theoretically. I investigate three broad topics in this thesis. First, I focus on how food webs with varying levels of functional diversity across three trophic levels buffer environmental changes, such as a sudden addition of nutrients or long-term changes (e.g. warming or eutrophication). I observed that functional diversity generally enhanced ecological stability (i.e. the buffering capacity of the food web) by increasing trophic coupling. More precisely, two aspects of ecological stability (resistance and resilience) increased even though a third aspect (the inverse of the time required for the system to reach its post-perturbation state) decreased with increasing functional diversity. Second, I explore how several diversity facets served as a raw material for different sources of adaptation and how these sources affected multiple ecosystem functions across two trophic levels. Considering several sources of adaptation enabled the interplay between ecological and evolutionary processes, which affected trophic coupling and thereby ecosystem functioning. Third, I reflect further on the multifaceted nature of diversity by developing an index K able to quantify the facet of functional diversity, which is itself multifaceted. K can provide a comprehensive picture of functional diversity and is a rather good predictor of ecosystem functioning. Finally I synthesise the interdependent mechanisms (complementarity and selection effects, trophic coupling and adaptation) underlying the relationships between multifaceted diversity, ecosystem functioning and the environment, and discuss the generalisation of my findings across ecosystems and further perspectives towards elaborating an operational biodiversity-ecosystem functioning framework for research and conservation.},
  language  = {en}
}