@phdthesis{Jozefczuk2009,
  author    = {J{\´o}zefczuk, Szymon},
  title     = {"Escherichia coli" stress response on the level of transcriptome and metabolome},
  pages     = {XV, 121 Bl. : graph. Darst.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Balk2015,
  author    = {Balk, Maria},
  title     = {3D structured shape-memory hydrogels with enzymatically-induced shape shifting},
  school      = {Universit{\"a}t Potsdam},
  pages     = {128},
  year      = {2015},
  language  = {en}
}
@phdthesis{Stephan2023,
  author    = {Stephan, Mareike Sophia},
  title     = {A bacterial mimetic system to study bacterial inactivation and infection},
  school      = {Universit{\"a}t Potsdam},
  pages     = {150},
  year      = {2023},
  abstract  = {The emerging threat of antibiotic-resistant bacteria has become a global challenge in the last decades, leading to a rising demand for alternative treatments for bacterial infections. One approach is to target the bacterial cell envelope, making understanding its biophysical properties crucial. Specifically, bacteriophages use the bacterial envelope as an entry point to initiate infection, and they are considered important building blocks of new antibiotic strategies against drug-resistant bacteria.. Depending on the structure of the cell wall, bacteria are classified as Gram-negative and Gram-positive. Gram-negative bacteria are equipped with a complex cell envelope composed of two lipid membranes enclosing a rigid peptidoglycan layer. The synthesis machinery of the Gram-negative cell envelope is the target of antimicrobial agents, including new physical sanitizing procedures addressing the outer membrane (OM). It is therefore very important to study the biophysical properties of the Gram-negative bacterial cell envelope. The high complexity of the Gram-negative OM sets the demand for a model system in which the contribution of individual components can be evaluated separately. In this respect, giant unilamellar vesicles (GUVs) are promising membrane systems to study membrane properties while controlling parameters such as membrane composition and surrounding medium conditions. The aim of this work was to develop methods and approaches for the preparation and characterization of a GUV-based membrane model that mimics the OM of the Gram-negative cell envelope. A major component of the OM is the lipopolysaccharide (LPS) on the outside of the OM heterobilayer. The vesicle model was designed to contain LPS in the outer leaflet and lipids in the inner leaflet. Furthermore, the interaction of the prepared LPS-GUVs with bacteriophages was tested. LPS containing GUVs were prepared by adapting the inverted emulsion technique to meet the challenging properties of LPS, namely their high self-aggregation rate in aqueous solutions. Notably, an additional emulsification step together with the adaption of solution conditions was employed to asymmetrically incorporate LPS containing long polysaccharide chains into the artificial membranes. GUV membrane asymmetry was verified with a fluorescence quenching assay. Since the necessary precautions for handling the quenching agent sodium dithionite are often underestimated and poorly described, important parameters were tested and identified to obtain a stable and reproducible assay. In the context of varied LPS incorporation, a microscopy-based technique was introduced to determine the LPS content on individual GUVs and to directly compare vesicle properties and LPS coverage. Diffusion coefficient measurements in the obtained GUVs showed that increasing LPS concentrations in the membranes resulted in decreased diffusivity. Employing LPS-GUVs we could demonstrate that a Salmonella bacteriophage bound with high specificity to its LPS receptor when presented at the GUV surface, and that the number of bound bacteriophages scaled with the amount of presented LPS receptor. In addition to binding, the bacteriophages were able to eject their DNA into the vesicle lumen. LPS-GUVs thus provide a starting platform for bottom-up approaches for the generation of more complex membranes, in which the effects of individual components on the membrane properties and the interaction with antimicrobial agents such as bacteriophages could be explored.},
  language  = {en}
}
@phdthesis{Eisinger2007,
  author    = {Eisinger, Dirk},
  title     = {A new management model for developing small scale contingency plans of rabies},
  address   = {Potsdam},
  pages     = {115 S. : graph. Darst.},
  year      = {2007},
  language  = {en}
}
@phdthesis{Pellizzer2016,
  author    = {Pellizzer, Tommaso},
  title     = {A novel approach to identify plastidic factors for plastome genome incompatibility and evidence for the central involvement of the chloroplast in leaf shaping},
  school      = {Universit{\"a}t Potsdam},
  pages     = {136},
  year      = {2016},
  language  = {en}
}
@phdthesis{Wang2013,
  author    = {Wang, Ting},
  title     = {A novel R2R3 MYB-like transcription factor regulates ABA mediated stress response and leaf growth in Arabidopsis},
  address   = {Potsdam},
  pages     = {102 S.},
  year      = {2013},
  language  = {en}
}
@phdthesis{Gaetjen2023,
  author    = {G{\"a}tjen, Dominic},
  title     = {A Pichia pastoris surface display system for the efficient screening of high-producing antibody clones},
  school      = {Universit{\"a}t Potsdam},
  pages     = {120},
  year      = {2023},
  abstract  = {Pichia pastoris (syn. Komagataella phaffi) is a distinguished expression system widely used in industrial production processes. Recent molecular research has focused on numerous approaches to increase recombinant protein yield in P. pastoris. For example, the design of expression vectors and synthetic genetic elements, gene copy number optimization, or co-expression of helper proteins (transcription factors, chaperones, etc.). However, high clonal variability of transformants and low screening throughput have hampered significant success. To enhance screening capacities, display-based methodologies inherit the potential for efficient isolation of producer clones via fluorescence-activated cell sorting (FACS). Therefore, this study focused on developing a novel clone selection method that is based on the non-covalent attachment of Fab fragments on the P. pastoris cell surface to be applicable for FACS. Initially, a P. pastoris display system was developed, which is a prerequisite for the surface capture of secreted Fabs. A Design of Experiments approach was applied to analyze the influence of various genetic elements on antibody fragment display. The combined P. pastoris formaldehyde dehydrogenase promoter (PFLD1), Saccharomyces cerevisiae invertase 2 signal peptide (ScSUC2), - agglutinin (ScSAG1) anchor protein, and the ARS of Kluyveromyces lactis (panARS) conferred highest display levels. Subsequently, eight single-chain variable fragments (scFv) specific for the constant part of the Fab heavy or light chain were individually displayed in P. pastoris. Among the tested scFvs, the anti-human CH1 IgG domain scFv allowed the most efficient Fab capture detected by flow cytometry. Irrespective of the Fab sequence, exogenously added as well as simultaneously secreted Fabs were successfully captured on the cell surface. Furthermore, Fab secretion capacities were shown to correlate to the level of surface-bound Fabs as demonstrated for characterized producer clones. Flow-sorted clones presenting high amounts of Fabs showed an increase in median Fab titers (factor of 21 to 49) compared to unsorted clones when screened in deep-well plates. For selected candidates, improved functional Fab yields of sorted cells vs. unsorted cells were confirmed in an upscaled shake flask production. Since the scFv capture matrix was encoded on an episomal plasmid with inherently unstable autonomously replicating sequences (ARS), efficient plasmid curing was observed after removing the selective pressure. Hence, sorted clones could be immediately used for production without the need to modify the expression host or vector. The resulting switchable display/secretion system provides a streamlined approach for the isolation of Fab producers and subsequent Fab production.},
  language  = {en}
}
@phdthesis{Zauber2013,
  author    = {Zauber, Henrik},
  title     = {A systems biology driven approach for analyzing lipid protein interactions in sterol biosynthesis mutants},
  address   = {Potsdam},
  pages     = {126 S.},
  year      = {2013},
  language  = {en}
}
@phdthesis{Mavrothalassiti2020,
  author    = {Mavrothalassiti, Eleni},
  title     = {A.thaliana root and shoot single-cell transcriptomes and detection of mobile transcripts},
  school      = {Universit{\"a}t Potsdam},
  pages     = {133},
  year      = {2020},
  language  = {en}
}
@phdthesis{Freudenberger2013,
  author    = {Freudenberger, Lisa},
  title     = {Adaptation of nature conservation to global change: an ecosystem-based approach to priority-setting},
  address   = {Potsdam},
  pages     = {253 S.},
  year      = {2013},
  language  = {en}
}