@phdthesis{Siemiatkowska2020,
  author    = {Siemiatkowska, Beata},
  title     = {Redox signalling in plants},
  doi       = {10.25932/publishup-48911},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-489119},
  school      = {Universit{\"a}t Potsdam},
  pages     = {127},
  year      = {2020},
  abstract  = {Once proteins are synthesized, they can additionally be modified by post-translational modifications (PTMs). Proteins containing reactive cysteine thiols, stabilized in their deprotonated form due to their local environment as thiolates (RS-), serve as redox sensors by undergoing a multitude of oxidative PTMs (Ox-PTMs). Ox-PTMs such as S-nitrosylation or formation of inter- or intra-disulfide bridges induce functional changes in these proteins. Proteins containing cysteines, whose thiol oxidation state regulates their functions, belong to the so-called redoxome. Such Ox-PTMs are controlled by site-specific cellular events that play a crucial role in protein regulation, affecting enzyme catalytic sites, ligand binding affinity, protein-protein interactions or protein stability. Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in all photosynthetic organisms. Therefore, studying PTMs will remain crucial for understanding plant adaptation to external stimuli like fluctuating light conditions. Optimizing methods suitable for studying plants Ox-PTMs is of high importance for elucidation of the redoxome in plants. This study focusses on thiol modifications occurring in plant and provides novel insight into in vivo redoxome of Arabidopsis thaliana in response to light vs. dark. This was achieved by utilizing a resin-assisted thiol enrichment approach. Furthermore, confirmation of candidates on the single protein level was carried out by a differential labelling approach. The thiols and disulfides were differentially labelled, and the protein levels were detected using immunoblot analysis. Further analysis was focused on light-reduced proteins. By the enrichment approach many well studied redox-regulated proteins were identified. Amongst those were fructose 1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) which have previously been described as thioredoxin system targeted enzymes. The redox regulated proteins identified in the current study were compared to several published, independent results showing redox regulated proteins in Arabidopsis leaves, root, mitochondria and specifically S-nitrosylated proteins. These proteins were excluded as potential new candidates but remain as a proof-of-concept to the enrichment experiments to be effective. Additionally, CSP41A and CSP41B proteins, which emerged from this study as potential targets of redox-regulation, were analyzed by Ribo-Seq. The active translatome study of csp41a mutant vs. wild-type showed most of the significant changes at end of the night, similarly as csp41b. Yet, in both mutants only several chloroplast-encoded genes were altered. Further studies of CSP41A and CSP41B proteins are needed to reveal their functions and elucidate the role of redox regulation of these proteins.},
  language  = {en}
}
@phdthesis{Siewert2011,
  author    = {Siewert, Katharina},
  title     = {Autoaggressive human t cell receptorrs and their antigen specificities},
  address   = {Potsdam},
  pages     = {145 S.},
  year      = {2011},
  language  = {en}
}
@phdthesis{SilvaIturriza2008,
  author    = {Silva Iturriza, Adriana Maria},
  title     = {Evolutionary relationships between haemosporidian parasites and Philippine birds},
  address   = {Potsdam},
  pages     = {130 Bl. : graph. Darst.},
  year      = {2008},
  language  = {en}
}
@phdthesis{SimonRosin2001,
  author    = {Simon-Rosin, Ulrike},
  title     = {Isolation and characterisation of ammonium transporters from the module legumen : lotus japanicus},
  pages     = {85 S.},
  year      = {2001},
  language  = {en}
}
@phdthesis{Sin2016,
  author    = {Sin, Celine},
  title     = {Post-transcriptional control of gene expression},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-102469},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xxv, 238},
  year      = {2016},
  abstract  = {Gene expression describes the process of making functional gene products (e.g. proteins or special RNAs) from instructions encoded in the genetic information (e.g. DNA). This process is heavily regulated, allowing cells to produce the appropriate gene products necessary for cell survival, adapting production as necessary for different cell environments. Gene expression is subject to regulation at several levels, including transcription, mRNA degradation, translation and protein degradation. When intact, this system maintains cell homeostasis, keeping the cell alive and adaptable to different environments. Malfunction in the system can result in disease states and cell death. In this dissertation, we explore several aspects of gene expression control by analyzing data from biological experiments. Most of the work following uses a common mathematical model framework based on Markov chain models to test hypotheses, predict system dynamics or elucidate network topology. Our work lies in the intersection between mathematics and biology and showcases the power of statistical data analysis and math modeling for validation and discovery of biological phenomena.},
  language  = {en}
}
@phdthesis{Skirycz2007,
  author    = {Skirycz, Aleksandra},
  title     = {Functional analysis of selected DOF transcription factors in the model plant Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16987},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Transcription factors (TFs) are global regulators of gene expression playing essential roles in almost all biological processes, and are therefore of great scientific and biotechnological interest. This project focused on functional characterisation of three DNA-binding-with-one-zinc-finger (DOF) TFs from the genetic model plant Arabidopsis thaliana, namely OBP1, OBP2 and AtDOF4;2. These genes were selected due to severe growth phenotypes conferred upon their constitutive over-expression. To identify biological processes regulated by OBP1, OBP2 and AtDOF4;2 in detail molecular and physiological characterization of transgenic plants with modified levels of OBP1, OBP2 and AtDOF4;2 expression (constitutive and inducible over-expression, RNAi) was performed using both targeted and profiling technologies. Additionally expression patterns of studied TFs and their target genes were analyzed using promoter-GUS lines and publicly available microarray data. Finally selected target genes were confirmed by chromatin immuno-precipitation and electrophoretic-mobility shift assays. This combinatorial approach revealed distinct biological functions of OBP1, OBP2 and AtDOF4;2. Specifically OBP2 controls indole glucosinolate / auxin homeostasis by directly regulating the enzyme at the branch of these pathways; CYP83B1 (Skirycz et al., 2006). Glucosinolates are secondary compounds important for defence against herbivores and pathogens in the plants order Caparales (e.g. Arabidopsis, canola and broccoli) whilst auxin is an essential plant hormone. Hence OBP2 is important for both response to biotic stress and plant growth. Similarly to OBP2 also AtDOF4;2 is involved in the regulation of plant secondary metabolism and affects production of various phenylpropanoid compounds in a tissue and environmental specific manner. It was found that under certain stress conditions AtDOF4;2 negatively regulates flavonoid biosynthetic genes whilst in certain tissues it activates hydroxycinnamic acid production. It was hypothesized that this dual function is most likely related to specific interactions with other proteins; perhaps other TFs (Skirycz et al., 2007). Finally OBP1 regulates both cell proliferation and cell expansion. It was shown that OBP1 controls cell cycle activity by directly targeting the expression of core cell cycle genes (CYCD3;3 and KRP7), other TFs and components of the replication machinery. Evidence for OBP1 mediated activation of cell cycle during embryogenesis and germination will be presented. Additionally and independently on its effects on cell proliferation OBP1 negatively affects cell expansion via reduced expression of cell wall loosening enzymes. Summing up this work provides an important input into our knowledge on DOF TFs function. Future work will concentrate on establishing exact regulatory networks of OBP1, OBP2 and AtDOF4;2 and their possible biotechnological applications.},
  language  = {en}
}
@phdthesis{Sklodowski2015,
  author    = {Sklodowski, Kamil},
  title     = {Regulation of plant potassium channels},
  school      = {Universit{\"a}t Potsdam},
  pages     = {115},
  year      = {2015},
  language  = {en}
}
@phdthesis{Smirnova2012,
  author    = {Smirnova, Julia},
  title     = {Carbohydrate-active enzymes metabolising maltose: kinetic and structural features},
  address   = {Potsdam},
  pages     = {162 S.},
  year      = {2012},
  language  = {en}
}
@phdthesis{Soja2014,
  author    = {Soja, Aleksandra Maria},
  title     = {Transcriptomic and metabolomic analysis of Arabidopsis thaliana during abiotic stress},
  pages     = {134},
  year      = {2014},
  language  = {en}
}
@phdthesis{Sokolowska2016,
  author    = {Sokolowska, Ewelina Maria},
  title     = {Implementation of a plasmodesmata gatekeeper system, and its effect on intercellular transport},
  school      = {Universit{\"a}t Potsdam},
  pages     = {143},
  year      = {2016},
  language  = {en}
}