@phdthesis{Šustr2020,
  author    = {Šustr, David},
  title     = {Molecular diffusion in polyelectrolyte multilayers},
  doi       = {10.25932/publishup-48903},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-489038},
  school      = {Universit{\"a}t Potsdam},
  pages     = {106},
  year      = {2020},
  abstract  = {Research on novel and advanced biomaterials is an indispensable step towards their applications in desirable fields such as tissue engineering, regenerative medicine, cell culture, or biotechnology. The work presented here focuses on such a promising material: polyelectrolyte multilayer (PEM) composed of hyaluronic acid (HA) and poly(L-lysine) (PLL). This gel-like polymer surface coating is able to accumulate (bio-)molecules such as proteins or drugs and release them in a controlled manner. It serves as a mimic of the extracellular matrix (ECM) in composition and intrinsic properties. These qualities make the HA/PLL multilayers a promising candidate for multiple bio-applications such as those mentioned above. The work presented aims at the development of a straightforward approach for assessment of multi-fractional diffusion in multilayers (first part) and at control of local molecular transport into or from the multilayers by laser light trigger (second part). The mechanism of the loading and release is governed by the interaction of bioactives with the multilayer constituents and by the diffusion phenomenon overall. The diffusion of a molecule in HA/PLL multilayers shows multiple fractions of different diffusion rate. Approaches, that are able to assess the mobility of molecules in such a complex system, are limited. This shortcoming motivated the design of a novel evaluation tool presented here. The tool employs a simulation-based approach for evaluation of the data acquired by fluorescence recovery after photobleaching (FRAP) method. In this approach, possible fluorescence recovery scenarios are primarily simulated and afterwards compared with the data acquired while optimizing parameters of a model until a sufficient match is achieved. Fluorescent latex particles of different sizes and fluorescein in an aqueous medium are utilized as test samples validating the analysis results. The diffusion of protein cytochrome c in HA/PLL multilayers is evaluated as well. This tool significantly broadens the possibilities of analysis of spatiotemporal FRAP data, which originate from multi-fractional diffusion, while striving to be widely applicable. This tool has the potential to elucidate the mechanisms of molecular transport and empower rational engineering of the drug release systems. The second part of the work focuses on the fabrication of such a spatiotemporarily-controlled drug release system employing the HA/PLL multilayer. This release system comprises different layers of various functionalities that together form a sandwich structure. The bottom layer, which serves as a reservoir, is formed by HA/PLL PEM deposited on a planar glass substrate. On top of the PEM, a layer of so-called hybrids is deposited. The hybrids consist of thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) -based hydrogel microparticles with surface-attached gold nanorods. The layer of hybrids is intended to serve as a gate that controls the local molecular transport through the PEM-solution-interface. The possibility of stimulating the molecular transport by near-infrared (NIR) laser irradiation is being explored. From several tested approaches for the deposition of hybrids onto the PEM surface, the drying-based approach was identified as optimal. Experiments, that examine the functionality of the fabricated sandwich at elevated temperature, document the reversible volume phase transition of the PEM-attached hybrids while sustaining the sandwich stability. Further, the gold nanorods were shown to effectively absorb light radiation in the tissue- and cell-friendly NIR spectral region while transducing the energy of light into heat. The rapid and reversible shrinkage of the PEM-attached hybrids was thereby achieved. Finally, dextran was employed as a model transport molecule. It loads into the PEM reservoir in a few seconds with the partition constant of 2.4, while it spontaneously releases in a slower, sustained manner. The local laser irradiation of the sandwich, which contains the fluorescein isothiocyanate tagged dextran, leads to a gradual reduction of fluorescence intensity in the irradiated region. The release system fabricated employs renowned photoresponsivity of the hybrids in an innovative setting. The results of the research are a step towards a spatially-controlled on-demand drug release system that paves the way to spatiotemporally controlled drug release. The approaches developed in this work have the potential to elucidate the molecular dynamics in ECM and to foster engineering of multilayers with properties tuned to mimic the ECM. The work aims at spatiotemporal control over the diffusion of bioactives and their presentation to the cells.},
  language  = {en}
}
@misc{ĆwiekKupczyńskaAltmannArendetal.2016,
  author    = {Ćwiek-Kupczyńska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bj{\"o}rn and Weise, Stephan and Kersey, Paul and Krajewski, Paweł},
  title     = {Measures for interoperability of phenotypic data},
  series = {Plant methods},
  journal   = {Plant methods},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407299},
  pages     = {18},
  year      = {2016},
  abstract  = {Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time ‑consuming experiments, the findings can be fostered by reusing and combin‑ ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑ ment called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA ‑Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA ‑Tab ‑formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.},
  language  = {en}
}
@misc{UestuenBartetzkoBoernke2015,
  author    = {{\"U}st{\"u}n, Suayib and Bartetzko, Verena and B{\"o}rnke, Frederik},
  title     = {The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid},
  series = {Frontiers in plant science},
  journal   = {Frontiers in plant science},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-406537},
  pages     = {11},
  year      = {2015},
  abstract  = {XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.},
  language  = {en}
}
@misc{ZorHeiskanenCavigliaetal.2014,
  author    = {Z{\´o}r, K. and Heiskanen, A. and Caviglia, Claudia and Vergani, M. and Landini, E. and Shah, F. and Carminati, Marco and Mart{\´i}nez-Serrano, A. and Ramos Moreno, T. and Kokaia, M. and Benayahu, Dafna and Keresztes, Zs. and Papkovsky, D. and Wollenberger, Ursula and Svendsen, W. E. and Dimaki, M. and Ferrari, G. and Raiteri, R. and Sampietro, M. and Dufva, M. and Emn{\´e}us, J.},
  title     = {A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-99492},
  pages     = {11},
  year      = {2014},
  abstract  = {Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring.},
  language  = {en}
}
@misc{ZwickelKahlKlaffkeetal.2017,
  author    = {Zwickel, Theresa and Kahl, Sandra and Klaffke, Horst and Rychlik, Michael and M{\"u}ller, Marina E. H.},
  title     = {Spotlight on the underdogs},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400438},
  pages     = {17},
  year      = {2017},
  abstract  = {Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions},
  language  = {en}
}
@misc{ZwaagHorstBlaženovićetal.2020,
  author    = {Zwaag, Jelle and Horst, Rob ter and Blaženović, Ivana and St{\"o}ßel, Daniel and Ratter, Jacqueline and Worseck, Josephine M. and Schauer, Nicolas and Stienstra, Rinke and Netea, Mihai G. and Jahn, Dieter and Pickkers, Peter and Kox, Matthijs},
  title     = {Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {4},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-51778},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-517784},
  pages     = {20},
  year      = {2020},
  abstract  = {We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.},
  language  = {en}
}
@misc{ZurellKoenigMalchowetal.2021,
  author    = {Zurell, Damaris and K{\"o}nig, Christian and Malchow, Anne-Kathleen and Kapitza, Simon and Bocedi, Greta and Travis, Justin M. J. and Fandos, Guillermo},
  title     = {Spatially explicit models for decision-making in animal conservation and restoration},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  volume    = {2022},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  edition   = {4},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-54991},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549915},
  pages     = {1 -- 16},
  year      = {2021},
  abstract  = {Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79\%), towards the species and population level (80\%) and towards conservation (rather than restoration) applications (71\%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10\% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes.},
  language  = {en}
}
@misc{Zinke2022,
  type      = {Master Thesis},
  author    = {Zinke, Jann Felix},
  title     = {Herstellung von Gießharzpr{\"a}paraten f{\"u}r den Einsatz im Biologieunterricht},
  doi       = {10.25932/publishup-61502},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-615028},
  school      = {Universit{\"a}t Potsdam},
  pages     = {101},
  year      = {2022},
  abstract  = {Das Ziel des hier beschriebenen Masterprojekts war es, eine Methode zu etablieren, mit der Insekten in Gießharz eingeschlossen werden k{\"o}nnen, damit sie dauerhaft konserviert f{\"u}r mikroskopische Untersuchungen im Biologieunterricht zur Verf{\"u}gung stehen. Die Masterarbeit enth{\"a}lt eine ausf{\"u}hrliche Anleitung zur Herstellung von Gießharzpr{\"a}paraten mit darin eingebetteten Insekten. Sie soll als Handreichung vor allem f{\"u}r Biologie-Lehrkr{\"a}fte dienen, um selbstst{\"a}ndig hochwertige Lehrpr{\"a}parate f{\"u}r ihren Unterricht herstellen zu k{\"o}nnen. Aufgrund der Komplexit{\"a}t des Themas werden Naturschutzbestimmungen und die Beschaffung der Insekten genauso beleuchtet wie deren anschließende Pr{\"a}paration, die Konstruktion einer eigenen Gießform, die Einbettung der Insekten in Gießharz und die Nachbehandlung des Gießlings. Wichtige Einflussfaktoren, die die Qualit{\"a}t der Pr{\"a}parate entscheidend beeinflussen und m{\"o}gliche Fehlerquellen, werden ausf{\"u}hrlich erl{\"a}utert. Mittels dieser detaillierten Eingießanleitung k{\"o}nnen mit relativ einfachen und kosteng{\"u}nstigen Mitteln faszinierende Studienobjekte f{\"u}r einen anschaulichen Biologieunterricht entstehen.},
  language  = {de}
}
@phdthesis{Ziege2022,
  author    = {Ziege, Ricardo},
  title     = {Growth dynamics and mechanical properties of E. coli biofilms},
  doi       = {10.25932/publishup-55986},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-559869},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 123},
  year      = {2022},
  abstract  = {Biofilms are complex living materials that form as bacteria get embedded in a matrix of self-produced protein and polysaccharide fibres. The formation of a network of extracellular biopolymer fibres contributes to the cohesion of the biofilm by promoting cell-cell attachment and by mediating biofilm-substrate interactions. This sessile mode of bacteria growth has been well studied by microbiologists to prevent the detrimental effects of biofilms in medical and industrial settings. Indeed, biofilms are associated with increased antibiotic resistance in bacterial infections, and they can also cause clogging of pipelines or promote bio-corrosion. However, biofilms also gained interest from biophysics due to their ability to form complex morphological patterns during growth. Recently, the emerging field of engineered living materials investigates biofilm mechanical properties at multiple length scales and leverages the tools of synthetic biology to tune the functions of their constitutive biopolymers. This doctoral thesis aims at clarifying how the morphogenesis of Escherichia coli (E. coli) biofilms is influenced by their growth dynamics and mechanical properties. To address this question, I used methods from cell mechanics and materials science. I first studied how biological activity in biofilms gives rise to non-uniform growth patterns. In a second study, I investigated how E. coli biofilm morphogenesis and its mechanical properties adapt to an environmental stimulus, namely the water content of their substrate. Finally, I estimated how the mechanical properties of E. coli biofilms are altered when the bacteria express different extracellular biopolymers. On nutritive hydrogels, micron-sized E. coli cells can build centimetre-large biofilms. During this process, bacterial proliferation and matrix production introduce mechanical stresses in the biofilm, which release through the formation of macroscopic wrinkles and delaminated buckles. To relate these biological and mechanical phenomena, I used time-lapse fluorescence imaging to track cell and matrix surface densities through the early and late stages of E. coli biofilm growth. Colocalization of high cell and matrix densities at the periphery precede the onset of mechanical instabilities at this annular region. Early growth is detected at this outer annulus, which was analysed by adding fluorescent microspheres to the bacterial inoculum. But only when high rates of matrix production are present in the biofilm centre, does overall biofilm spreading initiate along the solid-air interface. By tracking larger fluorescent particles for a long time, I could distinguish several kinematic stages of E. coli biofilm expansion and observed a transition from non-linear to linear velocity profiles, which precedes the emergence of wrinkles at the biofilm periphery. Decomposing particle velocities to their radial and circumferential components revealed a last kinematic stage, where biofilm movement is mostly directed towards the radial delaminated buckles, which verticalize. The resulting compressive strains computed in these regions were observed to substantially deform the underlying agar substrates. The co-localization of higher cell and matrix densities towards an annular region and the succession of several kinematic stages are thus expected to promote the emergence of mechanical instabilities at the biofilm periphery. These experimental findings are predicted to advance future modelling approaches of biofilm morphogenesis. E. coli biofilm morphogenesis is further anticipated to depend on external stimuli from the environment. To clarify how the water could be used to tune biofilm material properties, we quantified E. coli biofilm growth, wrinkling dynamics and rigidity as a function of the water content of the nutritive substrates. Time-lapse microscopy and computational image analysis revealed that substrates with high water content promote biofilm spreading kinetics, while substrates with low water content promote biofilm wrinkling. The wrinkles observed on biofilm cross-sections appeared more bent on substrates with high water content, while they tended to be more vertical on substrates with low water content. Both wet and dry biomass, accumulated over 4 days of culture, were larger in biofilms cultured on substrates with high water content, despite extra porosity within the matrix layer. Finally, the micro-indentation analysis revealed that substrates with low water content supported the formation of stiffer biofilms. This study shows that E. coli biofilms respond to the water content of their substrate, which might be used for tuning their material properties in view of further applications. Biofilm material properties further depend on the composition and structure of the matrix of extracellular proteins and polysaccharides. In particular, E. coli biofilms were suggested to present tissue-like elasticity due to a dense fibre network consisting of amyloid curli and phosphoethanolamine-modified cellulose. To understand the contribution of these components to the emergent mechanical properties of E. coli biofilms, we performed micro-indentation on biofilms grown from bacteria of several strains. Besides showing higher dry masses, larger spreading diameters and slightly reduced water contents, biofilms expressing both main matrix components also presented high rigidities in the range of several hundred kPa, similar to biofilms containing only curli fibres. In contrast, a lack of amyloid curli fibres provides much higher adhesive energies and more viscoelastic fluid-like material behaviour. Therefore, the combination of amyloid curli and phosphoethanolamine-modified cellulose fibres implies the formation of a composite material whereby the amyloid curli fibres provide rigidity to E. coli biofilms, whereas the phosphoethanolamine-modified cellulose rather acts as a glue. These findings motivate further studies involving purified versions of these protein and polysaccharide components to better understand how their interactions benefit biofilm functions. All three studies depict different aspects of biofilm morphogenesis, which are interrelated. The first work reveals the correlation between non-uniform biological activities and the emergence of mechanical instabilities in the biofilm. The second work acknowledges the adaptive nature of E. coli biofilm morphogenesis and its mechanical properties to an environmental stimulus, namely water. Finally, the last study reveals the complementary role of the individual matrix components in the formation of a stable biofilm material, which not only forms complex morphologies but also functions as a protective shield for the bacteria it contains. Our experimental findings on E. coli biofilm morphogenesis and their mechanical properties can have further implications for fundamental and applied biofilm research fields.},
  language  = {en}
}
@misc{ZiegeMahlowHennigeSulzetal.2009,
  author    = {Ziege, Madlen and Mahlow, Kristin and Hennige-Sulz, Carmen and Kronmarck, Claudia and Tiedemann, Ralph and Streit, Bruno and Plath, Martin},
  title     = {Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk?},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45171},
  year      = {2009},
  abstract  = {Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak.},
  language  = {en}
}
@misc{ZhuSchluppTiedemann2016,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97119},
  pages     = {19},
  year      = {2016},
  abstract  = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.},
  language  = {en}
}
@misc{ZhuSchluppTiedemann2017,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-403875},
  pages     = {14},
  year      = {2017},
  abstract  = {The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor.},
  language  = {en}
}
@misc{ZhangChenSiemiatkowskaetal.2020,
  author    = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair},
  title     = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {5},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52425},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-524254},
  pages     = {14},
  year      = {2020},
  abstract  = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.},
  language  = {en}
}
@phdthesis{Zhang2020,
  author    = {Zhang, Jianrui},
  title     = {Completely water-based emulsions as compartmentalized systems via pickering stabilization},
  doi       = {10.25932/publishup-47654},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476542},
  school      = {Universit{\"a}t Potsdam},
  pages     = {II, 119},
  year      = {2020},
  abstract  = {Completely water-based systems are of interest for the development of novel material for various reasons: On one hand, they provide benign environment for biological systems and on the other hand they facilitate effective molecular transport in a membrane-free environment. In order to investigate the general potential of aqueous two-phase systems (ATPSs) for biomaterials and compartmentalized systems, various solid particles were applied to stabilize all-aqueous emulsion droplets. The target ATPS to be investigated should be prepared via mixing of two aqueous solutions of water-soluble polymers, which turn biphasic when exceeding a critical polymer concentration. Hydrophilic polymers with a wide range of molar mass such as dextran/poly(ethylene glycol) (PEG) can therefore be applied. Solid particles adsorbed at the interfaces can be exceptionally efficient stabilizers forming so-called Pickering emulsions, and nanoparticles can bridge the correlation length of polymer solutions and are thereby the best option for water-in-water emulsions. The first approach towards the investigation of ATPS was conducted with all aqueous dextran-PEG emulsions in the presence of poly(dopamine) particles (PDP) in Chapter 4. The water-in-water emulsions were formed with a PEG/dextran system via utilizing PDP as stabilizers. Studies of the formed emulsions were performed via laser scanning confocal microscope (CLSM), optical microscope (OM), cryo-scanning electron microscope (SEM) and tensiometry. The stable emulsions (at least 16 weeks) were demulsified easily via dilution or surfactant addition. Furthermore, the solid PDP at the water-water interface were crosslinked in order to inhibit demulsification of the Pickering emulsion. Transmission electron microscope (TEM) and scanning electron microscope (SEM) were used to visualize the morphology of PDP before and after crosslinking. PDP stabilized water-in-water emulsions were utilized in the following Chapter 5 to form supramolecular compartmentalized hydrogels. Here, hydrogels were prepared in pre-formed water-in-water emulsions and gelled via α-cyclodextrin-PEG (α-CD-PEG) inclusion complex formation. Studies of the formed complexes were performed via X-ray powder diffraction (XRD) and the mechanical properties of the hydrogels were measured with oscillatory shear rheology. In order to verify the compartmentalized state and its triggered decomposition, hydrogels and emulsions were assessed via OM, SEM and CLSM. The last chapter broadens the investigations from the previous two systems by utilizing various carbon nitrides (CN) as different stabilizers in ATPS. CN introduces another way to trigger demulsification, namely irradiation with visible light. Therefore, emulsification and demulsification with various triggers were probed. The investigated all aqueous multi-phase systems will act as model for future fabrication of biocompatible materials, cell micropatterning as well as separation of compartmentalized systems.},
  language  = {en}
}
@misc{ZhangIgnatova2009,
  author    = {Zhang, Gong and Ignatova, Zoya},
  title     = {Generic algorithm to predict the speed of translational elongation : implications for protein biogenesis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45007},
  year      = {2009},
  abstract  = {Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.},
  language  = {en}
}
@phdthesis{Zhang2005,
  author    = {Zhang, Baichen},
  title     = {Dissection of phloem transport in cucurbitaceae by metabolomic analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6644},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {This thesis aimed to investigate several fundamental and perplexing questions relating to the phloem loading and transport mechanisms of Cucurbita maxima, by combining metabolomic analysis with cell biological techniques. This putative symplastic loading species has long been used for experiments on phloem anatomy, phloem biochemistry, phloem transport physiology and phloem signalling. Symplastic loading species have been proposed to use a polymer trapping mechanism to accumulate RFO (raffinose family oligosaccharides) sugars to build up high osmotic pressure in minor veins which sustains a concentration gradient that drives mass flow. However, extensive evidence indicating a low sugar concentration in their phloem exudates is a long-known problem that conflicts with this hypothesis. Previous metabolomic analysis shows the concentration of many small molecules in phloem exudates is higher than that of leaf tissues, which indicates an active apoplastic loading step. Therefore, in the view of the phloem metabolome, a symplastic loading mechanism cannot explain how small molecules other than RFO sugars are loaded into phloem. Most studies of phloem physiology using cucurbits have neglected the possible functions of vascular architecture in phloem transport. It is well known that there are two phloem systems in cucurbits with distinctly different anatomical features: central phloem and extrafascicular phloem. However, mistaken conclusions on sources of cucurbit phloem exudation from previous reports have hindered consideration of the idea that there may be important differences between these two phloem systems. The major results are summarized as below: 1) O-linked glycans in C.maxima were structurally identified as beta-1,3 linked glucose polymers, and the composition of glycans in cucurbits was found to be species-specific. Inter-species grafting experiments proved that these glycans are phloem mobile and transported uni-directionally from scion to stock. 2) As indicated by stable isotopic labelling experiments, a considerable amount of carbon is incorporated into small metabolites in phloem exudates. However, the incorporation of carbon into RFO sugars is much faster than for other metabolites. 3) Both CO2 labelling experiments and comparative metabolomic analysis of phloem exudates and leaf tissues indicated that metabolic processes other than RFO sugar metabolism play an important role in cucurbit phloem physiology. 4) The underlying assumption that the central phloem of cucurbits continuously releases exudates after physical incision was proved wrong by rigorous experiments including direct observation by normal microscopy and combined multiple-microscopic methods. Errors in previous experimental confirmation of phloem exudation in cucurbits are critically discussed. 5) Extrafascicular phloem was proved to be functional, as indicated by phloem-mobile carboxyfluorescein tracer studies. Commissural sieve tubes interconnect phloem bundles into a complete super-symplastic network. 6) Extrafascicular phloem represents the main source of exudates following physical incision. The major transported metabolites by these extrafacicular phloem are non-sugar compounds including amino acids, O-glycans, amines. 7) Central phloem contains almost exclusively RFO sugars, the estimated amount of which is up to 1 to 2 molar. The major RFO sugar present in central phloem is stachyose. 8) Cucurbits utilize two structurally different phloem systems for transporting different group of metabolites (RFO sugars and non-RFO sugar compounds). This implies that cucurbits may use spatially separated loading mechanisms (apoplastic loading for extrafascicular phloem and symplastic loading for central phloem) for supply of nutrients to sinks. 9) Along the transport systems, RFO sugars were mainly distributed within central phloem tissues. There were only small amounts of RFO sugars present in xylem tissues (millimolar range) and trace amounts of RFO sugars in cortex and pith. The composition of small molecules in external central phloem is very different from that in internal central phloem. 10) Aggregated P-proteins were manually dissected from central phloem and analysed by both SDS-PAGE and mass spectrometry. Partial sequences of peptides were obtained by QTOF de novo sequencing from trypsin digests of three SDS-PAGE bands. None of these partial sequences shows significant homology to known cucurbit phloem proteins or other plant proteins. This proves that these central phloem proteins are a completely new group of proteins different from those in extrafascicular phloem. The extensively analysed P-proteins reported in literature to date are therefore now shown to arise from extrafascicular phloem and not central phloem, and therefore do not appear to be involved in the occlusion processes in central phloem.},
  subject      = {phloem},
  language  = {en}
}
@phdthesis{Zemella2019,
  author    = {Zemella, Anne},
  title     = {Fluoreszenzmarkierung und Modifizierung von komplexen Proteinen in eukaryotischen zellfreien Systemen durch die Etablierung von orthogonalen tRNA/Aminoacyl-tRNA-Synthetase-Paaren},
  doi       = {10.25932/publishup-44236},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442361},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XI, 141},
  year      = {2019},
  abstract  = {Die funktionelle Charakterisierung von therapeutisch relevanten Proteinen kann bereits durch die Bereitstellung des Zielproteins in ad{\"a}quaten Mengen limitierend sein. Dies trifft besonders auf Membranproteine zu, die aufgrund von zytotoxischen Effekten auf die Produktionszelllinie und der Tendenz Aggregate zu bilden, in niedrigen Ausbeuten an aktivem Protein resultieren k{\"o}nnen. Der lebende Organismus kann durch die Verwendung von translationsaktiven Zelllysaten umgangen werden- die Grundlage der zellfreien Proteinsynthese. Zu Beginn der Arbeit wurde die ATP-abh{\"a}ngige Translation eines Lysates auf der Basis von kultivierten Insektenzellen (Sf21) analysiert. F{\"u}r diesen Zweck wurde ein ATP-bindendes Aptamer eingesetzt, durch welches die Translation der Nanoluziferase reguliert werden konnte. Durch die dargestellte Applizierung von Aptameren, k{\"o}nnten diese zuk{\"u}nftig in zellfreien Systemen f{\"u}r die Visualisierung der Transkription und Translation eingesetzt werden, wodurch zum Beispiel komplexe Prozesse validiert werden k{\"o}nnen. Neben der reinen Proteinherstellung k{\"o}nnen Faktoren wie posttranslationale Modifikationen sowie eine Integration in eine lipidische Membran essentiell f{\"u}r die Funktionalit{\"a}t des Membranproteins sein. Im zweiten Abschnitt konnte, im zellfreien Sf21-System, f{\"u}r den G-Protein-gekoppelten Rezeptor Endothelin B sowohl eine Integration in die endogen vorhandenen Endoplasmatisch Retikulum-basierten Membranstrukturen als auch Glykosylierungen, identifiziert werden. Auf der Grundlage der erfolgreichen Synthese des ET-B-Rezeptors wurden verschiedene Methoden zur Fluoreszenzmarkierung des Adenosin-Rezeptors A2a (Adora2a) angewandt und optimiert. Im dritten Abschnitt wurde der Adora2a mit Hilfe einer vorbeladenen tRNA, welche an eine fluoreszierende Aminos{\"a}ure gekoppelt war, im zellfreien Chinesischen Zwerghamster Ovarien (CHO)-System markiert. Zus{\"a}tzlich konnte durch den Einsatz eines modifizierten tRNA/Aminoacyl-tRNA-Synthetase-Paares eine nicht-kanonische Aminos{\"a}ure an Position eines integrierten Amber-Stopcodon in die Polypeptidkette eingebaut und die funktionelle Gruppe im Anschluss an einen Fluoreszenzfarbstoff gekoppelt werden. Aufgrund des offenen Charakters eignen sich zellfreie Proteinsynthesesysteme besonders f{\"u}r eine Integration von exogenen Komponenten in den Translationsprozess. Mit Hilfe der Fluoreszenzmarkierung wurde eine ligandvermittelte Konformations{\"a}nderung im Adora2a {\"u}ber einen Biolumineszenz-Resonanzenergietransfer detektiert. Durch die Etablierung der Amber-Suppression wurde dar{\"u}ber hinaus das Hormon Erythropoetin pegyliert, wodurch Eigenschaften wie Stabilit{\"a}t und Halbwertszeit des Proteins ver{\"a}ndert wurden. Zu guter Letzt wurde ein neues tRNA/Aminoacyl-tRNA-Synthetase-Paar auf Basis der Methanosarcina mazei Pyrrolysin-Synthetase etabliert, um das Repertoire an nicht-kanonischen Aminos{\"a}uren und den damit verbundenen Kopplungsreaktionen zu erweitern. Zusammenfassend wurden die Potenziale zellfreier Systeme in Bezug auf der Herstellung von komplexen Membranproteinen und der Charakterisierung dieser durch die Einbringung einer positionsspezifischen Fluoreszenzmarkierung verdeutlicht, wodurch neue M{\"o}glichkeiten f{\"u}r die Analyse und Funktionalisierung von komplexen Proteinen geschaffen wurden.},
  language  = {de}
}
@phdthesis{Zaupa2010,
  author    = {Zaupa, Alessandro},
  title     = {Physical crosslinking of gelatin : a supramolecular approach to biomaterials},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52888},
  school      = {Universit{\"a}t Potsdam},
  year      = {2010},
  abstract  = {This work describes the realization of physically crosslinked networks based on gelatin by the introduction of functional groups enabling specific supramolecular interactions. Molecular models were developed in order to predict the material properties and permit to establish a knowledge-based approach to material design. The effect of additional supramolecular interactions with hydroxyapaptite was then studied in composite materials. The calculated properties are compared to experimental results to validate the models. The models are then further used for the study of physically crosslinked networks. Gelatin was functionalized with desaminotyrosine (DAT) and desaminotyrosyl-tyrosine (DATT) side groups, derived from the natural amino acid tyrosine. These group can potentially undergo to π-π and hydrogen bonding interactions also under physiological conditions. Molecular dynamics (MD) simulations were performed on models with 0.8 wt.-\% or 25 wt.-\% water content, using the second generation forcefield CFF91. The validation of the models was obtained by the comparison with specific experimental data such as, density, peptide conformational angles and X-ray scattering spectra. The models were then used to predict the supramolecular organization of the polymer chain, analyze the formation of physical netpoints and calculate the mechanical properties. An important finding of simulation was that with the increase of aromatic groups also the number of observed physical netpoints increased. The number of relatively stable physical netpoints, on average zero 0 for natural gelatin, increased to 1 and 6 for DAT and DATT functionalized gelatins respectively. A comparison with the Flory-Rehner model suggested reduced equilibrium swelling by factor 6 of the DATT-functionalized materials in water. The functionalized gelatins could be synthesized by chemoselective coupling of the free carboxylic acid groups of DAT and DATT to the free amino groups of gelatin. At 25 wt.-\% water content, the simulated and experimentally determined elastic mechanical properties (e.g. Young Modulus) were both in the order of GPa and were not influenced by the degree of aromatic modification. The experimental equilibrium degree of swelling in water decreased with increasing the number of inserted aromatic functions (from 2800 vol.-\% for pure gelatin to 300 vol.-\% for the DATT modified gelatin), at the same time, Young's modulus, elongation at break, and maximum tensile strength increased. It could be show that the functionalization with DAT and DATT influences the chain organization of gelatin based materials together with a controlled drying condition. Functionalization with DAT and DATT lead to a drastic reduction of helical renaturation, that could be more finely controlled by the applied drying conditions. The properties of the materials could then be influenced by application of two independent methods. Composite materials of DAT and DATT functionalized gelatins with hydroxyapatite (HAp) show a drastic reduction of swelling degree. In tensile tests and rheological measurements, the composites equilibrated in water had increased Young's moduli (from 200 kPa up to 2 MPa) and tensile strength (from 57 kPa up to 1.1 MPa) compared to the natural polymer matrix without affecting the elongation at break. Furthermore, an increased thermal stability from 40 °C to 85 °C of the networks could be demonstrated. The differences of the behaviour of the functionalized gelatins to pure gelatin as matrix suggested an additional stabilizing bond between the incorporated aromatic groups to the hydroxyapatite.},
  language  = {en}
}
@misc{ZancolliBakerBarlowetal.2016,
  author    = {Zancolli, Giulia and Baker, Timothy G. and Barlow, Axel and Bradley, Rebecca K. and Calvete, Juan J. and Carter, Kimberley C. and de Jager, Kaylah and Owens, John Benjamin and Price, Jenny Forrester and Sanz, Libia and Scholes-Higham, Amy and Shier, Liam and Wood, Liam and W{\"u}ster, Catharine E. and W{\"u}ster, Wolfgang},
  title     = {Is hybridization a source of adaptive venom variation in rattlesnakes?},
  series = {Toxins},
  journal   = {Toxins},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407595},
  pages     = {16},
  year      = {2016},
  abstract  = {Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.},
  language  = {en}
}
@phdthesis{Yildiz2023,
  author    = {Yildiz, Tugba},
  title     = {Dissecting the role of the TusA protein for cell functionality and FtsZ ring assembly in Escherichia coli},
  doi       = {10.25932/publishup-61713},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-617135},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XI, 171},
  year      = {2023},
  abstract  = {In this work, the role of the TusA protein was investigated for the cell functionality and FtsZ ring assembly in Escherichia coli. TusA is the tRNA-2-thiouridine synthase that acts as a sulfur transferase in tRNA thiolation for the formation of 2-thiouridine at the position 34 (wobble base) of tRNALys, tRNAGlu and tRNAGln. It binds the persulfide form of sulfur and transfers it to further proteins during mnm5s2U tRNA modification at wobble position and for Moco biosynthesis. With this thiomodification of tRNA, the ribosome binding is more efficient and frameshifting is averted during the protein translation. Previous studies have revealed an essential role of TusA in bacterial cell physiology since deletion of the tusA gene resulted in retarded growth and filamentous cells during the exponential growth phase in a rich medium which suddenly disappeared during the stationary phase. This indicates a problem in the cell division process. Therefore the focus of this work was to investigate the role of TusA for cell functionality and FtsZ ring formation and thus the cell separation. The reason behind the filamentous growth of the tusA mutant strain was investigated by growth and morphological analyses. ΔtusA cells showed a retarded growth during the exponential phase compared to the WT strain. Also, morphological analysis of ΔtusA cells confirmed the filamentous cell shape. The growth and cell division defects in ΔtusA indicated a defect in FtsZ protein as a key player of cell division. The microscopic investigation revealed that filamentous ΔtusA cells possessed multiple DNA parts arranged next to each other. This suggested that although the DNA replication occurred correctly, there was a defect in the step where FtsZ should act; probably FtsZ is unable to assemble to the ring structure or the assembled ring is not able to constrict. All tested mutant strains (ΔtusD, ΔtusE and ΔmnmA) involved in the mnm5s2U34 tRNA modification pathway shared the similar retarded growth and filamentous cell shape like ΔtusA strain. Thus, the cell division defect arises from a defect in mnm5s2U34 tRNA thiolation. Since the FtsZ ring formation was supposed to be defective in filaments, a possible intracellular interaction of TusA and FtsZ was examined by fluorescent (EGFP and mCherry) fusion proteins expression and FRET. FtsZ expressing tusA mutant (DE3) cells showed a red mCherry signal at the cell poles, indicating that FtsZ is still in the assembling phase. Interestingly, the cellular region of EGFP-TusA fusion protein expressed in ΔtusA (DE3) was conspicuous; the EGFP signal was spread throughout the whole cell and, in addition, a slight accumulation of the EGFP-TusA fluorescence was detectable at the cell poles, the same part of the cell as for mCherry-FtsZ. Thus, this strongly suggested an interaction of TusA and FtsZ. Furthermore, the cellular FtsZ and Fis concentrations, and their change during different growth phases were determined via immunoblotting. All tested deletion strains of mnm5s2U34 tRNA modification show high cellular FtsZ and Fis levels in the exponential phase, shifting to the later growth phases. This shift reflects the retarded growth, whereby the deletion strains reach later the exponential phase. Conclusively, the growth and cell division defect, and thus the formation of filaments, is most likely caused by changes in the cellular FtsZ and Fis concentrations. Finally, the translation efficiencies of certain proteins (RpoS, Fur, Fis and mFis) in tusA mutant and in additional gene deletion strains were studied whether they were affected by using unmodified U34 tRNAs of Lys, Glu and Gln. The translation efficiency is decreased in mnm5s2U34 tRNA modification-impaired strains in addition to their existing growth and cell division defect due to the elimination of these three amino acids. Finally, these results confirm and reinforce the importance of Lys, Glu and Gln and the mnm5s2U34 tRNA thiolation for efficient protein translation. Thus, these findings verify that the translation of fur, fis and rpoS is regulated by mnm5s2U34 tRNA modifications, which is growth phase-dependent. In total, this work showed the importance of the role of TusA for bacterial cell functionality and physiology. The deletion of the tusA gene disrupted a complex regulatory network within the cell, that most influenced by the decreased translation of Fis and RpoS, caused by the absence of mnm5s2U34 tRNA modifications. The disruption of RpoS and Fis cellular network influences in turn the cellular FtsZ level in the early exponential phase. Finally, the reduced FtsZ concentration leads to elongated, filamentous E. coli cells, which are unable to divide.},
  language  = {en}
}
@misc{YarmanScheller2014,
  author    = {Yarman, Aysu and Scheller, Frieder W.},
  title     = {The first electrochemical MIP sensor for tamoxifen},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1046},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47617},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476173},
  pages     = {10},
  year      = {2014},
  abstract  = {We present an electrochemical MIP sensor for tamoxifen (TAM)-a nonsteroidal anti-estrogen-which is based on the electropolymerisation of an O-phenylenediamine. resorcinol mixture directly on the electrode surface in the presence of the template molecule. Up to now only. bulk. MIPs for TAM have been described in literature, which are applied for separation in chromatography columns. Electro-polymerisation of the monomers in the presence of TAM generated a film which completely suppressed the reduction of ferricyanide. Removal of the template gave a markedly increased ferricyanide signal, which was again suppressed after rebinding as expected for filling of the cavities by target binding. The decrease of the ferricyanide peak of the MIP electrode depended linearly on the TAM concentration between 1 and 100 nM. The TAM-imprinted electrode showed a 2.3 times higher recognition of the template molecule itself as compared to its metabolite 4-hydroxytamoxifen and no cross-reactivity with the anticancer drug doxorubucin was found. Measurements at + 1.1 V caused a fouling of the electrode surface, whilst pretreatment of TAM with peroxide in presence of HRP generated an oxidation product which was reducible at 0 mV, thus circumventing the polymer formation and electrochemical interferences.},
  language  = {en}
}
@misc{YarmanJetzschmannNeumannetal.2017,
  author    = {Yarman, Aysu and Jetzschmann, Katharina J. and Neumann, Bettina and Zhang, Xiaorong and Wollenberger, Ulla and Cordin, Aude and Haupt, Karsten and Scheller, Frieder W.},
  title     = {Enzymes as tools in MIP-sensors},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1098},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47464},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474642},
  pages     = {18},
  year      = {2017},
  abstract  = {Molecularly imprinted polymers (MIPs) have the potential to complement antibodies in bioanalysis, are more stable under harsh conditions, and are potentially cheaper to produce. However, the affinity and especially the selectivity of MIPs are in general lower than those of their biological pendants. Enzymes are useful tools for the preparation of MIPs for both low and high-molecular weight targets: As a green alternative to the well-established methods of chemical polymerization, enzyme-initiated polymerization has been introduced and the removal of protein templates by proteases has been successfully applied. Furthermore, MIPs have been coupled with enzymes in order to enhance the analytical performance of biomimetic sensors: Enzymes have been used in MIP-sensors as tracers for the generation and amplification of the measuring signal. In addition, enzymatic pretreatment of an analyte can extend the analyte spectrum and eliminate interferences.},
  language  = {en}
}
@misc{YanChenKaufmann2016,
  author    = {Yan, Wenhao and Chen, Dijun and Kaufmann, Kerstin},
  title     = {Efficient multiplex mutagenesis by RNA‑guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-90895},
  year      = {2016},
  abstract  = {Background: The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its 'endogenous' environment. Results: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable largefragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 \% decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions: Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants.},
  language  = {en}
}
@misc{WurzbacherFuchsAttermeyeretal.2017,
  author    = {Wurzbacher, Christian and Fuchs, Andrea and Attermeyer, Katrin and Frindte, Katharina and Grossart, Hans-Peter and Hupfer, Michael and Casper, Peter and Monaghan, Michael T.},
  title     = {Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1111},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43196},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431965},
  pages     = {18},
  year      = {2017},
  abstract  = {Background Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.},
  language  = {en}
}
@phdthesis{Wunderlich2014,
  author    = {Wunderlich, Kai},
  title     = {Entwicklung einer parallelen Mehrkomponentenanalyse von Antigen-Antik{\"o}rper-Reaktionen in der Dopinganalyse},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76869},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, 130},
  year      = {2014},
  abstract  = {Weltweit streben Anti-Doping Institute danach jene Sportler zu {\"u}berf{\"u}hren, welche sich unerlaubter Mittel oder Methoden bedienen. Die hierf{\"u}r notwendigen Testsysteme werden kontinuierlich weiterentwickelt und neue Methoden aufgrund neuer Wirkstoffe der Pharmaindustrie etabliert. Gegenstand dieser Arbeit war es, eine parallele Mehrkomponentenanalyse auf Basis von Antigen-Antik{\"o}rper Reaktionen zu entwickeln, bei dem es prim{\"a}r um Verringerung des ben{\"o}tigten Probevolumens und der Versuchszeit im Vergleich zu einem Standard Nachweis-Verfahren ging. Neben der Verwendung eines Multiplex Ansatzes und der Mikroarraytechnologie stellten ebenfalls die Genauigkeit aller Messparameter, die Stabilit{\"a}t des Versuchsaufbaus sowie die Performance {\"u}ber einen Einfach-Blind-Ansatz Herausforderungen dar. Die Anforderung an den Multiplex Ansatz, keine falschen Signale trotz {\"a}hnlicher Strukturen zu messen, konnte durch die gezielte Kombination von spezifischen Antik{\"o}rpern realisiert werden. Hierf{\"u}r wurden neben Kreuzreaktivit{\"a}tstests auf dem Mikroarray parallel erfolgreich Western Blot Versuche durchgef{\"u}hrt. Jene Antik{\"o}rper, welche in diesen Versuchen die gesetzten Anforderungen erf{\"u}llten, wurden f{\"u}r das Ermitteln der kleinsten nachweisbaren Konzentration verwendet. {\"U}ber das Optimieren der Versuchsbedingungen konnte unter Verwendung von Tween in der Waschl{\"o}sung sowohl auf Glas als auch auf Kunststoff die Hintergrundfluoreszenz reduziert und somit eine Steigerung des Signal/Hintergrundverh{\"a}ltnisses erreicht werden. In den Versuchen zu Ermittlung der Bestimmungsgrenze wurde f{\"u}r das humane Choriongonadotropin (hCG-i) eine Konzentration von 10 mU/ml, f{\"u}r dessen beta-Untereinheit (hCG-beta) eine Konzentration von 3,6 mU/ml und f{\"u}r das luteinisierende Hormon (LH) eine Konzentration von 10 mU/ml bestimmt. Den ermittelten Wert im Serum f{\"u}r das hCG-i entspricht dem von der Welt-Anti-Dopin-Agentur (WADA) geforderten Wert in Urin von 5 mU/ml. Neben der Ermittlung von Bestimmungsgrenzen wurden diese hinsichtlich auftretender Matrixeffekte in Serum und Blut gemessen. Wie aus den Versuchen zur Ermittlung von Kreuzreaktivit{\"a}ten auf dem Mikroarray zu entnehmen ist, lassen sich das LH, das hCG-i und hCG-β ebenfalls in Serum und Blut messen. Die Durchf{\"u}hrung einer Performance-Analyse {\"u}ber einem Einfach-Blind-Ansatz mit 130 Serum Proben, wurde ebenfalls {\"u}ber dieses System realisiert. Die ausgewerteten Proben wurden anschließend {\"u}ber eine Grenzwertoptimierungskurve analysiert und die diagnostische Spezifit{\"a}t ermittelt. F{\"u}r die Messungen des LH konnte eine Sensitivit{\"a}t und Spezifit{\"a}t von 100\% erreicht werden. Demnach wurden alle negativen und positiven Proben eindeutig interpretiert. F{\"u}r das hCG-β konnte ebenfalls eine Spezifit{\"a}t von 100\% und eine Sensitivit{\"a}t von 97\% erreicht werden. Die hCG-i Proben wurden mit einer Spezifit{\"a}t von 100\% und eine Sensitivit{\"a}t von 97,5\% gemessen. Um den Nachweis zu erbringen, dass dieser Versuchsaufbau {\"u}ber mehrere Wochen stabile Signale bei Vermessen von identischen Proben liefert, wurde ein {\"u}ber zw{\"o}lf Wochen angesetzter Stabilit{\"a}tstest f{\"u}r alle Parameter erfolgreich in Serum und Blut durchgef{\"u}hrt. Zusammenfassend konnte in dieser Arbeit erfolgreich eine Mehrkomponentenanalyse als Multiplex Ansatz auf einem Mikroarray entwickelt werden. Die Durchf{\"u}hrung der Performance-Analyse und des Stabilit{\"a}tstests zeigen bereits die m{\"o}gliche Einsatzf{\"a}higkeit dieses Tests im Kontext einer Dopinganalyse.},
  language  = {de}
}
@misc{WulfHeinken2008,
  author    = {Wulf, Monika and Heinken, Thilo},
  title     = {Colonization of recent coniferous versus deciduous forest stands by vascular plants at the local scale},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46080},
  year      = {2008},
  abstract  = {Questions: 1. Are there differences among species in their preference for coniferous vs. deciduous forest? 2. Are tree and shrub species better colonizers of recent forest stands than herbaceous species? 3. Do colonization patterns of plant species groups depend on tree species composition? Location: Three deciduous and one coniferous recent forest areas in Brandenburg, NE Germany. Methods: In 34 and 21 transects in coniferous and deciduous stands, respectively, we studied the occurrence and percentage cover of vascular plants in a total of 150 plots in ancient stands, 315 in recent stands and 55 at the ecotone. Habitat preference, diaspore weight, generative dispersal potential and clonal extension were used to explain mechanisms of local migration. Regression analysis was conducted to test whether migration distance was related to species' life-history traits. Results: 25 species were significantly associated with ancient stands and ten species were significantly more frequent in recent stands. Tree and shrub species were good colonizers of recent coniferous and deciduous stands. In the coniferous stands, all herbaceous species showed a strong dispersal limitation during colonization, whereas in the deciduous stands generalist species may have survived in the grasslands which were present prior to afforestation. Conclusions: The fast colonization of recent stands by trees and shrubs can be explained by their effective dispersal via wind and animals. This, and the comparably efficient migration of herbaceous forest specialists into recent coniferous stands, implies that the conversion of coniferous into deciduous stands adjacent to ancient deciduous forests is promising even without planting of trees.},
  language  = {en}
}
@misc{WolffGastEversetal.2021,
  author    = {Wolff, Martin and Gast, Klaus and Evers, Andreas and Kurz, Michael and Pfeiffer-Marek, Stefania and Sch{\"u}ler, Anja and Seckler, Robert and Thalhammer, Anja},
  title     = {A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {9},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52208},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522081},
  pages     = {22},
  year      = {2021},
  abstract  = {Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.},
  language  = {en}
}
@misc{WojcikCeulemansGaedke2021,
  author    = {Wojcik, Laurie Anne Myriam and Ceulemans, Ruben and Gaedke, Ursula},
  title     = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1251},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-55373},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-553730},
  pages     = {25},
  year      = {2021},
  abstract  = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
  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}
}
@phdthesis{Woehlecke2021,
  author    = {Woehlecke, Sandra},
  title     = {Das erweiterte Fachwissen f{\"u}r den schulischen Kontext als Leitlinie f{\"u}r eine additive fachliche Lehrveranstaltung im Lehramtsstudium Biologie},
  doi       = {10.25932/publishup-52120},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-521209},
  school      = {Universit{\"a}t Potsdam},
  pages     = {304},
  year      = {2021},
  abstract  = {Das Fachwissen von Lehrkr{\"a}ften weist f{\"u}r die Auspr{\"a}gung fachdidaktischer Expertise eine hohe Bedeutung auf. Welche Merkmale universit{\"a}re Lehrveranstaltungen aufweisen sollten, um Lehramtsstudierenden ein berufsspezifisches Fachwissen zu vermitteln, ist jedoch {\"u}berwiegend noch unklar. Innerhalb des Projekts PSI-Potsdam wurde auf theoretischer Grundlage das fach{\"u}bergreifende Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext entwickelt. Als Ansatz zur Verbesserung des Biologie-Lehramtsstudiums diente dieses Modell als Konzeptionsgrundlage f{\"u}r eine additive Lehrveranstaltung. Hierbei werden Lerngelegenheiten geboten, um das universit{\"a}r erworbene Fachwissen {\"u}ber zellbiologische Inhalte auf schulische Kontexte anzuwenden, z.B. durch die Dekonstruktion und anschließende Rekonstruktion von schulischen Lerntexten. Die Wirkung des Seminars wurde in mehreren Zyklen im Forschungsformat der Fachdidaktischen Entwicklungsforschung beforscht. Eine der zentralen Forschungsfragen lautet dabei: Wie kann eine Lerngelegenheit f{\"u}r Lehramtsstudierende der Biologie gestaltet sein, um ein erweitertes Fachwissen f{\"u}r den schulischen Kontext f{\"u}r den zellbiologischen Themenbereich „Struktur und Funktion der Biomembran" zu f{\"o}rdern? Anhand fall{\"u}bergreifender Analysen (n = 29) wird im empirischen Teil aufgezeigt, welche Einstellungen zum Lehramtsstudium in der Stichprobe bestehen. Als ein wichtiges Ergebnis kann hierbei herausgestellt werden, dass sich das Fachinteresse hinsichtlich schulisch und universit{\"a}r vermittelter Inhalte bei den untersuchten Studierenden auffallend unterscheidet, wobei dem Schulwissen ein deutlich h{\"o}heres Interesse entgegengebracht wird. Die Berufsrelevanz fachlicher Inhalte wird seitens der Studierenden h{\"a}ufig am Schulwissen festgemacht. Innerhalb konkreter Einzelfallanalysen (n = 6) wird anhand von Lernpfaden dargestellt, wie sich {\"u}ber mehrere Design-Experimente hinweg fachliche Konzepte entwickelt haben. Bei der Beschreibung wird vor allem auf Schl{\"u}sselstellen und H{\"u}rden im Lernprozess fokussiert. Aus diesen Ergebnissen folgend werden vorgenommene Iterationen f{\"u}r die einzelnen Zyklen beschrieben, die ebenfalls anhand der iterativen Entwicklung der Design-Prinzipien dargelegt werden. Es konnte gezeigt werden, dass die Schl{\"u}sselstellen sehr individuell aufgrund der subjektiv fokussierten Inhalte zu Tage treten. Meist treten sie jedoch im Zusammenhang mit der Verkn{\"u}pfung verschiedener fachlicher Konzepte oder durch kooperative Aufschl{\"u}sselungen von Konzepten auf. Fachliche H{\"u}rden konnten hingegen in Form von fachlich unangemessenen Vorstellungen fall{\"u}bergreifend identifiziert werden. Dies betrifft unter anderem die Vorstellung der Biomembran als Wand, die mit den Vorstellungen einer Schutzfunktion und einer formgebenden Funktion der Biomembran einhergeht. Weiterhin wird beleuchtet, wie das erweiterte Fachwissen f{\"u}r den schulischen Kontext zur Bearbeitung der Lernaufgaben angewendet wurde. Es hat sich gezeigt, dass sich bestimmte Lerngelegenheiten eigenen, um bestimmte Facetten des erweiterten Fachwissens zu f{\"o}rdern. Insgesamt scheint das Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext {\"a}ußerst geeignet zu sein, um anhand der Facetten und deren Beschreibungen Lerngelegenheiten oder Gestaltungsprinzipien f{\"u}r diese zu konzipieren. F{\"u}r das untersuchte Lehr-Lernarrangement haben sich kleinere Adaptationen des Modells als sinnvoll erwiesen. Hinsichtlich der Methodologie konnten Ableitungen f{\"u}r die Anwendung der fachdidaktischen Entwicklungsforschung f{\"u}r additive fachliche Lehrveranstaltungen dieser Art herausgestellt werden. Um den Professionsbezug der fachwissenschaftlichen Anteile im Lehramtsstudium zu verbessern, ist der weitere Einbezug des erweiterten Fachwissens f{\"u}r den schulischen Kontext in die fachwissenschaftlichen Studienanteile {\"u}beraus w{\"u}nschenswert.},
  language  = {de}
}
@phdthesis{Witte2009,
  author    = {Witte, Jeannine},
  title     = {Rhabdomerorganisation und -morphogenese im Komplexauge von Drosophila},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41847},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Sehzellen von Insekten sind epitheliale Zellen mit einer charakteristischen, hochpolaren Morphologie und Organisation. Die molekularen Komponenten der Sehkaskade befinden sich im Rhabdomer, einem Saum dicht gepackter Mikrovilli entlang der Sehzelle. Bereits in den 70er Jahren des letzten Jahrhunderts wurde beschrieben, dass die Mikrovilli entlang einer Sehzelle eine unterschiedliche Ausrichtung besitzen, oder in anderen Worten, die Rhabdomere entlang der Sehzell-L{\"a}ngsachse verdreht sind. So sind in den Sehzellen R1-R6 bei dipteren Fliegen (Calliphora, Drosophila) die Mikrovilli im distalen und proximalen Bereich eines Rhabdomers etwa rechtwinkelig zueinander angeordnet. Dieses Ph{\"a}nomen wird in der Fachliteratur als rhabdomere twisting bezeichnet und reduziert die Empfindlichkeit f{\"u}r polarisiertes Licht. Es wurde f{\"u}r das Drosophila-Auge gezeigt, dass diese strukturelle Asymmetrie der Sehzellen mit einer molekularen Asymmetrie in der Verteilung phosphotyrosinierter Proteine an die Stielmembran (einem nicht-mikrovill{\"a}ren Bereich der apikalen Plasmamembran) einhergeht. Zudem wurde gezeigt, dass die immuncytochemische Markierung mit anti-Phosphotyrosin (anti-PY) als lichtmikroskopischer Marker f{\"u}r das rhabdomere twisting verwendet werden kann. Bisher wurde haupts{\"a}chlich die physiologische Bedeutung der Rhabdomerverdrehung untersucht. Es ist wenig {\"u}ber die entwicklungs- und zellbiologischen Grundlagen bekannt. Ziel der vorliegenden Arbeit war es, die Identit{\"a}t der phosphotyrosinierten Proteine an der Stielmembran zu kl{\"a}ren und ihre funktionelle Bedeutung f{\"u}r die Entwicklung des rhabdomere twisting zu analysieren. Zudem sollte untersucht werden, welchen Einfluss die inneren Sehzellen R7 und R8 auf die Verdrehung der Rhabdomere von R1-R6 haben. F{\"u}r die zwei Proteinkinasen Rolled (ERK) und Basket (JNK) vom Typ der Mitogen-aktivierten Proteinkinasen (MAPK) konnte ich zeigen, dass sie in ihrer aktivierten (= phosphorylierten) Form (pERK bzw. pJNK) eine asymmetrische Verteilung an der Stielmembran aufweisen vergleichbar der Markierung mit anti-PY. Weiterhin wurde diese asymmetrische Verteilung von pERK und pJNK ebenso wie die von PY erst kurz vor Schlupf der Fliegen (bei ca. 90\% pupaler Entwicklung) etabliert. Durch Pr{\"a}inkubationsexperimente mit anti-PY wurde die Markierung mit anti-pERK bzw. anti-pJNK unterbunden. Diese Ergebnisse sprechen daf{\"u}r, dass pERK und pJNK zu den Proteinen geh{\"o}ren, die von anti-PY an der Stielmembran erkannt werden. Da es sich bei ERK und JNK um Kinasen handelt, ist es naheliegend, dass diese an der Entwicklung des rhabdomere twisting beteiligt sein k{\"o}nnten. Diese Hypothese wurde durch die Analyse von hypermorphen (rl SEM)und hypomorphen (rl 1/rl 10a) Rolled-Mutanten {\"u}berpr{\"u}ft. In der rl SEM-Mutante mit erh{\"o}hter Aktivit{\"a}t der Proteinkinase erfolgte die asymmetrische Positionierung von pERK an der Stielmembran sowie die Mikrovillikippung schon zu einem fr{\"u}heren Zeitpunkt in der pupalen Entwicklung. Im adulten Auge war die anti-PY-Markierung im distalen Bereich der Sehzellen intensiver sowie der Kippwinkel vergr{\"o}ßert. In der rl 1/rl 10a-Mutanten mit reduzierter Kinaseaktivit{\"a}t waren die anti-PY-Markierung und der Kippwinkel im proximalen Bereich der Sehzellen verringert. Die Proteinkinase ERK hat somit einen Einfluss auf die zeitliche Etablierung des rhabdomere twisting wie auch auf dessen Auspr{\"a}gung im Adulttier. Die Rhabdomerverdrehung sowie die {\"A}nderung im anti-PY-Markierungsmuster erfolgen an den Sehzellen R1-R6 relativ abrupt auf halber Ommatidienl{\"a}nge, dort wo das Rhabdomer von R7 endet und das von R8 beginnt. Es stellte sich deshalb die Frage, ob die Rhabdomerverdrehung an R1-R6 durch die Sehzelle R7 und/oder R8 beeinflusst wird. Um dieser Frage nachzugehen wurden Mutanten analysiert, denen die R7- oder die R8-Photorezeptoren bzw. R7 und R8 fehlten. Das wichtigste Ergebnis dieser Untersuchungen war, dass bei Fehlen von R8 die Rhabdomerverdrehung bei R1-R6 nach keinen erkennbaren Regeln erfolgt. R8 ist somit Voraussetzung f{\"u}r die Etablierung der Rhabdomerverdrehung in R1-R6. Folgendes Modell wurde auf Grundlage dieses und weiterer Ergebnisse erarbeitet: Im dritten Larvenstadium rekrutiert R8 die Sehzellpaare R2/R5, R3/R4 und R1/R6. Dabei werden R1-R6 durch den Kontakt zu R8 „polarisiert". Abschließend wird R7 durch R8 rekrutiert. Dies f{\"u}hrt zu einer Fixierung der Polarit{\"a}t von R1-R6 durch R7. Die Ausf{\"u}hrung der Mikrovillikippung anhand der festgelegten Polarit{\"a}t erfolgt in der sp{\"a}ten Puppenphase. Die Proteinkinase ERK ist an diesem letzten Morphogeneseprozess beteiligt.},
  language  = {de}
}
@phdthesis{Witt2009,
  author    = {Witt, Sandra},
  title     = {Die Rolle der DGDG Synthase DGD1 bei der Galaktolipid Synthese in den H{\"u}llmembranen von Chloroplasten},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33447},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {In den Chloroplasten von h{\"o}heren Pflanzen sind die Galaktolipide Monogalaktosyldiacylglycerol (MGDG) und Digalaktosyldiacylglycerol (DGDG) die am weitesten verbreiteten Lipide. In dieser Forschungsarbeit wurde die Funktion der DGDG Synthase DGD1, und insbesondere die Funktion des N-terminalen Bereichs dieses Enzyms in der Modellpflanze Arabidopsis thaliana untersucht. Die {\"U}berexpression des N-terminalen Bereichs von DGD1 in WT-Col2 resultierte in einem reduzierten Wachstum, welches sich jedoch von der dgd1-1 Mutante unterschied. Dies legte bereits nahe, dass die Expression von N-DGD1 einen negativen Einfluss auf das Wachstum hat. Durch Studien in einem heterologen E.coli Expressionssystem konnte diese These best{\"a}tigt werden. Zellen, die ausschließlich N-DGD1 zusammen mit einer MGD Synthase aus Gurke exprimierten, waren im Wachstum stark beeintr{\"a}chtigt. Nicht nur der N-terminale Bereich von DGD1, auch der N-terminale Bereich von MGD1 besitzt eine Funktion als Transitpeptid und ist somit ein wichtiger Faktor zur korrekten Lokalisierung des MGD1 Proteins. In dieser Arbeit ist es gelungen, ein Fusionskonstrukt aus N-MGD1 und DGD2 in die dgd1-1 Mutante zu transferieren und damit das reduzierte Wachstum zu komplementieren. Fr{\"u}here Versuche, ein reduziertes dgd1-1 Wachstum mit DGD2 allein zu komplementieren, scheiterten. Somit gibt dies einen Hinweis darauf, dass N-MGD1 als Transitpeptid fungieren kann. Bindungsstudien zur Interaktion von DGD1 und N-DGD1 Protein zeigten, dass die polaren Lipide MGDG und DGDG in Wechselwirkung mit dem N-terminalen Bereich von DGD1 treten. Bis zum heutigen Zeitpunkt ist nicht erforscht, wie der Transport von DGDG und MGDG zwischen den H{\"u}llmembranen des Chloroplasten erfolgt. Die in dieser Arbeit angefertigen Bindungsstudien konnten Hinweise darauf geben, dass N-DGD1 als eine Art „Antiporter" fungiert, um MGDG und DGDG zwischen den H{\"u}llmembranen zu transportieren. Weiterhin wurden Bindungsstudien zur Erforschung von Interaktionen der Glykosyltransferasen DGD1, DGD2, MGD1, MGD2 und MGD3 angefertigt. Dabei wurden Wechselwirkungen zwischen den Glykosyltransferasen DGD1, DGD2 und MGD2 detektiert. Interessant ist, dass Hinweise auf eine Dimerbildung bestimmter Enzyme gefunden wurden, so f{\"u}r DGD1 und MGD2. Ein weiterer Ansatz zur Erforschung von Wechselwirkungen von DGD1 Protein mit bis jetzt unbekannten Proteinen war die Expression von DGD1-StrepIITag und DGD1-CTAPTag Fusionsproteinen in dgd1-1 Mutanten. Es wurden f{\"u}r beide Tags transgene Linien generiert, die im Wachstum komplementiert waren und wildtyp{\"a}hnliche Mengen an DGDG akkumulierten. Die Expression der verschiedenen Tags in den Pflanzen war sehr unterschiedlich, wobei der DGD1-CTAP-Tag am st{\"a}rksten exprimiert war. Mit Pflanzenmaterial dieser Linien kann nun eine Aufreinigung des getaggten Proteins und eventueller Interaktionspartner erfolgen.},
  language  = {de}
}
@misc{WinklerHeinken2007,
  author    = {Winkler, Eckart and Heinken, Thilo},
  title     = {Spread of an ant-dispersed annual herb : an individual-based simulation study on population development of Melampyrum pratense L.},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-46491},
  year      = {2007},
  abstract  = {The paper presents a simulation and parameter-estimation approach for evaluating stochastic patterns of population growth and spread of an annual forest herb, Melampyrum pratense (Orobanchaceae). The survival of a species during large-scale changes in land use and climate will depend, to a considerable extent, on its dispersal and colonisation abilities. Predictions on species migration need a combination of field studies and modelling efforts. Our study on the ability of M. pratense to disperse into so far unoccupied areas was based on experiments in secondary woodland in NE Germany. Experiments started in 1997 at three sites where the species was not yet present, with 300 seeds sown within one square meter. Population development was then recorded until 2001 by mapping of individuals with a resolution of 5 cm. Additional observations considered density dependence of seed production. We designed a spatially explicit individual-based computer simulation model to explain the spatial patterns of population development and to predict future population spread. Besides primary drop of seeds (barochory) it assumed secondary seed transport by ants (myrmecochory) with an exponentially decreasing dispersal tail. An important feature of populationpattern explanation was the simultaneous estimation of both population-growth and dispersal parameters from consistent spatio-temporal data sets. As the simulation model produced stochastic time series and random spatially discrete distributions of individuals we estimated parameters by minimising the expectation of weighted sums of squares. These sums-ofsquares criteria considered population sizes, radial population distributions around the area of origin and distributions of individuals within squares of 25*25 cm, the range of density action. Optimal parameter values, together with the precision of the estimates, were obtained from calculating sums of squares in regular grids of parameter values. Our modelling results showed that transport of fractions of seeds by ants over distances of 1…2 m was indispensable for explaining the observed population spread that led to distances of at most 8 m from population origin within 3 years. Projections of population development over 4 additional years gave a diffusion-like increase of population area without any "outposts". This prediction generated by the simulation model gave a hypothesis which should be revised by additional field observations. Some structural deviations between observations and model output already indicated that for full understanding of population spread the set of dispersal mechanisms assumed in the model may have to be extended by additional features of plant-animal mutualism.},
  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{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{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}
}
@misc{Wickert2007,
  type      = {Master Thesis},
  author    = {Wickert, Claudia},
  title     = {Breeding white storks in former East Prussia : comparing predicted relative occurrences across scales and time using a stochastic gradient boosting method (TreeNet), GIS and public data},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13532},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {In dieser Arbeit wurden verschiedene GIS-basierte Habitatmodelle f{\"u}r den Weißstorch (Ciconia ciconia) im Gebiet der ehemaligen deutschen Provinz Ostpreußen (ca. Gebiet der russischen Exklave Kaliningrad und der polnischen Woiwodschaft Ermland-Masuren) erstellt. Zur Charakterisierung der Beziehung zwischen dem Weißstorch und der Beschaffenheit seiner Umwelt wurden verschiedene historische Datens{\"a}tze {\"u}ber den Bestand des Weißstorches in den 1930er Jahren sowie ausgew{\"a}hlte Variablen zur Habitat-Beschreibung genutzt. Die Aufbereitung und Modellierung der verwendeten Datens{\"a}tze erfolgte mit Hilfe eines geographischen Informationssystems (ArcGIS) und einer statistisch-mathematischen Methode aus den Bereichen „Machine Learning" und „Data-Mining" (TreeNet, Salford Systems Ltd.). Unter Verwendung der historischen Habitat-Parameter sowie der Daten zum Vorkommen des Weißstorches wurden quantitative Modelle auf zwei Maßstabs-Ebenen erstellt: (i) auf Punktskala unter Verwendung eines Rasters mit einer Zellgr{\"o}ße von 1 km und (ii) auf Verwaltungs-Kreisebene basierend auf der Gliederung der Provinz Ostpreußen in ihre Landkreise. Die Auswertung der erstellten Modelle zeigt, dass das Vorkommen von Storchennestern im ehemaligen Ostpreußen, unter Ber{\"u}cksichtigung der hier verwendeten Variablen, maßgeblich durch die Variablen ‚forest', ‚settlement area', ‚pasture land' und ‚coastline' bestimmt wird. Folglich l{\"a}sst sich davon ausgehen, dass eine gute Nahrungsverf{\"u}gbarkeit, wie der Weißstorch sie auf Wiesen und Weiden findet, sowie die N{\"a}he zu menschlichen Siedlungen ausschlaggebend f{\"u}r die Nistplatzwahl des Weißstorches in Ostpreußen sind. Geschlossene Waldgebiete zeigen sich in den Modellen als Standorte f{\"u}r Horste des Weißstorches ungeeignet. Der starke Einfluss der Variable ‚coastline' l{\"a}sst sich h{\"o}chstwahrscheinlich durch die starke naturr{\"a}umliche Gliederung Ostpreußens parallel zur K{\"u}stenlinie erkl{\"a}ren. In einem zweiten Schritt konnte unter Verwendung der in dieser Arbeit erstellten Modelle auf beiden Skalen Vorhersagen f{\"u}r den Zeitraum 1981-1993 getroffen werden. Dabei wurde auf dem Punktmaßstab eine Abnahme an potentiellem Bruthabitat vorhergesagt. Im Gegensatz dazu steigt die vorhergesagte Weißstorchdichte unter Verwendung des Modells auf Verwaltungs-Kreisebene. Der Unterschied zwischen beiden Vorhersagen beruht vermutlich auf der Verwendung unterschiedlicher Skalen und von zum Teil voneinander verschiedenen erkl{\"a}renden Variablen. Weiterf{\"u}hrende Untersuchungen sind notwendig, um diesen Sachverhalt zu kl{\"a}ren. Des Weiteren konnten die Modellvorhersagen f{\"u}r den Zeitraum 1981-1993 mit den vorliegenden Bestandserfassungen aus dieser Zeit deskriptiv verglichen werden. Es zeigt sich hierbei, dass die hier vorhergesagten Bestandszahlen h{\"o}her sind als die in den Z{\"a}hlungen ermittelten. Die hier erstellten Modelle beschreiben somit vielmehr die Kapazit{\"a}t des Habitats. Andere Faktoren, die die Gr{\"o}ße der Weißstorch-Population bestimmen, wie z.B. Bruterfolg oder Mortalit{\"a}t sollten in zuk{\"u}nftige Untersuchungen mit einbezogen werden. Es wurde ein m{\"o}glicher Ansatz aufgezeigt, wie man mit den hier vorgestellten Methoden und unter Verwendung historischer Daten wertvolle Habitatmodelle erstellen sowie die Auswirkung von Landnutzungs{\"a}nderungen auf den Weißstorch beurteilen kann. Die hier erstellten Modelle sind als erste Grundlage zu sehen und lassen sich mit Hilfe weitere Daten hinsichtlich Habitatstruktur und mit exakteren r{\"a}umlich expliziten Angaben zu Neststandorten des Weißstorches weiter verfeinern. In einem weiteren Schritt sollte außerdem ein Habitatmodell f{\"u}r die heutige Zeit erstellt werden. Dadurch w{\"a}re ein besserer Vergleich m{\"o}glich hinsichtlich erdenklicher Auswirkungen von {\"A}nderungen der Landnutzung und relevanten Umweltbedingungen auf den Weißstorch im Gebiet des ehemaligen Ostpreußens sowie in seinem gesamten Verbreitungsgebiet.},
  language  = {en}
}
@misc{WeyrichYasarLenzetal.2020,
  author    = {Weyrich, Alexandra and Yasar, Selma and Lenz, Dorina and Fickel, J{\"o}rns},
  title     = {Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {5-6},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-51652},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516525},
  pages     = {15},
  year      = {2020},
  abstract  = {External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.},
  language  = {en}
}
@misc{WeyrichJeschekSchrapersetal.2018,
  author    = {Weyrich, Alexandra and Jeschek, Marie and Schrapers, Katharina T. and Lenz, Dorina and Chung, Tzu Hung and Ruebensam, Kathrin and Yasar, Sermin and Schneemann, Markus and Ortmann, Sylvia and Jewgenow, Katarina and Fickel, J{\"o}rns},
  title     = {Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1065},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-46003},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460031},
  pages     = {14},
  year      = {2018},
  abstract  = {Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.},
  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{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}
}
@misc{WessigBaderKlieretal.2016,
  author    = {Wessig, Pablo and Bader, Denise and Klier, Dennis Tobias and Hettrich, Cornelia and Bier, Frank Fabian},
  title     = {Detecting carbohydrate-lectin interactions using a fluorescent probe based on DBD dyes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-394382},
  pages     = {1235 -- 1238},
  year      = {2016},
  abstract  = {Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein - a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.},
  language  = {en}
}
@phdthesis{Werner2002,
  author    = {Werner, Deljana},
  title     = {Versuche zur Gewinnung von katalytischen Antik{\"o}rpern zur Hydrolyse von Arylcarbamaten und Arylharnstoffen},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000463},
  school      = {Universit{\"a}t Potsdam},
  year      = {2002},
  abstract  = {Im Rahmen dieser Arbeit gelang es, katalytische Antik{\"o}rper zur Hydrolyse von Benzylphenylcarbamaten sowie zahlreiche monoklonale Antik{\"o}rper gegen Haptene herzustellen. Es wurden verschiedene Hapten-Protein-Konjugate unter Verwendung unterschiedlicher Kopplungsmethoden hergestellt und charakterisiert. Zur Generierung der hydrolytisch aktiven Antik{\"o}rper wurden Inzuchtm{\"a}use mit KLH-Konjugaten von 4 {\"U}bergangszustandsanaloga ({\"U}ZA) immunisiert. Mit Hilfe der Hybridomtechnik wurden verschiedene monoklonale Antik{\"o}rper gegen diese {\"U}ZA gewonnen. Dabei wurden sowohl verschiedene Immunisierungsschemata als auch verschiedene Inzuchtmausst{\"a}mme und Fusionstechniken verwendet. Insgesamt wurden 32 monoklonale Antik{\"o}rper gegen die verwendeten {\"U}ZA selektiert. Diese Antik{\"o}rper wurden in großen Mengen hergestellt und gereinigt. Zum Nachweis der Antik{\"o}rper-vermittelten Katalyse wurden verschiedene Methoden entwickelt und eingesetzt, darunter immunologische Nachweismethoden mit Anti-Substrat- und Anti-Produkt-Antik{\"o}rpern und eine photometrische Methode mit Dimethylaminozimtaldehyd. Der Nachweis der hydrolytischen Aktivit{\"a}t gelang mit Hilfe eines Enzymsensors, basierend auf immobilisierter Tyrosinase. Die Antik{\"o}rper N1-BC1-D11, N1-FA7-C4, N1-FA7-D12 und R3-LG2-F9 hydrolysierten die Benzylphenylcarbamate POCc18, POCc19 und Substanz 27. Der Nachweis der hydrolytischen Aktivit{\"a}t dieser Antik{\"o}rper gelang auch mit Hilfe der HPLC. Der katalytische Antik{\"o}rper N1-BC1-D11 wurde kinetisch und thermodynamisch untersucht. Es wurde eine Michaelis-Menten-Kinetik mit Km von 210 \&\#181;M, vmax von 3 mM/min und kcat von 222 min-1 beobachtet. Diese Werte korrelieren mit den Werten der wenigen bekannten Diphenylcarbamat-spaltenden Abzyme. Die Beschleunigungsrate des Antik{\"o}rpers N1-BC1-D11 betrug 10. Das {\"U}ZA Hei3 hemmte die hydrolytische Aktivit{\"a}t. Dies beweist, dass die Hydrolyse in der Antigenbindungsstelle stattfindet. Weiter wurde zwischen der Antik{\"o}rperkonzentration und der Umsatzgeschwindigkeit eine lineare Abh{\"a}ngigkeit festgestellt. Die thermodynamische Gleichtgewichtsdissoziationskonstante KD des Abzyms von 2,6 nM zeugt von einer sehr guten Affinit{\"a}t zum {\"U}ZA. Hydrolytisch aktiv waren nur Antik{\"o}rper, die gegen das {\"U}bergangszustandsanalogon Hei3 hergestellt worden waren. Es wird vermutet, dass die Hydrolyse der Benzylphenylcarbamate {\"u}ber einen Additions-Eliminierungsmechanismus unter Ausbildung eines tetraedrischen {\"U}bergangszustandes verl{\"a}uft, dessen analoge Verbindung Hei3 ist. Im Rahmen der Generierung von Nachweisantik{\"o}rpern zur Detektion der Substratabnahme bei der Hydrolyse wurden Anti-Diuron-Antik{\"o}rper hergestellt. Einer der Antik{\"o}rper (B91-CG5) ist spezifisch f{\"u}r das Herbizid Diuron und hat einen IC50-Wert von 0,19 \&\#181;g/l und eine untere Nachweisgrenze von 0,04 \&\#181;g/l. Ein anderer Antik{\"o}rper (B91-KF5) reagiert kreuz mit einer Palette {\"a}hnlicher Herbizide. Mit diesen Antik{\"o}rpern wurde ein empfindlicher Labortest, der ein Monitoring von Diuron auf Grundlage des durch die Trinkwasserverordnung festgeschriebenen Wertes f{\"u}r Pflanzenschutzmittel von 0,1 \&\#181;g/l erlaubt, aufgebaut. Der Effekt der Anti-Diuron-Antik{\"o}rper auf die Diuron-inhibierte Photosynthese wurde in vitro und in vivo untersucht. Es wurde nachgewiesen, dass sowohl in isolierten Thylakoiden, als auch in intakten Algen eine Vorinkubation der Anti-Diuron-Antik{\"o}rper mit Diuron zur Inaktivierung seiner Photosynthese-hemmenden Wirkung f{\"u}hrt. Wurde der Elektronentransport in den isolierten Thylakoiden oder in Algen durch Diuron unterbrochen, so f{\"u}hrte die Zugabe der Anti-Diuron-Antik{\"o}rper zur Reaktivierung der Elektronen{\"u}bertragung.},
  language  = {de}
}
@misc{WergerBergmannWeberetal.2020,
  author    = {Werger, Luise and Bergmann, Joana and Weber, Ewald and Heinze, Johannes},
  title     = {Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1019},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-48409},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-484092},
  pages     = {14},
  year      = {2020},
  abstract  = {Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant-soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant-soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant-soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant-soil interactions under changing environmental conditions.},
  language  = {en}
}
@article{WendlandGlowinski2022,
  author    = {Wendland, Mirko and Glowinski, Ingrid},
  title     = {Professionsorientierung von Praxisphasen - Ergebnisse einer Fragenbogenstudie},
  series = {Professionalisierung in Praxisphasen : Ergebnisse der Lehrerbildungsforschung an der Universit{\"a}t Potsdam (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 2)},
  journal   = {Professionalisierung in Praxisphasen : Ergebnisse der Lehrerbildungsforschung an der Universit{\"a}t Potsdam (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 2)},
  number    = {2},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-508-8},
  issn      = {2626-3556},
  doi       = {10.25932/publishup-57087},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-570876},
  pages     = {287 -- 321},
  year      = {2022},
  abstract  = {Die Professionsorientierung der Lehramtsstudieng{\"a}nge ist ein zentrales Anliegen der universit{\"a}ren Potsdamer Lehrkr{\"a}ftebildung. Seit 1999 finden Evaluationen zur Professionsorientierung statt, die Diskrepanzen zwischen der gew{\"u}nschten und der erfahrenen Professionsorientierung durch die Studierenden aufzeigen. Im Wintersemester 2013/14 wurden neue Studieng{\"a}nge an der Universit{\"a}t Potsdam eingef{\"u}hrt. Inwieweit damit auch eine st{\"a}rkere Professionsorientierung und ein st{\"a}rkerer Berufsbezug erfolgt ist, ist bislang ungekl{\"a}rt. In einer Onlinebefragung im Dezember 2018 wurden Studierende der Lehramtsstudieng{\"a}nge der Universit{\"a}t Potsdam gebeten, die inhaltliche Gestaltung der Lehramtsstudieng{\"a}nge sowie die Professionsorientierung der Praxisphasen, die Betreuung und Beratung im Rahmen der Praktika, den Nutzen der Praktika f{\"u}r Studium und Beruf und ihre Lehrer:innenkompetenz einzusch{\"a}tzen. Der Beitrag stellt erste empirische Analysen dar und diskutiert Anregungen zur Weiterentwicklung der Studieng{\"a}nge mit Bezug auf die Praxisstudien.},
  language  = {de}
}
@phdthesis{Wende2003,
  author    = {Wende, Hagen},
  title     = {Genetische Charakterisierung des "Leukocyte Receptor Complex" und Entwicklung einer Methode zum Nachweis seiner Produkte im Einzelzellmaßstab},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001298},
  school      = {Universit{\"a}t Potsdam},
  year      = {2003},
  abstract  = {Der "Leukocyte Receptor Complex" (LRC) ist ein DNA-Sequenzabschnitt auf dem Chromosom 19 des Menschen, der eine L{\"a}nge von {\"u}ber 900.000 Basenpaaren umfaßt. In diesem Chromosomenabschnitt ist eine Vielzahl von Genen lokalisiert, die f{\"u}r die Funktion verschiedener weißer Blutzellen (Leukozyten) von entscheidender Bedeutung sind. Bei den aus diesen Genen synthetisierten Proteinen (Eiweißen) handelt es sich um Strukturen, die auf der Oberfl{\"a}che dieser Zellen lokalisiert sind und zur Interaktion der Leukozyten mit ihrer Umgebung dienen. Diese auch als Rezeptoren bezeichneten Proteine k{\"o}nnen mit Oberfl{\"a}chenproteinen auf anderen K{\"o}rperzellen wechselwirken und daraus resultierende Signale in das Innere der Blutzelle weiterleiten. In der vorliegenden Doktorarbeit wurde der LRC im Detail untersucht. Hierzu wurde zun{\"a}chst der gesamte Chromosomenabschnitt aus kleineren, einander {\"u}berlappenden DNA-Fragmenten rekonstruiert. Aufgrund der in diesen DNA-Fragmenten enthaltenen DNA-Sequenzen war es m{\"o}glich, den gesamten Chromosomenabschnitt {\"a}hnlich einem Puzzle zusammenzusetzen. Die anschließende Analyse des LRC zeigte, daß sich dieser in drei Bereiche, sogenannte Cluster, unterteilen l{\"a}ßt. Diese Cluster sind dadurch gekennzeichnet, daß in ihnen jeweils nur Gene eines Rezeptortyps vorkommen. Hierbei handelt es sich um ‚immunoglobulin-like transcript′ -Gene (ILT) und ‚killer cell Ig-like receptor′-Gene (KIR). Die KIR- und ILT-Cluster werden von weiteren stammesgeschichtlich verwandten Genen unterbrochen und flankiert. Je nach Individuum k{\"o}nnen im LRC bis zu 31 solcher verwandten Rezeptorgene lokalisiert sein. Auf der Grundlage der Kartierungsdaten und von Daten des humanen Genomprojekts war es zudem m{\"o}glich, evolution{\"a}re Untersuchungen zur Entwicklung des LRC durchzuf{\"u}hren. Dabei wurde eine Hypothese zur Entstehung des LRC entworfen und zu anderen Spezies in Beziehung gesetzt. Im zweiten Teil der Arbeit habe ich aufbauend auf der sogenannten HRCA-Methode eine Technik entwickelt, die es erlaubt kleinste Unterschiede zwischen DNA-Sequenzen, sogenannte Einzelbasenpaaraustausche, nachzuweisen. Die entwickelte Methode kann verwendet werden, um sehr {\"a}hnliche DNA-Sequenzen, wie z.B. verschiedene KIR-Sequenzen, zu unterscheiden und ihre Menge zu bestimmen. Sie ist außerdem geeignet Mutationen, die mit bestimmten Krankheiten assoziiert sind, nachzuweisen und k{\"o}nnte somit in der Diagnostik Anwendung finden.},
  language  = {de}
}
@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{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}
}
@misc{WeithoffBell2022,
  author    = {Weithoff, Guntram and Bell, Elanor Margaret},
  title     = {Complex Trophic Interactions in an Acidophilic Microbial Community},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-56994},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569945},
  pages     = {1 -- 10},
  year      = {2022},
  abstract  = {Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.},
  language  = {en}
}
@misc{WeiseAugeBaessleretal.2020,
  author    = {Weise, Hanna and Auge, Harald and Baessler, Cornelia and B{\"a}rlund, Ilona and Bennett, Elena M. and Berger, Uta and Bohn, Friedrich and Bonn, Aletta and Borchardt, Dietrich and Brand, Fridolin and Jeltsch, Florian and Joshi, Jasmin Radha and Grimm, Volker},
  title     = {Resilience trinity},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {4},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-51528},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515284},
  pages     = {14},
  year      = {2020},
  abstract  = {Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.},
  language  = {en}
}