@misc{SchefflerBoginHermanussen2020, author = {Scheffler, Christiane and Bogin, Barry and Hermanussen, Michael}, title = {Catch-up growth is a better indicator of undernutrition than thresholds for stunting}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-55049}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-550495}, pages = {12}, year = {2020}, abstract = {Objective: Stunting (height-for-age < -2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < -2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala - different socio-economic status (SES). Participants: 1716 Indonesian children (6·0-13·2 years) and 3838 Guatemalan children (4·0-18·9 years) with up to 50 \% stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting.}, language = {en} } @misc{ChorusSpijkerman2020, author = {Chorus, Ingrid and Spijkerman, Elly}, title = {What Colin Reynolds could tell us about nutrient limitation, N:P ratios and eutrophication control}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-54197}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-541979}, pages = {19}, year = {2020}, abstract = {Colin Reynolds exquisitely consolidated our understanding of driving forces shaping phytoplankton communities and those setting the upper limit to biomass yield, with limitation typically shifting from light in winter to phosphorus in spring. Nonetheless, co-limitation is frequently postulated from enhanced growth responses to enrichments with both N and P or from N:P ranging around the Redfield ratio, concluding a need to reduce both N and P in order to mitigate eutrophication. Here, we review the current understanding of limitation through N and P and of co-limitation. We conclude that Reynolds is still correct: (i) Liebig's law of the minimum holds and reducing P is sufficient, provided concentrations achieved are low enough; (ii) analyses of nutrient limitation need to exclude evidently non-limiting situations, i.e. where soluble P exceeds 3-10 mu g/l, dissolved N exceeds 100-130 mu g/l and total P and N support high biomass levels with self-shading causing light limitation; (iii) additionally decreasing N to limiting concentrations may be useful in specific situations (e.g. shallow waterbodies with high internal P and pronounced denitrification); (iv) management decisions require local, situation-specific assessments. The value of research on stoichiometry and co-limitation lies in promoting our understanding of phytoplankton ecophysiology and community ecology.}, language = {en} } @misc{HornBecherJohstetal.2020, author = {Horn, Juliane and Becher, Matthias A. and Johst, Karin and Kennedy, Peter J. and Osborne, Juliet L. and Radchuk, Viktoriia and Grimm, Volker}, title = {Honey bee colony performance affected by crop diversity and farmland structure}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-55694}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-556943}, pages = {24}, year = {2020}, abstract = {Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps.}, language = {en} } @misc{JannaschNickelSchulze2020, author = {Jannasch, Franziska and Nickel, Daniela and Schulze, Matthias B.}, title = {The reliability and relative validity of predefined dietary patterns were higher than that of exploratory dietary patterns in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam population}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {125}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {11}, issn = {1866-8372}, doi = {10.25932/publishup-55003}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-550030}, pages = {13}, year = {2020}, abstract = {The aim of this study was to assess the ability of the FFQ to describe reliable and valid dietary pattern (DP) scores. In a total of 134 participants of the European Prospective Investigation into Cancer and Nutrition-Potsdam study aged 35-67 years, the FFQ was applied twice (baseline and after 1 year) to assess its reliability. Between November 1995 and March 1997, twelve 24-h dietary recalls (24HDR) as reference instrument were applied to assess the validity of the FFQ. Exploratory DP were derived by principal component analyses. Investigated predefined DP were the Alternative Healthy Eating Index (AHEI) and two Mediterranean diet indices. From dietary data of each FFQ, two exploratory DP were retained, but differed in highly loading food groups, resulting in moderate correlations (r 0 center dot 45-0 center dot 58). The predefined indices showed higher correlations between the FFQ (r(AHEI) 0 center dot 62, r(Mediterranean Diet Pyramid Index (MedPyr)) 0 center dot 62 and r(traditional Mediterranean Diet Score (tMDS)) 0 center dot 51). From 24HDR dietary data, one exploratory DP retained differed in composition to the first FFQ-based DP, but showed similarities to the second DP, reflected by a good correlation (r 0 center dot 70). The predefined DP correlated moderately (r 0 center dot 40-0 center dot 60). To conclude, long-term analyses on exploratory DP should be interpreted with caution, due to only moderate reliability. The validity differed extensively for the two exploratory DP. The investigated predefined DP showed a better reliability and a moderate validity, comparable to other studies. Within the two Mediterranean diet indices, the MedPyr performed better than the tMDs in this middle-aged, semi-urban German study population.}, language = {en} } @phdthesis{Kiss2024, author = {Kiss, Andrea}, title = {Moss-associated bacterial and archaeal communities of northern peatlands: key taxa, environmental drivers and potential functions}, doi = {10.25932/publishup-63064}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-630641}, school = {Universit{\"a}t Potsdam}, pages = {XX, 139, liv}, year = {2024}, abstract = {Moss-microbe associations are often characterised by syntrophic interactions between the microorganisms and their hosts, but the structure of the microbial consortia and their role in peatland development remain unknown. In order to study microbial communities of dominant peatland mosses, Sphagnum and brown mosses, and the respective environmental drivers, four study sites representing different successional stages of natural northern peatlands were chosen on a large geographical scale: two brown moss-dominated, circumneutral peatlands from the Arctic and two Sphagnum-dominated, acidic peat bogs from subarctic and temperate zones. The family Acetobacteraceae represented the dominant bacterial taxon of Sphagnum mosses from various geographical origins and displayed an integral part of the moss core community. This core community was shared among all investigated bryophytes and consisted of few but highly abundant prokaryotes, of which many appear as endophytes of Sphagnum mosses. Moreover, brown mosses and Sphagnum mosses represent habitats for archaea which were not studied in association with peatland mosses so far. Euryarchaeota that are capable of methane production (methanogens) displayed the majority of the moss-associated archaeal communities. Moss-associated methanogenesis was detected for the first time, but it was mostly negligible under laboratory conditions. Contrarily, substantial moss-associated methane oxidation was measured on both, brown mosses and Sphagnum mosses, supporting that methanotrophic bacteria as part of the moss microbiome may contribute to the reduction of methane emissions from pristine and rewetted peatlands of the northern hemisphere. Among the investigated abiotic and biotic environmental parameters, the peatland type and the host moss taxon were identified to have a major impact on the structure of moss-associated bacterial communities, contrarily to archaeal communities whose structures were similar among the investigated bryophytes. For the first time it was shown that different bog development stages harbour distinct bacterial communities, while at the same time a small core community is shared among all investigated bryophytes independent of geography and peatland type. The present thesis displays the first large-scale, systematic assessment of bacterial and archaeal communities associated both with brown mosses and Sphagnum mosses. It suggests that some host-specific moss taxa have the potential to play a key role in host moss establishment and peatland development.}, language = {en} } @phdthesis{Hammel2024, author = {Hammel, Alexander}, title = {Establishing the red microalga Porphyridium purpureum as a novel platform for the production of recombinant proteins}, doi = {10.25932/publishup-63270}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-632709}, school = {Universit{\"a}t Potsdam}, pages = {ix, 159}, year = {2024}, abstract = {Microalgae have been recognized as a promising green production platform for recombinant proteins. The majority of studies on recombinant protein expression have been conducted in the green microalga C. reinhardtii. While promising improvement regarding nuclear transgene expression in this alga has been made, it is still inefficient due to epigenetic silencing, often resulting in low yields that are not competitive with other expressor organisms. Other microalgal species might be better suited for high-level protein expression, but are limited in their availability of molecular tools. The red microalga Porphyridium purpureum recently emerged as candidate for the production of recombinant proteins. It is promising in that transformation vectors are episomally maintained as autonomously replicating plasmids in the nucleus at a high copy number, thus leading to high expression values in this red alga. In this work, we expand the genetic tools for P. purpureum and investigate parameters that govern efficient transgene expression. We provide an improved transformation protocol to streamline the generation of transgenic lines in this organism. After being able to efficiently generate transgenic lines, we showed that codon usage is a main determinant of high-level transgene expression, not only at the protein level but also at the level of mRNA accumulation. The optimized expression constructs resulted in YFP accumulation up to an unprecedented 5\% of the total soluble protein. Furthermore, we designed new constructs conferring efficient transgene expression into the culture medium, simplifying purification and harvests of recombinant proteins. To further improve transgene expression, we tested endogenous promoters driving the most highly transcribed genes in P. purpureum and found minor increase of YFP accumulation. We employed the previous findings to express complex viral antigens from the hepatitis B virus and the hepatitis C virus in P. purpureum to demonstrate its feasibility as producer of biopharmaceuticals. The viral glycoproteins were successfully produced to high levels and could reach their native confirmation, indicating a functional glycosylation machinery and an appropriate folding environment in this red alga. We could successfully upscale the biomass production of transgenic lines and with that provide enough material for immunization trials in mice that were performed in collaboration. These trials showed no toxicity of neither the biomass nor the purified antigens, and, additionally, the algal-produced antigens were able to elicit a strong and specific immune response. The results presented in this work pave the way for P. purpureum as a new promising producer organism for biopharmaceuticals in the microalgal field.}, language = {en} } @misc{SchornSalmanCarvalhoLittmannetal.2019, author = {Schorn, Sina and Salman-Carvalho, Verena and Littmann, Sten and Ionescu, Danny and Grossart, Hans-Peter and Cypionka, Heribert}, title = {Cell architecture of the giant sulfur bacterium achromatium oxaliferum}, 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 = {2}, issn = {1866-8372}, doi = {10.25932/publishup-54993}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549935}, pages = {10}, year = {2019}, abstract = {Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.}, language = {en} } @phdthesis{Cheng2024, author = {Cheng, Feng}, title = {Evolution and ontogeny of electric organ discharge in African weakly electric fish genus Campylomormyrus: a genomic and transcriptomic perspective}, doi = {10.25932/publishup-63017}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-630172}, school = {Universit{\"a}t Potsdam}, pages = {176}, year = {2024}, abstract = {The African weakly electric fishes (Mormyridae) exhibit a remarkable adaptive radiation possibly due to their species-specific electric organ discharges (EODs). It is produced by a muscle-derived electric organ that is located in the caudal peduncle. Divergence in EODs acts as a pre-zygotic isolation mechanism to drive species radiations. However, the mechanism behind the EOD diversification are only partially understood. The aim of this study is to explore the genetic basis of EOD diversification from the gene expression level across Campylomormyrus species/hybrids and ontogeny. I firstly produced a high quality genome of the species C. compressirostris as a valuable resource to understand the electric fish evolution. The next study compared the gene expression pattern between electric organs and skeletal muscles in Campylomormyrus species/hybrids with different types of EOD duration. I identified several candidate genes with an electric organ-specific expression, e.g. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. The overall genes expression pattern exhibited a significant association with EOD duration in all analyzed species/hybrids. The expression of several candidate genes, e.g. KCNJ2, KLF5, KCNK6 and KCNQ5, possibly contribute to the regulation of EOD duration in Campylomormyrus due to their increasing or decreasing expression. Several potassium channel genes showed differential expression during ontogeny in species and hybrid with EOD alteration, e.g. KCNJ2. I next explored allele specific expression of intragenus hybrids by crossing the duration EOD species C. compressirostris with the medium duration EOD species C. tshokwe and the elongated duration EOD species C. rhynchophorus. The hybrids exhibited global expression dominance of the C. compressirostris allele in the adult skeletal muscle and electric organ, as well as in the juvenile electric organ. Only the gene KCNJ2 showed dominant expression of the allele from C. rhynchophorus, and this was increasingly dominant during ontogeny. It hence supported our hypothesis that KCNJ2 is a key gene of regulating EOD duration. Our results help us to understand, from a genetic perspective, how gene expression effect the EOD diversification in the African weakly electric fish.}, language = {en} } @misc{LenznerMagallonDawsonetal.2020, author = {Lenzner, Bernd and Magallon, Susana and Dawson, Wayne and Kreft, Holger and K{\"o}nig, Christian and Pergl, Jan and Pysek, Petr and Weigelt, Patrick and van Kleunen, Mark and Winter, Marten and Dullinger, Stefan and Essl, Franz}, title = {Role of diversification rates and evolutionary history as a driver of plant naturalization success}, 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}, issn = {1866-8372}, doi = {10.25932/publishup-56999}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569996}, pages = {13}, year = {2020}, abstract = {Human introductions of species beyond their natural ranges and their subsequent establishment are defining features of global environmental change. However, naturalized plants are not uniformly distributed across phylogenetic lineages, with some families contributing disproportionately more to the global alien species pool than others. Additionally, lineages differ in diversification rates, and high diversification rates have been associated with characteristics that increase species naturalization success. Here, we investigate the role of diversification rates in explaining the naturalization success of angiosperm plant families. We use five global data sets that include native and alien plant species distribution, horticultural use of plants, and a time-calibrated angiosperm phylogeny. Using phylogenetic generalized linear mixed models, we analysed the effect of diversification rate, different geographical range measures, and horticultural use on the naturalization success of plant families. We show that a family's naturalization success is positively associated with its evolutionary history, native range size, and economic use. Investigating interactive effects of these predictors shows that native range size and geographic distribution additionally affect naturalization success. High diversification rates and large ranges increase naturalization success, especially of temperate families. We suggest this may result from lower ecological specialization in temperate families with large ranges, compared with tropical families with smaller ranges.}, language = {en} } @misc{RomeroMunozFandosBenitezLopezetal.2020, author = {Romero-Munoz, Alfredo and Fandos, Guillermo and Ben{\´i}tez-L{\´o}pez, Ana and Kuemmerle, Tobias}, title = {Habitat destruction and overexploitation drive widespread declines in all facets of mammalian diversity in the Gran Chaco}, 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-56769}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-567696}, pages = {15}, year = {2020}, abstract = {Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50\% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57\%, similar to 37\%, and similar to 6\% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23\% of the Chaco would have to be protected to safeguard the top 17\% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them.}, language = {en} } @misc{EckertHerdenStiftetal.2020, author = {Eckert, Silvia and Herden, Jasmin and Stift, Marc and Joshi, Jasmin Radha and van Kleunen, Mark}, title = {Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-56952}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569528}, pages = {17}, year = {2020}, abstract = {Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.}, language = {en} } @misc{FichtnerBarbierAnnunziataetal.2020, author = {Fichtner, Franziska and Barbier, Francois F. and Annunziata, Maria Grazia and Feil, Regina and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Stitt, Mark and Beveridge, Christine A. and Lunn, John Edward}, title = {Regulation of shoot branching in arabidopsis by trehalose 6-phosphate}, 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-56956}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569564}, pages = {19}, year = {2020}, abstract = {Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood. We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds. TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous Tre6P phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and upregulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds. These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT.}, language = {en} } @misc{ZaplataNhabangaStalmansetal.2020, author = {Zaplata, Markus Klemens and Nhabanga, Abel and Stalmans, Marc and Volpers, Thomas and Burkart, Michael and Sperfeld, Erik}, title = {Grasses cope with high-contrast ecosystem conditions in the large outflow of the Banhine wetlands, Mozambique}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-57351}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-573515}, pages = {16}, year = {2020}, abstract = {Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock.}, language = {en} } @phdthesis{Stange2024, author = {Stange, Maike}, title = {A study on Coronin-A and Aip1 function in motility of Dictyostelium discoideum and on Aip1 interchangeability between Dictyostelium discoideum and Arabidopsis thaliana}, doi = {10.25932/publishup-62856}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-628569}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 168}, year = {2024}, abstract = {Actin is one of the most highly conserved proteins in eukaryotes and distinct actin-related proteins with filament-forming properties are even found in prokaryotes. Due to these commonalities, actin-modulating proteins of many species share similar structural properties and proposed functions. The polymerization and depolymerization of actin are critical processes for a cell as they can contribute to shape changes to adapt to its environment and to move and distribute nutrients and cellular components within the cell. However, to what extent functions of actin-binding proteins are conserved between distantly related species, has only been addressed in a few cases. In this work, functions of Coronin-A (CorA) and Actin-interacting protein 1 (Aip1), two proteins involved in actin dynamics, were characterized. In addition, the interchangeability and function of Aip1 were investigated in two phylogenetically distant model organisms. The flowering plant Arabidopsis thaliana (encoding two homologs, AIP1-1 and AIP1-2) and in the amoeba Dictyostelium discoideum (encoding one homolog, DdAip1) were chosen because the functions of their actin cytoskeletons may differ in many aspects. Functional analyses between species were conducted for AIP1 homologs as flowering plants do not harbor a CorA gene. In the first part of the study, the effect of four different mutation methods on the function of Coronin-A protein and the resulting phenotype in D. discoideum was revealed in two genetic knockouts, one RNAi knockdown and a sudden loss-of-function mutant created by chemical-induced dislocation (CID). The advantages and disadvantages of the different mutation methods on the motility, appearance and development of the amoebae were investigated, and the results showed that not all observed properties were affected with the same intensity. Remarkably, a new combination of Selection-Linked Integration and CID could be established. In the second and third parts of the thesis, the exchange of Aip1 between plant and amoeba was carried out. For A. thaliana, the two homologs (AIP1-1 and AIP1-2) were analyzed for functionality as well as in D. discoideum. In the Aip1-deficient amoeba, rescue with AIP1-1 was more effective than with AIP1-2. The main results in the plant showed that in the aip1-2 mutant background, reintroduced AIP1-2 displayed the most efficient rescue and A. thaliana AIP1-1 rescued better than DdAip1. The choice of the tagging site was important for the function of Aip1 as steric hindrance is a problem. The DdAip1 was less effective when tagged at the C-terminus, while the plant AIP1s showed mixed results depending on the tag position. In conclusion, the foreign proteins partially rescued phenotypes of mutant plants and mutant amoebae, despite the organisms only being very distantly related in evolutionary terms.}, language = {en} } @misc{EhrlichKathGaedke2020, author = {Ehrlich, Elias and Kath, Nadja Jeanette and Gaedke, Ursula}, title = {The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton}, 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 = {6}, issn = {1866-8372}, doi = {10.25932/publishup-51395}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-513956}, pages = {14}, year = {2020}, abstract = {Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change.}, language = {en} } @misc{MasigolKhodaparastMostowfizadehGhalamfarsaetal.2020, author = {Masigol, Hossein and Khodaparast, Seyed Akbar and Mostowfizadeh-Ghalamfarsa, Reza and Rojas-Jimenez, Keilor and Woodhouse, Jason Nicholas and Neubauer, Darshan and Grossart, Hans-Peter}, title = {Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51582}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515820}, pages = {16}, year = {2020}, abstract = {Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50\% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.}, language = {en} } @misc{CrawfordKaramatLehotaietal.2020, author = {Crawford, Tim and Karamat, Fazeelat and Lehotai, N{\´o}ra and Rentoft, Matilda and Blomberg, Jeanette and Strand, {\AA}sa and Bj{\"o}rklund, Stefan}, title = {Specific functions for mediator complex subunits from different modules in the transcriptional response of arabidopsis thaliana to abiotic stress}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51366}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-513666}, pages = {20}, year = {2020}, abstract = {Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.}, language = {en} } @misc{MoradianRochLendleinetal.2020, author = {Moradian, Hanieh and Roch, Toralf and Lendlein, Andreas and Gossen, Manfred}, title = {mRNA transfection-induced activation of primary human monocytes and macrophages}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51569}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515694}, pages = {17}, year = {2020}, abstract = {Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications.}, language = {en} } @misc{BaeurleTrindade2020, author = {B{\"a}urle, Isabel and Trindade, In{\^e}s}, title = {Chromatin regulation of somatic abiotic stress memory}, 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 = {17}, issn = {1866-8372}, doi = {10.25932/publishup-51666}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516668}, pages = {13}, year = {2020}, abstract = {In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.}, language = {en} } @misc{ObbardShiRobertsetal.2020, author = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.}, title = {A new lineage of segmented RNA viruses infecting animals}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51604}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516040}, pages = {12}, year = {2020}, abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.}, 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{AmenNagelHedtetal.2020, author = {Amen, Rahma and Nagel, Rebecca and Hedt, Maximilian and Kirschbaum, Frank and Tiedemann, Ralph}, title = {Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences}, 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 = {3}, issn = {1866-8372}, doi = {10.25932/publishup-51871}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-518714}, pages = {13}, year = {2020}, abstract = {Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated.}, language = {en} } @misc{MorenoRomeroProbstTrindadeetal.2020, author = {Moreno-Romero, Jordi and Probst, Aline V. and Trindade, In{\^e}s and Kalyanikrishna, and Engelhorn, Julia and Farrona, Sara}, title = {Looking At the Past and Heading to the Future}, 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-51194}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-511942}, pages = {14}, year = {2020}, abstract = {In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.}, language = {en} } @misc{CaoTianAndreevetal.2020, author = {Cao, Xianyong and Tian, Fang and Andreev, Andrei and Anderson, Patricia M. and Lozhkin, Anatoly V. and Bezrukova, Elena and Ni, Jian and Rudaya, Natalia and Stobbe, Astrid and Wieczorek, Mareike and Herzschuh, Ulrike}, title = {A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr}, 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 = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51243}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-512438}, pages = {19}, year = {2020}, abstract = {Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 \% of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 \% were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 \%) and lake sediments (33 \%). Most of the records (83 \%) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.}, 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{FichtnerOlasFeiletal.2020, author = {Fichtner, Franziska and Olas, Justyna Jadwiga and Feil, Regina and Watanabe, Mutsumi and Krause, Ursula and Hoefgen, Rainer and Stitt, Mark and Lunn, John Edward}, title = {Functional features of Trehalose-6-Phosphate Synthase 1}, 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 = {6}, issn = {1866-8372}, doi = {10.25932/publishup-51653}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516532}, pages = {26}, year = {2020}, abstract = {Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.}, language = {en} } @misc{Leimkuehler2020, author = {Leimk{\"u}hler, Silke}, title = {The biosynthesis of the molybdenum cofactors in Escherichia coli}, 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 = {6}, issn = {1866-8372}, doi = {10.25932/publishup-51655}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516559}, pages = {22}, year = {2020}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.}, 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} } @misc{KunstmannEngstroemWehleetal.2020, author = {Kunstmann, Ruth Sonja and Engstr{\"o}m, Olof and Wehle, Marko and Widmalm, G{\"o}ran and Santer, Mark and Barbirz, Stefanie}, title = {Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein}, 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 = {32}, issn = {1866-8372}, doi = {10.25932/publishup-51941}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-519418}, pages = {13}, year = {2020}, abstract = {Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.}, language = {en} } @phdthesis{Stiegler2023, author = {Stiegler, Jonas}, title = {Mobile link functions in unpredictable agricultural landscapes}, doi = {10.25932/publishup-62202}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-622023}, school = {Universit{\"a}t Potsdam}, pages = {155}, year = {2023}, abstract = {Animal movement is a crucial aspect of life, influencing ecological and evolutionary processes. It plays an important role in shaping biodiversity patterns, connecting habitats and ecosystems. Anthropogenic landscape changes, such as in agricultural environments, can impede the movement of animals by affecting their ability to locate resources during recurring movements within home ranges and, on a larger scale, disrupt migration or dispersal. Inevitably, these changes in movement behavior have far-reaching consequences on the mobile link functions provided by species inhabiting such extensively altered matrix areas. In this thesis, I investigate the movement characteristics and activity patterns of the European hare (Lepus europaeus), aiming to understand their significance as a pivotal species in fragmented agricultural landscapes. I reveal intriguing results that shed light on the importance of hares for seed dispersal, the influence of personality traits on behavior and space use, the sensitivity of hares to extreme weather conditions, and the impacts of GPS collaring on mammals' activity patterns and movement behavior. In Chapter I, I conducted a controlled feeding experiment to investigate the potential impact of hares on seed dispersal. By additionally utilizing GPS data of hares in two contrasting landscapes, I demonstrated that hares play a vital role, acting as effective mobile linkers for many plant species in small and isolated habitat patches. The analysis of seed intake and germination success revealed that distinct seed traits, such as density, surface area, and shape, profoundly affect hares' ability to disperse seeds through endozoochory. These findings highlight the interplay between hares and plant communities and thus provide valuable insights into seed dispersal mechanisms in fragmented landscapes. By employing standardized behavioral tests in Chapter II, I revealed consistent behavioral responses among captive hares while simultaneously examining the intricate connection between personality traits and spatial patterns within wild hare populations. This analysis provides insights into the ecological interactions and dynamics within hare populations in agricultural habitats. Examining the concept of animal personality, I established a link between personality traits and hare behavior. I showed that boldness, measured through standardized tests, influences individual exploration styles, with shy and bold hares exhibiting distinct space use patterns. In addition to providing valuable insights into the role of animal personality in heterogeneous environments, my research introduced a novel approach demonstrating the feasibility of remotely assessing personality types using animal-borne sensors without additional disturbance of the focal individual. While climate conditions severely impact the activity and, consequently, the fitness of wildlife species across the globe, in Chapter III, I uncovered the sensitivity of hares to temperature, humidity, and wind speed during their peak reproduction period. I found a strong response in activity to high temperatures above 25°C, with a particularly pronounced effect during temperature extremes of over 35°C. The non-linear relationship between temperature and activity was characterized by contrasting responses observed for day and night. These findings emphasize the vulnerability of hares to climate change and the potential consequences for their fitness and population dynamics with the ongoing rise of temperature. Since such insights can only be obtained through capturing and tagging free-ranging animals, I assessed potential impacts and the recovery process post-collar attachment in Chapter IV. For this purpose, I examined the daily distances moved and the temporal-associated activity of 1451 terrestrial mammals out of 42 species during their initial tracking period. The disturbance intensity and the speed of recovery varied across species, with herbivores, females, and individuals captured and collared in relatively secluded study areas experiencing more pronounced disturbances due to limited anthropogenic influences. Mobile linkers are essential for maintaining biodiversity as they influence the dynamics and resilience of ecosystems. Furthermore, their ability to move through fragmented landscapes makes them a key component for restoring disturbed sites. Individual movement decisions determine the scale of mobile links, and understanding variations in space use among individuals is crucial for interpreting their functions. Climate change poses further challenges, with wildlife species expected to adjust their behavior, especially in response to high-temperature extremes, and comprehending the anthropogenic influence on animal movements will remain paramount to effective land use planning and the development of successful conservation strategies. This thesis provides a comprehensive ecological understanding of hares in agricultural landscapes. My research findings underscore the importance of hares as mobile linkers, the influence of personality traits on behavior and spatial patterns, the vulnerability of hares to extreme weather conditions, and the immediate consequences of collar attachment on mammalian movements. Thus, I contribute valuable insights to wildlife conservation and management efforts, aiding in developing strategies to mitigate the impact of environmental changes on hare populations. Moreover, these findings enable the development of methodologies aimed at minimizing the impacts of collaring while also identifying potential biases in the data, thereby benefiting both animal welfare and the scientific integrity of localization studies.}, language = {en} } @phdthesis{Schaefer2024, author = {Sch{\"a}fer, Marj{\"a}nn Helena}, title = {Untersuchungen zur Evolution der 15-Lipoxygenase (ALOX15) bei S{\"a}ugetieren und funktionelle Charakterisierung von Knock-in-M{\"a}usen mit humanisierter Reaktionsspezifit{\"a}t der 15-Lipoxygenase-2 (Alox15b)}, doi = {10.25932/publishup-62034}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-620340}, school = {Universit{\"a}t Potsdam}, pages = {XVII, 280}, year = {2024}, abstract = {Arachidons{\"a}urelipoxygenasen (ALOX-Isoformen) sind Lipid-peroxidierenden Enzyme, die bei der Zelldifferenzierung und bei der Pathogenese verschiedener Erkrankungen bedeutsam sind. Im menschlichen Genom gibt es sechs funktionelle ALOX-Gene, die als Einzelkopiegene vorliegen. F{\"u}r jedes humane ALOX-Gen gibt es ein orthologes Mausgen. Obwohl sich die sechs humanen ALOX-Isoformen strukturell sehr {\"a}hnlich sind, unterscheiden sich ihre funktionellen Eigenschaften deutlich voneinander. In der vorliegenden Arbeit wurden vier unterschiedliche Fragestellungen zum Vorkommen, zur biologischen Rolle und zur Evolutionsabh{\"a}ngigkeit der enzymatischen Eigenschaften von S{\"a}ugetier-ALOX-Isoformen untersucht: 1) Spitzh{\"o}rnchen (Tupaiidae) sind evolution{\"a}r n{\"a}her mit dem Menschen verwandt als Nagetiere und wurden deshalb als Alternativmodelle f{\"u}r die Untersuchung menschlicher Erkrankungen vorgeschlagen. In dieser Arbeit wurde erstmals der Arachidons{\"a}urestoffwechsel von Spitzh{\"o}rnchen untersucht. Dabei wurde festgestellt, dass im Genom von Tupaia belangeri vier unterschiedliche ALOX15-Gene vorkommen und die Enzyme sich hinsichtlich ihrer katalytischen Eigenschaften {\"a}hneln. Diese genomische Vielfalt, die weder beim Menschen noch bei M{\"a}usen vorhanden ist, erschwert die funktionellen Untersuchungen zur biologischen Rolle des ALOX15-Weges. Damit scheint Tupaia belangeri kein geeigneteres Tiermodel f{\"u}r die Untersuchung des ALOX15-Weges des Menschen zu sein. 2) Entsprechend der Evolutionshypothese k{\"o}nnen S{\"a}ugetier-ALOX15-Orthologe in Arachidons{\"a}ure-12-lipoxygenierende- und Arachidons{\"a}ure-15-lipoxygenierende Enzyme eingeteilt werden. Dabei exprimieren S{\"a}ugetierspezies, die einen h{\"o}heren Evolutionsgrad als Gibbons aufweisen, Arachidons{\"a}ure-15-lipoxygenierende ALOX15-Orthologe, w{\"a}hrend evolution{\"a}r weniger weit entwickelte S{\"a}ugetiere Arachidons{\"a}ure-12 lipoxygenierende Enzyme besitzen. In dieser Arbeit wurden elf neue ALOX15-Orthologe als rekombinante Proteine exprimiert und funktionell charakterisiert. Die erhaltenen Ergebnisse f{\"u}gen sich widerspruchsfrei in die Evolutionshypothese ein und verbreitern deren experimentelle Basis. Die experimentellen Daten best{\"a}tigen auch das Triadenkonzept. 3) Da humane und murine ALOX15B-Orthologe unterschiedliche funktionelle Eigenschaften aufweisen, k{\"o}nnen Ergebnisse aus murinen Krankheitsmodellen zur biologischen Rolle der ALOX15B nicht direkt auf den Menschen {\"u}bertragen werden. Um die ALOX15B-Orthologen von Maus und Mensch funktionell einander anzugleichen, wurden im Rahmen der vorliegenden Arbeit Knock-in M{\"a}use durch die In vivo Mutagenese mittels CRISPR/Cas9-Technik hergestellt. Diese exprimieren eine humanisierte Mutante (Doppelmutation von Tyrosin603Asparagins{\"a}ure+Histidin604Valin) der murinen Alox15b. Diese M{\"a}use waren lebens- und fortpflanzungsf{\"a}hig, zeigten aber geschlechtsspezifische Unterschiede zu ausgekreuzten Wildtyp-Kontrolltieren im Rahmen ihre Individualentwicklung. 4) In vorhergehenden Untersuchungen zur Rolle der ALOX15B in Rahmen der Entz{\"u}ndungsreaktion wurde eine antiinflammatorische Wirkung des Enzyms postuliert. In der vorliegenden Arbeit wurde untersucht, ob eine Humanisierung der murinen Alox15b die Entz{\"u}ndungsreaktion in zwei verschiedenen murinen Entz{\"u}ndungsmodellen beeinflusst. Eine Humanisierung der murinen Alox15b f{\"u}hrte zu einer verst{\"a}rkten Ausbildung von Entz{\"u}ndungssymptomen im induzierten Dextran-Natrium-Sulfat-Kolitismodell. Im Gegensatz dazu bewirkte die Humanisierung der Alox15b eine Abschw{\"a}chung der Entz{\"u}ndungssymptome im Freund'schen Adjuvans Pfoten{\"o}demmodell. Diese Daten deuten darauf hin, dass sich die Rolle der ALOX15B in verschiedenen Entz{\"u}ndungsmodellen unterscheidet.}, language = {de} } @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} } @phdthesis{Sureshkumar2023, author = {Sureshkumar, Priyavathi}, title = {Erweiterung der zellbasierten Calcium-Imaging-Methode im eukaryotischen zellfreien Proteinsynthese-System f{\"u}r die transient-receptor-potential (TRP) - Ionenkan{\"a}le}, doi = {10.25932/publishup-61987}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-619872}, school = {Universit{\"a}t Potsdam}, pages = {x, 110}, year = {2023}, abstract = {Die Fluoreszenz-Calcium-Imaging-Methode wird auch heute noch als g{\"a}ngige Methode verwendet, vor allem wegen der geringeren Kosten f{\"u}r das Wirkstoffscreening in der pharmazeutischen Forschung, wobei Ionenkan{\"a}le sowie einige der G-Protein gekoppelte Rezeptoren (GPCRs) die Mehrzahl der Wirkstoffziele ansprechen. Die zellfreie Synthese eukaryotischer Proteine hat nicht die Nachteile, die bei der {\"U}berexpression dieser ionenpermeablen Proteine in Zellen auftreten k{\"o}nnen, wie z. B. Zelltoxizit{\"a}t, geringere Proteinexpression und die Beseitigung der exprimierten Proteine aufgrund ver{\"a}nderter Dom{\"a}nen sowie die zeitaufw{\"a}ndige Pflege von Zelllinien. Die Synthese von Ionenkan{\"a}len in zellfreien Proteinsyntheseplattformen f{\"u}r das k{\"u}nftige Wirkstoffscreening ist noch in der Grundlagenforschung. Obwohl die Fluoreszenz-Calcium-Imaging-Methode in zellbasierten Assays weit verbreitet ist, wurde diese Methode bisher noch nicht in zellfreien Proteinexpressionssystemen verwendet. Insgesamt ist die neue Anwendung der Calcium-Imaging-Methode in eukaryontischen zellfreien Systemen eine Voraussetzung f{\"u}r die schnelle pharmakologische Analyse von Wirkstoffen. Das erste Ziel dieser wissenschaftlichen Arbeit bestand darin, die grundlegenden Prinzipien der Calcium-Imaging-Methode zur Untersuchung von Ionenkan{\"a}len in zellbasierten Systemen zu untersuchen. Hierf{\"u}r wurden zwei Tumorzelllinien des Auges verwendet, und zwar benigne Pterygiumzellen und maligne Aderhautmelanom 92.1 Zellen. In diesen Studien wurde die Interaktion zwischen den nativ {\"u}berexprimierten transient-receptor-potential-Ionenkan{\"a}len (TRPs) wie TRP Vanilliod 1 (TRPV1) (Capsaicinrezeptor) und TRP Melastatin 8 (TRPM8) (Mentholrezeptor) in diesen Tumorzellen nach Zugabe von verschiedenen Medikamenten und Hormonen untersucht. Das zweite Ziel dieser Arbeit war es, den Calcium-Mechanismus von GPCRs in den Zellen zu untersuchen. Zu diesem Zweck wurde Mas, ein GPCR und Angiotensin (1-7) -Hormonrezeptor, aus dem renin-angiotensin-aldosteron-system (RAAS) in der Human Embryonic Kidney-293 (HEK293) Zelllinie {\"u}berexprimiert. In dieser Studie wurden insbesondere die Aktivierung klassischer GPCR-Signalwege wie Phospholipase C und Proteinkinase C durch Angiotensin-(1-7) {\"u}ber Mas und die Beteiligung von TRP-Kan{\"a}len nachgewiesen. Die zellbasierte-Calcium-Imaging-Methode f{\"u}r chemische Calcium-Indikatoren ließ sich aufgrund der Anwesenheit einer großen Menge cytosolischer Carboxylesterasen gut anwenden. Carboxylesterase ist das wichtigste Enzym in der Calcium Imaging Methode, das die Verarbeitung chemischen Calcium-Farbstoffe behandelt. Dieses Enzym fehlt jedoch in Mikrosomen, die als Basismembran f{\"u}r die Integration synthetisierter Ionenkan{\"a}le in eukaryontischen zellfreien Systemen verwendet werden. Das dritte Ziel dieser Forschungsarbeit war die Umsetzung der zellbasierten Calcium-Imaging Methode und der Calcium-Signalwege in zellfreie Systeme. Hier wurde die zellfrei synthetisierte Carboxylesterase in Mikrosomen von Spodoptera frugiperda (Sf21) als praktikables Calcium-Imaging-Werkzeug etabliert, um sowohl native ionenpermeable Proteine als auch zellfrei-synthetisierte Ionenkan{\"a}le zu untersuchen. Die Enzymaktivit{\"a}t der zellfrei-synthetisierten Carboxylesterase in Mikrosomen wurde durch Esterase-Assays und den Calcium-Fluoreszenzfarbstoff Fluo-5N Acetoxymethylester (Fluo-5N AM) Belastungstests nachgewiesen. Das Calcium-Imaging der nativ vorhandenen Ca2+-ATPase des sarkoplasmatischen/endoplasmatischen Retikulums (SERCA) und der Ryanodin-Rezeptoren (RyR) in den Mikrosomen sowie der zell-frei exprimierten TRP-Ionenkan{\"a}le wurden mit dem Fura-5N-AM- Fluoreszenzfarbstoff in mit Carboxylesterase vorsynthetisierten Mikrosomen nachgewiesen. Zusammenfassend l{\"a}sst sich sagen, dass das Prinzip der zellbasierten Calcium-Imaging -Methode vielversprechend an das eukaryotische zellfreie Sf21-System angepasst werden konnte, um Ionenkan{\"a}le zu analysieren. Nach entsprechender Forschung k{\"o}nnte die etablierte Methode in Zukunft auch auf andere Membranproteine ausgeweitet werden. Dies umfasst die Untersuchung anderer zell-frei exprimierte GPCRs oder anderer Ionenkan{\"a}le wie Kalium-, Natrium- und Chlorid-Ionenkan{\"a}le.}, language = {de} } @phdthesis{CalderonQuinonez2023, author = {Calder{\´o}n Qui{\~n}{\´o}nez, Ana Patricia}, title = {Ecology and conservation of the jaguar (Panthera onca) in Central America}, doi = {10.25932/publishup-61367}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-613671}, school = {Universit{\"a}t Potsdam}, pages = {140}, year = {2023}, abstract = {Conservation of the jaguar relies on holistic and transdisciplinary conservation strategies that integratively safeguard essential, connected habitats, sustain viable populations and their genetic exchange, and foster peaceful human-jaguar coexistence. These strategies define four research priorities to advance jaguar conservation throughout the species' range. In this thesis I provide several relevant ecological and sociological insights into these research priorities, each addressed in a separate chapter. I focus on the effects of anthropogenic landscapes on jaguar habitat use and population gene flow, spatial patterns of jaguar habitat suitability and functional population connectivity, and on innovative governance approaches which can work synergistically to help achieve human-wildlife conviviality. Furthermore, I translate these insights into recommendations for conservation practice by providing tools and suggestions that conservation managers and stakeholders can use to implement local actions but also make broad scale conservation decisions in Central America. In Chapter 2, I model regional habitat use of jaguars, producing spatially-explicit maps for management of key areas of habitat suitability. Using an occupancy model of 13-year-camera-trap occurrence data, I show that human influence has the strongest impact on jaguar habitat use, and that Jaguar Conservation Units are the most important reservoirs of high quality habitat in this region. I build upon these results by zooming in to an area of high habitat suitability loss in Chapter 3, northern Central America. Here I study the drivers of jaguar gene flow and I produce spatially-explicit maps for management of key areas of functional population connectivity in this region. I use microsatellite data and pseudo-optimized multiscale, multivariate resistance surfaces of gene flow to show that jaguar gene flow is influenced by environmental, and even more strongly, by human influence variables; and that the areas of lowest gene flow resistance largely coincide with the location of the Jaguar Conservation Units. Given that human activities significantly impact jaguar habitat use and gene flow, securing viable jaguar populations in anthropogenic landscapes also requires fostering peaceful human-wildlife coexistence. This is a complex challenge that cannot be met without transdisciplinary academic research and cross-sectoral, collaborative governance structures that effectively respond to the multiple challenges of such coexistence. With this in mind, I focus in Chapter 4 on carnivore conservation initiatives that apply transformative governance approaches to enact transformative change towards human-carnivore coexistence. Using the frameworks of transformative biodiversity governance and convivial conservation, I highlight in this chapter concrete pathways, supported by more inclusive, democratic forms of conservation decision-making and participation that promote truly transformative changes towards human-jaguar conviviality.}, language = {en} } @phdthesis{FloresCastellanos2023, author = {Flores Castellanos, Junio}, title = {Potato tuber (Solanum tuberosum L. cv Desiree) — characterization of starch interacting proteins and maltodextrin metabolism}, doi = {10.25932/publishup-61505}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-615055}, school = {Universit{\"a}t Potsdam}, pages = {XV, 69}, year = {2023}, abstract = {Starch is a biopolymer for which, despite its simple composition, understanding the precise mechanism behind its formation and regulation has been challenging. Several approaches and bioanalytical tools can be used to expand the knowledge on the different parts involved in the starch metabolism. In this sense, a comprehensive analysis targeting two of the main groups of molecules involved in this process: proteins, as effectors/regulators of the starch metabolism, and maltodextrins as starch components and degradation products, was conducted in this research work using potato plants (Solanum tuberosum L. cv. Desiree) as model of study. On one side, proteins physically interacting to potato starch were isolated and analyzed through mass spectrometry and western blot for their identification. Alternatively, starch interacting proteins were explored in potato tubers from transgenic plants having antisense inhibition of starch-related enzymes and on tubers stored under variable environmental conditions. Most of the proteins recovered from the starch granules corresponded to previously described proteins having a specific role in the starch metabolic pathway. Another set of proteins could be grouped as protease inhibitors, which were found weakly interacting to starch. Variations in the protein profile obtained after electrophoresis separation became clear when tubers were stored under different temperatures, indicating a differential expression of proteins in response to changing environmental conditions. On the other side, since maltodextrin metabolism is thought to be involved in both starch initiation and degradation, soluble maltooligosaccharide content in potato tubers was analyzed in this work under diverse experimental variables. For this, tuber disc samples from wild type and transgenic lines strongly repressing either the plastidial or cytosolic form of the -glucan phosphorylase and phosphoglucomutase were incubated with glucose, glucose-6-phosphate, and glucose-1-phosphate solutions to evaluate the influence of such enzymes on the conversion of the carbon sources into soluble maltodextrins, in comparison to wild-type samples. Relative maltodextrin amounts analyzed through capillary electrophoresis equipped with laser-induced fluorescence (CE-LIF) revealed that tuber discs could immediately uptake glucose-1-phosphate and use it to produce maltooligosaccharides with a degree of polymerization of up to 30 (DP30), in contrast to transgenic tubers with strong repression of the plastidial glucan phosphorylase. The results obtained from the maltodextrin analysis support previous indications that a specific transporter for glucose-1-phosphate may exist in both the plant cells and the plastidial membranes, thereby allowing a glucose-6-phosphate independent transport. Furthermore, it confirms that the plastidial glucan phosphorylase is responsible for producing longer maltooligosaccharides in the plastids by catalyzing a glucan polymerization reaction when glucose-1-phosphate is available. All these findings contribute to a better understanding of the role of the plastidial glucan phosphorylase as a key enzyme directly involved in the synthesis and degradation of glucans and their implication on starch metabolism.}, language = {en} } @phdthesis{Stanke2023, author = {Stanke, Sandra}, title = {AC electrokinetic immobilization of influenza viruses and antibodies on nanoelectrode arrays for on-chip immunoassays}, doi = {10.25932/publishup-61716}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-617165}, school = {Universit{\"a}t Potsdam}, pages = {x, 115}, year = {2023}, abstract = {In the present thesis, AC electrokinetic forces, like dielectrophoresis and AC electroosmosis, were demonstrated as a simple and fast method to functionalize the surface of nanoelectrodes with submicrometer sized biological objects. These nanoelectrodes have a cylindrical shape with a diameter of 500 nm arranged in an array of 6256 electrodes. Due to its medical relevance influenza virus as well as anti-influenza antibodies were chosen as a model organism. Common methods to bring antibodies or proteins to biosensor surfaces are complex and time-consuming. In the present work, it was demonstrated that by applying AC electric fields influenza viruses and antibodies can be immobilized onto the nanoelectrodes within seconds without any prior chemical modification of neither the surface nor the immobilized biological object. The distribution of these immobilized objects is not uniform over the entire array, it exhibits a decreasing gradient from the outer row to the inner ones. Different causes for this gradient have been discussed, such as the vortex-shaped fluid motion above the nanoelectrodes generated by, among others, electrothermal fluid flow. It was demonstrated that parts of the accumulated material are permanently immobilized to the electrodes. This is a unique characteristic of the presented system since in the literature the AC electrokinetic immobilization is almost entirely presented as a method just for temporary immobilization. The spatial distribution of the immobilized viral material or the anti-influenza antibodies at the electrodes was observed by either the combination of fluorescence microscopy and deconvolution or by super-resolution microscopy (STED). On-chip immunoassays were performed to examine the suitability of the functionalized electrodes as a potential affinity-based biosensor. Two approaches were pursued: A) the influenza virus as the bio-receptor or B) the influenza virus as the analyte. Different sources of error were eliminated by ELISA and passivation experiments. Hence, the activity of the immobilized object was inspected by incubation with the analyte. This resulted in the successful detection of anti-influenza antibodies by the immobilized viral material. On the other hand, a detection of influenza virus particles by the immobilized anti-influenza antibodies was not possible. The latter might be due to lost activity or wrong orientation of the antibodies. Thus, further examinations on the activity of by AC electric fields immobilized antibodies should follow. When combined with microfluidics and an electrical read-out system, the functionalized chips possess the potential to serve as a rapid, portable, and cost-effective point-of-care (POC) device. This device can be utilized as a basis for diverse applications in diagnosing and treating influenza, as well as various other pathogens.}, language = {en} } @article{GlowinskiAutenrieth2023, author = {Glowinski, Ingrid and Autenrieth, Marijke}, title = {Eigene Forschung im Labor, um naturwissenschaftliche Erkenntnisgewinnung kompetent unterrichten zu k{\"o}nnen?}, series = {PSI-Potsdam: Ergebnisbericht zu den Aktivit{\"a}ten im Rahmen der Qualit{\"a}tsoffensive Lehrerbildung (2019-2023) (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 3)}, journal = {PSI-Potsdam: Ergebnisbericht zu den Aktivit{\"a}ten im Rahmen der Qualit{\"a}tsoffensive Lehrerbildung (2019-2023) (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 3)}, number = {3}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-568-2}, issn = {2626-3556}, doi = {10.25932/publishup-61792}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-617922}, pages = {273 -- 293}, year = {2023}, abstract = {Im Rahmen des PSI-Projekts wurde eine Lehrveranstaltung konzipiert, die Lehramtsstudierenden einen vertieften Einblick sowohl in den Ablauf von Forschung als auch eine Bearbeitung einer eigenen experimentellen Forschungsaufgabe erm{\"o}glichen soll. Anlass waren die Ber{\"u}cksichtigung eines „Wissens {\"u}ber Erkenntnisgewinnung in der Disziplin" im Modell des „Erweiterten Fachwissens f{\"u}r den schulischen Kontext" (PSI) sowie Erkenntnisse empirischer Studien, die die Relevanz eigener Forschungserfahrung f{\"u}r das Unterrichten naturwissenschaftlicher Erkenntnisgewinnungsprozesse zeigen. Hier stellen wir eine neue Lehrveranstaltung (4 SWS) vor, die den angehenden Lehrkr{\"a}ften Forschungserfahrung erm{\"o}glicht (Seminar und Praktikum). Die Lehrveranstaltung vermittelt Einblicke in Forschung und die „Natur der Naturwissenschaften", erm{\"o}glicht das Durchf{\"u}hren eigener wissenschaftlicher und schulrelevanter Experimente und bietet eine angemessene Reflexion {\"u}ber die verschiedenen Kurselemente. Die Evaluationsergebnisse sind {\"u}berwiegend positiv, zeigen aber auch, dass f{\"u}r die Studierenden die wahrgenommene Schulrelevanz und die fachdidaktischen Aspekte ein wichtiges Kriterium f{\"u}r die positive Bewertung sind.}, language = {de} } @phdthesis{Pruefer2023, author = {Pr{\"u}fer, Mareike}, title = {Charakterisierung und wechselfeldgest{\"u}tzte Herstellung von Enzym-Nanoarrays}, doi = {10.25932/publishup-61232}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-612329}, school = {Universit{\"a}t Potsdam}, pages = {104}, year = {2023}, abstract = {Dielektrophorese ist die Manipulation polarisierbarer Partikel durch inhomogene elektrische Wechselfelder. In dieser Arbeit wurden drei verschiedene Enzyme durch Dielektrophorese immobilisiert und anschließend hinsichtlich ihrer katalytischen Aktivit{\"a}t untersucht: Meerrettichperoxidase, Cholinoxidase aus Alcaligenes sp. und Glucoseoxidase aus Aspergillus niger. Die Immobilisierung erfolgte durch Dielektrophorese auf nano-Elektrodenarrays aus Wolfram-Zylindern mit 500 nm Durchmesser oder aus Titannitrid-Ringen mit 20 nm Breite. Die Immobilisierung der Enzyme konnte fluoreszenzmikroskopisch entweder anhand der intrinsischen Fluoreszenz oder aufgrund einer Fluoreszenzmarkierung vor oder nach der Immobilisierung f{\"u}r alle getesteten Enzyme nachgewiesen werden. Die Messung der Enzymaktivit{\"a}t erfolgte quantitativ durch den direkten oder indirekten Nachweis des gebildeten Produktes oder, im Falle der Cholinoxidase, durch Beobachtung der intrinsischen Fluoreszenz des Cofaktors FAD, die vom Oxidationszustand dieses Enzyms abh{\"a}ngt. F{\"u}r die Meerrettichperoxidase konnte so eine hohe erhaltene Enzymaktivit{\"a}t nach der Immobilisierung nachgewiesen werden. Die Aktivit{\"a}t der permanent immobilisierten Fraktion der Meerrettichperoxidase entsprach bis zu 47 \% der h{\"o}chstm{\"o}glichen Aktivit{\"a}t einer Monolage dieses Enzyms auf den Elektroden des Chips. Diese Aktivit{\"a}t kann als aktive, aber zuf{\"a}llig gegen{\"u}ber der Oberfl{\"a}che ausgerichtete Enzymschicht interpretiert werden. F{\"u}r die permanent immobilisierte Glucoseoxidase wurde nur eine Aktivit{\"a}t entsprechend <1,3 \% der Aktivit{\"a}t einer solchen Enzymschicht detektiert, w{\"a}hrend f{\"u}r die immobilisierte Cholinoxidase gar keine Aktivit{\"a}t nachgewiesen werden konnte. Die Aktivit{\"a}t der durch DEP immobilisierten Enzyme konnte somit quantitativ bestimmt werden. Der Anteil an erhaltener Aktivit{\"a}t h{\"a}ngt dabei stark vom verwendeten Enzym ab.}, language = {de} } @phdthesis{Dreymann2023, author = {Dreymann, Nico}, title = {Identification and functional characterization of aptamers targeting human urokinase and NDM-1 for therapeutic and diagnostic applications}, doi = {10.25932/publishup-61291}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-612919}, school = {Universit{\"a}t Potsdam}, pages = {IX, 130}, year = {2023}, abstract = {Aptamers are single-stranded DNA (ssDNA) or RNA molecules that can bind specifically and with high affinity to target molecules due to their unique three-dimensional structure. For this reason, they are often compared to antibodies and sometimes even referred to as "chemical antibodies". They are simple and inexpensive to synthesize, easy to modify, and smaller than conventional antibodies. Enzymes, especially hydrolases, are interesting targets in this context. This class of enzymes is capable of hydrolytically cleaving various macromolecules such as proteins, as well as smaller molecules such as antibiotics. Hence, they play an important role in many biological processes including diseases and their treatment. Hydrolase detection as well as the understanding of their function is therefore of great importance for diagnostics and therapy. Due to their various desirable features compared to antibodies, aptamers are being discussed as alternative agents for analytical and diagnostic use in various applications. The use of aptamers in therapy is also frequently investigated, as the binding of aptamers can have effects on the catalytic activity, protein-protein interactions, or proteolytic cascades. Aptamers are generated by an in vitro selection process. Potential aptamer candidates are selected from a pool of enriched nucleic acid sequences with affinity to the target, and their binding affinity and specificity is investigated. This is one of the most important steps in aptamer generation to obtain specific aptamers with high affinity for use in analytical and diagnostic applications. The binding properties or binding domains and their effects on enzyme functions form the basis for therapeutic applications. In this work, the binding properties of DNA aptamers against two different hydrolases were investigated. In view of their potential utility for analytical methods, aptamers against human urokinase (uPA) and New Delhi metallo-β-lactamase-1 (NDM-1) were evaluated for their binding affinity and specificity using different methods. Using the uPA aptamers, a protocol for measuring the binding kinetics of an aptamer-protein-interaction by surface plasmon resonance spectroscopy (SPR) was developed. Based on the increased expression of uPA in different types of cancer, uPA is discussed as a prognostic and diagnostic tumor marker. As uPA aptamers showed different binding sites on the protein, microtiter plate-based aptamer sandwich assay systems for the detection of uPA were developed. Because of the function of urokinase in cancer cell proliferation and metastasis, uPA is also discussed as a therapeutic target. In this regard, the different binding sites of aptamers showed different effects on uPA function. In vitro experiments demonstrated both inhibition of uPA binding to its receptor as well as the inhibition of uPA catalytic activity for different aptamers. Thus, in addition to their specificity and affinity for their targets, the utility of the aptamers for potential diagnostic and therapeutic applications was demonstrated. First, as an alternative inhibitor of human urokinase for therapeutic purposes, and second, as valuable recognition molecules for the detection of urokinase, as a prognostic and diagnostic marker for cancer, and for NDM-1 to detect resistance to carbapenem antibiotics.}, 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{Stuebler2023, author = {St{\"u}bler, Sabine}, title = {Mathematical model of the mucosal immune response to study inflammatory bowel diseases and their treatments}, doi = {10.25932/publishup-61230}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-612301}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 194}, year = {2023}, abstract = {Inflammatory bowel diseases (IBD), characterised by a chronic inflammation of the gut wall, develop as consequence of an overreacting immune response to commensal bacteria, caused by a combination of genetic and environmental conditions. Large inter-individual differences in the outcome of currently available therapies complicate the decision for the best option for an individual patient. Predicting the prospects of therapeutic success for an individual patient is currently only possible to a limited extent; for this, a better understanding of possible differences between responders and non-responders is needed. In this thesis, we have developed a mathematical model describing the most important processes of the gut mucosal immune system on the cellular level. The model is based on literature data, which were on the one hand used (qualitatively) to choose which cell types and processes to incorporate and to derive the model structure, and on the other hand (quantitatively) to derive the parameter values. Using ordinary differential equations, it describes the concentration-time course of neutrophils, macrophages, dendritic cells, T cells and bacteria, each subdivided into different cell types and activation states, in the lamina propria and mesenteric lymph nodes. We evaluate the model by means of simulations of the healthy immune response to salmonella infection and mucosal injury. A virtual population includes IBD patients, which we define through their initially asymptomatic, but after a trigger chronically inflamed gut wall. We demonstrate the model's usefulness in different analyses: (i) The comparison of virtual IBD patients with virtual healthy individuals shows that the disease is elicited by many small or fewer large changes, and allows to make hypotheses about dispositions relevant for development of the disease. (ii) We simulate the effects of different therapeutic targets and make predictions about the therapeutic outcome based on the pre-treatment state. (iii) From the analysis of differences between virtual responders and non-responders, we derive hypotheses about reasons for the inter-individual variability in treatment outcome. (iv) For the example of anti-TNF-alpha therapy, we analyse, which alternative therapies are most promising in case of therapeutic failure, and which therapies are most suited for combination therapies: For drugs also directly targeting the cytokine levels or inhibiting the recruitment of innate immune cells, we predict a low probability of success when used as alternative treatment, but a large gain when used in a combination treatment. For drugs with direct effects on T cells, via modulation of the sphingosine-1-phosphate receptor or inhibition of T cell proliferation, we predict a considerably larger probability of success when used as alternative treatment, but only a small additional gain when used in a combination therapy.}, language = {en} } @phdthesis{Petrich2023, author = {Petrich, Annett}, title = {Quantitative fluorescence microscopy methods to investigate molecular interactions and dynamics in living cells}, doi = {10.25932/publishup-61180}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-611800}, school = {Universit{\"a}t Potsdam}, pages = {244}, year = {2023}, abstract = {Biomolecules such as proteins and lipids have vital roles in numerous cellular functions, including biomolecule transport, protein functions, cellular homeostasis and biomembrane integrity. Traditional biochemistry methods do not provide precise information about cellular biomolecule distribution and behavior under native environmental conditions since they are not transferable to live cell samples. Consequently, this can lead to inaccuracies in quantifying biomolecule interactions due to potential complexities arising from the heterogeneity of native biomembranes. To overcome these limitations, minimal invasive microscopic techniques, such as fluorescence fluctuation spectroscopy (FFS) in combination with fluorescence proteins (FPs) and fluorescence lipid analogs, have been developed. FFS techniques and membrane property sensors enable the quantification of various parameters, including concentration, dynamics, oligomerization, and interaction of biomolecules in live cell samples. In this work, several FFS approaches and membrane property sensors were implemented and employed to examine biological processes of diverse context. Multi-color scanning fluorescence fluctuation spectroscopy (sFCS) was used the examine protein oligomerization, protein-protein interactions (PPIs) and protein dynamics at the cellular plasma membrane (PM). Additionally, two-color number and brightness (N\&B) analysis was extended with the cross-correlation analysis in order to quantify hetero-interactions of proteins in the PM with very slow motion, which would not accessible with sFCS due strong initial photobleaching. Furthermore, two semi-automatic analysis pipelines were designed: spectral F{\"o}rster resonance energy transfer (FRET) analysis to study changes in membrane charge at the inner leaflet of the PM, and spectral generalized polarization (GP) imaging and spectral phasor analysis to monitor changes in membrane fluidity and order. An important parameter for studying PPIs is molecular brightness, which directly determines oligomerization and can be extracted from FFS data. However, FPs often display complex photophysical transitions, including dark states. Therefore, it is crucial to characterize FPs for their dark-states to ensure reliable oligomerization measurements. In this study, N\&B and sFCS analysis were applied to determine photophysical properties of novel green FPs under different conditions (i.e., excitation power and pH) in living cells. The results showed that the new FPs, mGreenLantern (mGL) and Gamillus, exhibited the highest molecular brightness at the cost of lower photostability. The well-established monomeric enhanced green fluorescent protein (mEGFP) remained the best option to investigate PPIs at lower pH, while mGL was best suited for neutral pH, and Gamillus for high pH. These findings provide guidance for selecting an appropriate FP to quantify PPIs via FFS under different environmental conditions. Next, several biophysical fluorescence microscopy approaches (i.e., sFCS, GP imaging, membrane charge FRET) were employed to monitor changes in lipid-lipid-packing in biomembranes in different biological context. Lipid metabolism in cancer cells is known to support rapid proliferation and metastasis. Therefore, targeting lipid synthesis or membrane integrity holds immense promise as an anticancer strategy. However, the mechanism of action of the novel agent erufosine (EPC3) on membrane stability is not fully under stood. The present work revealed that EPC3 reduces lipid packing and composition as well as increased membrane fluidity and dynamic, hence, modifies lipid-lipid-interaction. These effects on membrane integrity were likely triggered by modulations in lipid metabolism and membrane organization. In the case of influenza A virus (IAV) infection, regulation of lipid metabolism is crucial for multiple steps in IAV replication and is related to the pathogenicity of IAV. Here, it is shown for the first time that IAV infection triggers a local enrichment of negatively charged lipids at the inner leaflet of the PM, which decreases membrane fluidity and dynamic, as well as increases lipid packing at the assembly site in living cells. This suggests that IAV alters lipid-lipid interactions and organization at the PM. Overall, this work highlights the potential of biophysical techniques as a screening platform for studying membrane properties in living cells at the single-cell level. Finally, this study addressed remaining questions about the early stage of IAV assembly. The recruitment of matrix protein 1 (M1) and its interaction with other viral surface proteins, hemagglutinin (HA), neuraminidase (NA), and matrix protein 2 (M2), has been a subject of debate due to conflicting results. In this study, different FFS approaches were performed in transfected cells to investigate interactions between IAV proteins themselves and host factors at the PM. FFS measurements revealed that M2 interacts strongly with M1, leading to the translocation of M1 to the PM. This interaction likely took place along the non-canonical pathway, as evidenced by the detection of an interaction between M2 and the host factor LC3-II, leading to the recruitment of LC3-II to the PM. Moreover, weaker interaction was observed between HA and membrane-bound M1, and no interaction between NA and M1. Interestingly, higher oligomeric states of M1 were only detectable in infected cells. These results indicate that M2 initiates virion assembly by recruiting M1 to the PM, which may serve as a platform for further interactions with viral proteins and host factors.}, language = {en} } @phdthesis{Pramanik2023, author = {Pramanik, Shreya}, title = {Protein reconstitution in giant vesicles}, doi = {10.25932/publishup-61278}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-612781}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 132}, year = {2023}, abstract = {Das Leben auf der Erde ist vielf{\"a}ltig und reicht von einzelligen Organismen bis hin zu mehrzelligen Lebewesen wie dem Menschen. Obwohl es Theorien dar{\"u}ber gibt, wie sich diese Organismen entwickelt haben k{\"o}nnten, verstehen wir nur wenig dar{\"u}ber, wie "Leben" aus Molek{\"u}len entstanden ist. Die synthetische Bottom-up-Biologie zielt darauf ab, minimale Zellen zu schaffen, indem sie verschiedene Module wie Kompartimentierung, Wachstum, Teilung und zellul{\"a}re Kommunikation kombiniert. Alle lebenden Zellen haben eine Membran, die sie von dem sie umgebenden w{\"a}ssrigen Medium trennt und sie sch{\"u}tzt. Dar{\"u}ber hinaus haben alle eukaryotischen Zellen Organellen, die von intrazellul{\"a}ren Membranen umschlossen sind. Jede Zellmembran besteht haupts{\"a}chlich aus einer Lipiddoppelschicht mit Membranproteinen. Lipide sind amphiphile Molek{\"u}le, die molekulare Doppelschichten aus zwei Lipid-Monoschichten oder Bl{\"a}ttchen bilden. Die hydrophoben Ketten der Lipide sind einander zugewandt, w{\"a}hrend ihre hydrophilen Kopfgruppen die Grenzfl{\"a}chen zur w{\"a}ssrigen Umgebung bilden. Riesenvesikel sind Modellmembransysteme, die Kompartimente mit einer Gr{\"o}ße von mehreren Mikrometern bilden und von einer einzigen Lipiddoppelschicht umgeben sind. Die Gr{\"o}ße der Riesenvesikel ist mit der Gr{\"o}ße von Zellen vergleichbar und macht sie zu guten Membranmodellen, die mit einem Lichtmikroskop untersucht werden k{\"o}nnen. Allerdings fehlen den Riesenvesikelmembranen nach der ersten Pr{\"a}paration Membranproteine, die in weiteren Pr{\"a}parationsschritten in diese Membranen eingebaut werden m{\"u}ssen. Je nach Protein kann es entweder {\"u}ber Ankerlipide an eines der Membranbl{\"a}ttchen gebunden oder {\"u}ber seine Transmembrandom{\"a}nen in die Lipiddoppelschicht eingebaut werden. Diese Arbeit befasst sich mit der Herstellung von Riesenvesikeln und der Rekonstitution von Proteinen in diesen Vesikeln. Außerdem wird ein mikrofluidischer Chip entworfen, der in verschiedenen Experimenten verwendet werden kann. Die Ergebnisse dieser Arbeit werden anderen Forschern helfen, die Protokolle f{\"u}r die Herstellung von GUVs zu verstehen, Proteine in GUVs zu rekonstituieren und Experimente mit dem mikrofluidischen Chip durchzuf{\"u}hren. Auf diese Weise wird die vorliegende Arbeit f{\"u}r das langfristige Ziel von Nutzen sein, die verschiedenen Module der synthetischen Biologie zu kombinieren, um eine Minimalzelle zu schaffen.}, language = {en} } @phdthesis{Ogunkola2023, author = {Ogunkola, Moses}, title = {Role of the tRNA thiouridine modification protein (TUM1) as a sulfurtransferase in humans}, doi = {10.25932/publishup-61135}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-611357}, school = {Universit{\"a}t Potsdam}, pages = {XII, 82}, year = {2023}, abstract = {Sulfur is essential for the functionality of some important biomolecules in humans. Biomolecules like the Iron-sulfur clusters, tRNAs, Molybdenum cofactor, and some vitamins. The trafficking of sulfur involves proteins collectively called sulfurtransferase. Among these are TUM1, MOCS3, and NFS1. This research investigated the role of TUM1 for molybdenum cofactor biosynthesis and cytosolic tRNA thiolation in humans. The rhodanese-like protein MOCS3 and the L-cysteine desulfurase (NFS1) have been previously demonstrated to interact with TUM1. These interactions suggested a dual function of TUM1 in sulfur transfer for Moco biosynthesis and cytosolic tRNA thiolation. TUM1 deficiency has been implicated to be responsible for a rare inheritable disorder known as mercaptolactate cysteine disulfiduria (MCDU), which is associated with a mental disorder. This mental disorder is similar to the symptoms of sulfite oxidase deficiency which is characterised by neurological disorders. Therefore, the role of TUM1 as a sulfurtransferase in humans was investigated, in CRISPR/Cas9 generated TUM1 knockout HEK 293T cell lines. For the first time, TUM1 was implicated in Moco biosynthesis in humans by quantifying the intermediate product cPMP and Moco using HPLC. Comparing the TUM1 knockout cell lines to the wild-type, accumulation and reduction of cPMP and Moco were observed respectively. The effect of TUM1 knockout on the activity of a Moco-dependent enzyme, Sulfite oxidase, was also investigated. Sulfite oxidase is essential for the detoxification of sulfite to sulfate. Sulfite oxidase activity and protein abundance were reduced due to less availability of Moco. This shows that TUM1 is essential for efficient sulfur transfer for Moco biosynthesis. Reduction in cystathionin -lyase in TUM1 knockout cells was quantified, a possible coping mechanism of the cell against sulfite production through cysteine catabolism. Secondly, the involvement of TUM1 in tRNA thio-modification at the wobble Uridine-34 was reported by quantifying the amount of mcm5s2U and mcm5U via HPLC. The reduction and accumulation of mcm5s2U and mcm5U in TUM1 knockout cells were observed in the nucleoside analysis. Herein, exogenous treatment with NaHS, a hydrogen sulfide donor, rescued the Moco biosynthesis, cytosolic tRNA thiolation, and cell proliferation deficits in TUM1 knockout cells. Further, TUM1 was shown to impact mitochondria bioenergetics through the measurement of the oxygen consumption rate and extracellular acidification rate (ECAR) via the seahorse cell Mito stress analyzer. Reduction in total ATP production was also measured. This reveals how important TUM1 is for H2S biosynthesis in the mitochondria of HEK 293T. Finally, the inhibition of NFS1 in HEK 293T and purified NFS1 protein by 2-methylene 3-quinuclidinone was demonstrated via spectrophotometric and radioactivity quantification. Inhibition of NFS1 by MQ further affected the iron-sulfur cluster-dependent enzyme aconitase activity.}, language = {en} } @phdthesis{MendesFerreira2023, author = {Mendes Ferreira, Clara}, title = {Indirect, tri-trophic effects of fear on biodiversity}, doi = {10.25932/publishup-61102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-611020}, school = {Universit{\"a}t Potsdam}, pages = {119}, year = {2023}, abstract = {Predator-forager interactions are a major factor in evolutionary adaptation of many species, as predators need to gain energy by consuming prey species, and foragers needs to avoid the worst fate of mortality while still consuming resources for energetic gains. In this evolutionary arms race, the foragers have constantly evolved anti-predator behaviours (e.g. foraging activity changes). To describe all these complex changes, researchers developed the framework of the landscape of fear, that is, the spatio-temporal variation of perceived predation risk. This concept simplifies all the involved ecological processes into one framework, by integrating animal biology and distribution with habitat characteristics. Researchers can then evaluate the perception of predation risk in prey species, what are the behavioural responses of the prey and, therefore, understand the cascading effects of landscapes of fear at the resource levels (tri-trophic effects). Although tri-trophic effects are well studied at the predator-prey interaction level, little is known on how the forager-resource interactions are part of the overall cascading effects of landscapes of fear, despite the changes of forager feeding behaviour - that occur with perceived predation risk - affecting directly the level of the resources. This thesis aimed to evaluate the cascading effects of the landscape of fear on biodiversity of resources, and how the feeding behaviour and movement of foragers shaped the final resource species composition (potential coexistence mechanisms). We studied the changes caused by landscapes of fear on wild and captive rodent communities and evaluated: the cascading effects of different landscapes of fear on a tri-trophic system (I), the effects of fear on a forager's movement patterns and dietary preferences (II) and cascading effects of different types of predation risk (terrestrial versus avian, III). In Chapter I, we applied a novel measure to evaluate the cascading effects of fear at the level of resources, by quantifying the diversity of resources left after the foragers gave-up on foraging (diversity at the giving-up density). We tested the measure at different spatial levels (local and regional) and observed that with decreased perceived predation risk, the density and biodiversity of resources also decreased. Foragers left a very dissimilar community of resources based on perceived risk and resources functional traits, and therefore acted as an equalising mechanism. In Chapter II, we wanted to understand further the decision-making processes of rodents in different landscapes of fear, namely, in which resource species rodents decided to forage on (based on three functional traits: size, nutrients and shape) and how they moved depending on perceived predation risk. In safe landscapes, individuals increased their feeding activity and movements and despite the increased costs, they visited more often patches that were further away from their central-place. Despite a preference for the bigger resources regardless of risk, when perceived predation risk was low, individuals changed their preference to fat-rich resources. In Chapter III, we evaluated the cascading effects of two different types of predation risk in rodents: terrestrial (raccoon) versus avian predation risk. Raccoon presence or absence did not alter the rodents feeding behaviour in different landscapes of fear. Rodent's showed risk avoidance behaviours towards avian predators (spatial risk avoidance), but not towards raccoons (lack of temporal risk avoidance). By analysing the effects of fear in tri-trophic systems, we were able to deepen the knowledge of how non-consumptive effects of predators affect the behaviour of foragers, and quantitatively measure the cascading effects at the level of resources with a novel measure. Foragers are at the core of the ecological processes and responses to the landscape of fear, acting as variable coexistence agents for resource species depending on perceived predation risk. This newly found measures and knowledge can be applied to more trophic chains, and inform researchers on biodiversity patterns originating from landscapes of fear.}, language = {en} } @phdthesis{Riedel2023, author = {Riedel, Soraya Lisanne}, title = {Development of electrochemical antibody-based and enzymatic assays for mycotoxin analysis in food}, doi = {10.25932/publishup-60747}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-607477}, school = {Universit{\"a}t Potsdam}, pages = {XV, 95}, year = {2023}, abstract = {Electrochemical methods are promising to meet the demand for easy-to-use devices monitoring key parameters in the food industry. Many companies run own lab procedures for mycotoxin analysis, but it is a major goal to simplify the analysis. The enzyme-linked immunosorbent assay using horseradish peroxidase as enzymatic label, together with 3,3',5,5' tetramethylbenzidine (TMB)/H2O2 as substrates allows sensitive mycotoxin detection with optical detection methods. For the miniaturization of the detection step, an electrochemical system for mycotoxin analysis was developed. To this end, the electrochemical detection of TMB was studied by cyclic voltammetry on different screen-printed electrodes (carbon and gold) and at different pH values (pH 1 and pH 4). A stable electrode reaction, which is the basis for the further construction of the electrochemical detection system, could be achieved at pH 1 on gold electrodes. An amperometric detection method for oxidized TMB, using a custom-made flow cell for screen-printed electrodes, was established and applied for a competitive magnetic bead-based immunoassay for the mycotoxin ochratoxin A. A limit of detection of 150 pM (60 ng/L) could be obtained and the results were verified with optical detection. The applicability of the magnetic bead-based immunoassay was tested in spiked beer using a handheld potentiostat connected via Bluetooth to a smartphone for amperometric detection allowing to quantify ochratoxin A down to 1.2 nM (0.5 µg/L). Based on the developed electrochemical detection system for TMB, the applicability of the approach was demonstrated with a magnetic bead-based immunoassay for the ergot alkaloid, ergometrine. Under optimized assay conditions a limit of detection of 3 nM (1 µg/L) was achieved and in spiked rye flour samples ergometrine levels in a range from 25 to 250 µg/kg could be quantified. All results were verified with optical detection. The developed electrochemical detection method for TMB gives great promise for the detection of TMB in many other HRP-based assays. A new sensing approach, based on an enzymatic electrochemical detection system for the mycotoxin fumonisin B1 was established using an Aspergillus niger fumonisin amine oxidase (AnFAO). AnFAO was produced recombinantly in E. coli as maltose-binding protein fusion protein and catalyzes the oxidative deamination of fumonisins, producing hydrogen peroxide. It was found that AnFAO has a high storage and temperature stability. The enzyme was coupled covalently to magnetic particles, and the enzymatically produced H2O2 in the reaction with fumonisin B1 was detected amperometrically in a flow injection system using Prussian blue/carbon electrodes and the custom-made wall-jet flow cell. Fumonisin B1 could be quantified down to 1.5 µM (≈ 1 mg/L). The developed system represents a new approach to detect mycotoxins using enzymes and electrochemical methods.}, language = {en} } @phdthesis{Soltani2023, author = {Soltani, Ouad}, title = {BLF1-Mode of Action in Barley Leaf Size Control}, doi = {10.25932/publishup-60705}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-607054}, school = {Universit{\"a}t Potsdam}, pages = {110}, year = {2023}, abstract = {Establishment of final leaf size in plants represents a complex mechanism that relies on the precise regulation of two interconnected cellular processes, cell division and cell expansion. In previous work, the barley protein BROAD LEAF1 (BLF1) was identified as a novel negative regulator of cell proliferation, that mainly limits leaf growth in the width direction. Here I identified a novel RING/U-box protein that interacts with BLF1 through a yeast two hybrid screen. Using BiFC, Co-IP and FRET I confirmed the interaction of the two proteins in planta. Enrichment of the BLF1-mEGFP fusion protein and the increase of the FRET signal upon MG132 treatment of tobacco plants, together with an in vivo ubiquitylation assay in bacteria, confirmed that the RING/U-box E3 interacts with BLF1 to mediate its ubiquitylation and degradation by the 26S proteasome system. Consistent with regulation of endogenous BLF1 in barley by proteasomal degradation, inhibition of the proteasome by bortezomib treatment on BLF1-vYFP transgenic barley plants also resulted in an enrichment of the BLF1 protein. I thus demonstrated that RING/U-box E3 is colocalized with BLF1 in nuclei and negatively regulates BLF1 protein levels. Analysis of ring-e3_1 knock-out mutants suggested the involvement of the RING/U-box E3 gene in leaf growth control, although the effect was mainly on leaf length. Together, my results suggest that proteasomal degradation, possibly mediated by RING/U-box E3, contributes to fine-tuning BLF1 protein-level in barley.}, language = {en} } @phdthesis{Carrasco2023, author = {Carrasco, Tomas}, title = {Genome structure analysis and patterns of transposable elements evolution in the slow-evolving Testudines clade}, doi = {10.25932/publishup-60657}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-606577}, school = {Universit{\"a}t Potsdam}, pages = {144}, year = {2023}, abstract = {Transposable elements (TEs) are loci that can replicate and multiply within the genome of their host. Within the host, TEs through transposition are responsible for variation on genomic architecture and gene regulation across all vertebrates. Genome assemblies have increased in numbers in recent years. However, to explore in deep the variations within different genomes, such as SNPs (single nucleotide polymorphism), INDELs (Insertion-deletion), satellites and transposable elements, we need high-quality genomes. Studies of molecular markers in the past 10 years have limitations to correlate with biological differences because molecular markers rely on the accuracy of the genomic resources. This has generated that a substantial part of the studies of TE in recent years have been on high quality genomic resources such as Drosophila, zebrafinch and maize. As testudine have a slow mutation rate lower only to crocodilians, with more than 300 species, adapted to different environments all across the globe, the testudine clade can help us to study variation. Here we propose Testudines as a clade to study variation and the abundance of TE on different species that diverged a long time ago. We investigated the genomic diversity of sea turtles, identifying key genomic regions associated to gene family duplication, specific expansion of particular TE families for Dermochelyidae and that are important for phenotypic differentiation, the impact of environmental changes on their populations, and the dynamics of TEs within different lineages. In chapter 1, we identify that despite high levels of genome synteny within sea turtles, we identified that regions of reduced collinearity and microchromosomes showed higher concentrations of multicopy gene families, as well as genetic distances between species, indicating their potential importance as sources of variation underlying phenotypic differentiation. We found that differences in the ecological niches occupied by leatherback and green turtles have led to contrasting evolutionary paths for their olfactory receptor genes. We identified in leatherback turtles a long-term low population size. Nonetheless, we identify no correlation between the regions of reduced collinearity with abundance of TEs or an accumulation of a particular TE group. In chapter 2, we identified that sea turtle genomes contain a significant proportion of TEs, with differences in TE abundance between species, and the discovery of a recent expansion of Penelope-like elements (PLEs) in the highly conserved sea turtle genome provides new insights into the dynamics of TEs within Testudines. In chapter 3, we compared the proportion of TE across the Testudine clade, and we identified that the proportion of transposable elements within the clade is stable, regardless of the quality of the assemblies. However, we identified that the proportion of TEs orders has correlation with genome quality depending of their expanded abundancy. For retrotransposon, a highly abundant element for this clade, we identify no correlation. However, for DNA elements a rarer element on this clade, correlate with the quality of the assemblies. Here we confirm that high-quality genomes are fundamental for the study of transposable element evolution and the conservation within the clade. The detection and abundance of specific orders of TEs are influenced by the quality of the genomes. We identified that a reduction in the population size on D. coriacea had left signals of long-term low population sizes on their genomes. On the same note we identified an expansion of TE on D. coriacea, not present in any other member of the available genomes of Testudines, strongly suggesting that it is a response of deregulation of TE on their genomes as consequences of the low population sizes. Here we have identified important genomic regions and gene families for phenotypic differentiation and highlighted the impact of environmental changes on the populations of sea turtles. We stated that accurate classification and analysis of TE families are important and require high-quality genome assemblies. Using TE analysis we manage to identify differences in highly syntenic species. These findings have significant implications for conservation and provide a foundation for further research into genome evolution and gene function in turtles and other vertebrates. Overall, this study contributes to our understanding of evolutionary change and adaptation mechanisms.}, language = {en} } @phdthesis{Malchow2023, author = {Malchow, Anne-Kathleen}, title = {Developing an integrated platform for predicting niche and range dynamics}, doi = {10.25932/publishup-60273}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-602737}, school = {Universit{\"a}t Potsdam}, pages = {xiv, 169}, year = {2023}, abstract = {Species are adapted to the environment they live in. Today, most environments are subjected to rapid global changes induced by human activity, most prominently land cover and climate changes. Such transformations can cause adjustments or disruptions in various eco-evolutionary processes. The repercussions of this can appear at the population level as shifted ranges and altered abundance patterns. This is where global change effects on species are usually detected first. To understand how eco-evolutionary processes act and interact to generate patterns of range and abundance and how these processes themselves are influenced by environmental conditions, spatially-explicit models provide effective tools. They estimate a species' niche as the set of environmental conditions in which it can persist. However, the currently most commonly used models rely on static correlative associations that are established between a set of spatial predictors and observed species distributions. For this, they assume stationary conditions and are therefore unsuitable in contexts of global change. Better equipped are process-based models that explicitly implement algorithmic representations of eco-evolutionary mechanisms and evaluate their joint dynamics. These models have long been regarded as difficult to parameterise, but an increased data availability and improved methods for data integration lessen this challenge. Hence, the goal of this thesis is to further develop process-based models, integrate them into a complete modelling workflow, and provide the tools and guidance for their successful application. With my thesis, I presented an integrated platform for spatially-explicit eco-evolutionary modelling and provided a workflow for their inverse calibration to observational data. In the first chapter, I introduced RangeShiftR, a software tool that implements an individual-based modelling platform for the statistical programming language R. Its open-source licensing, extensive help pages and available tutorials make it accessible to a wide audience. In the second chapter, I demonstrated a comprehensive workflow for the specification, calibration and validation of RangeShiftR by the example of the red kite in Switzerland. The integration of heterogeneous data sources, such as literature and monitoring data, allowed to successfully calibrate the model. It was then used to make validated, spatio-temporal predictions of future red kite abundance. The presented workflow can be adopted to any study species if data is available. In the third chapter, I extended RangeShiftR to directly link demographic processes to climatic predictors. This allowed me to explore the climate-change responses of eight Swiss breeding birds in more detail. Specifically, the model could identify the most influential climatic predictors, delineate areas of projected demographic suitability, and attribute current population trends to contemporary climate change. My work shows that the application of complex, process-based models in conservation-relevant contexts is feasible, utilising available tools and data. Such models can be successfully calibrated and outperform other currently used modelling approaches in terms of predictive accuracy. Their projections can be used to predict future abundances or to assess alternative conservation scenarios. They further improve our mechanistic understanding of niche and range dynamics under climate change. However, only fully mechanistic models, that include all relevant processes, allow to precisely disentangle the effects of single processes on observed abundances. In this respect, the RangeShiftR model still has potential for further extensions that implement missing influential processes, such as species interactions. Dynamic, process-based models are needed to adequately model a dynamic reality. My work contributes towards the advancement, integration and dissemination of such models. This will facilitate numeric, model-based approaches for species assessments, generate ecological insights and strengthen the reliability of predictions on large spatial scales under changing conditions.}, language = {en} } @misc{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and M{\"u}ller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, 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 = {1334}, issn = {1866-8372}, doi = {10.25932/publishup-43931}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439317}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @misc{GambaJonesTeasdaleetal.2014, author = {Gamba, Cristina and Jones, Eppie R. and Teasdale, Matthew D. and McLaughlin, Russell L. and Gonz{\´a}lez-Fortes, Gloria M. and Mattiangeli, Valeria and Dombor{\´o}czki, L{\´a}szl{\´o} and Kőv{\´a}ri, Ivett and Pap, Ildik{\´o} and Anders, Alexandra and Whittle, Alasdair and Dani, J{\´a}nos and Raczky, P{\´a}l and Higham, Thomas F. G. and Hofreiter, Michael and Bradley, Daniel G. and Pinhasi, Ron}, title = {Genome flux and stasis in a five millennium transect of European prehistory}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {5}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1332}, issn = {1866-8372}, doi = {10.25932/publishup-43799}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437999}, pages = {9}, year = {2014}, abstract = {The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.}, language = {en} } @phdthesis{Parry2023, author = {Parry, Victor}, title = {From individual to community level: Assessing swimming movement, dispersal and fitness of zooplankton}, doi = {10.25932/publishup-59769}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-597697}, school = {Universit{\"a}t Potsdam}, pages = {ix, 118}, year = {2023}, abstract = {Movement is a mechanism that shapes biodiversity patterns across spatialtemporal scales. Thereby, the movement process affects species interactions, population dynamics and community composition. In this thesis, I disentangled the effects of movement on the biodiversity of zooplankton ranging from the individual to the community level. On the individual movement level, I used video-based analysis to explore the implication of movement behavior on preypredator interactions. My results showed that swimming behavior was of great importance as it determined their survival in the face of predation. The findings also additionally highlighted the relevance of the defense status/morphology of prey, as it not only affected the prey-predator relationship by the defense itself but also by plastic movement behavior. On the community movement level, I used a field mesocosm experiment to explore the role of dispersal (time i.e., from the egg bank into the water body and space i.e., between water bodies) in shaping zooplankton metacommunities. My results revealed that priority effects and taxon-specific dispersal limitation influenced community composition. Additionally, different modes of dispersal also generated distinct community structures. The egg bank and biotic vectors (i.e. mobile links) played significant roles in the colonization of newly available habitat patches. One crucial aspect that influences zooplankton species after arrival in new habitats is the local environmental conditions. By using common garden experiments, I assessed the performance of zooplankton communities in their home vs away environments in a group of ponds embedded within an agricultural landscape. I identified environmental filtering as a driving factor as zooplankton communities from individual ponds developed differently in their home and away environments. On the individual species level, there was no consistent indication of local adaptation. For some species, I found a higher abundance/fitness in their home environment, but for others, the opposite was the case, and some cases were indifferent. Overall, the thesis highlights the links between movement and biodiversity patterns, ranging from the individual active movement to the community level.}, language = {en} } @misc{HartmannHasenkampMayeretal.2015, author = {Hartmann, Stefanie and Hasenkamp, Natascha and Mayer, Jens and Michaux, Johan and Morand, Serge and Mazzoni, Camila J. and Roca, Alfred L. and Greenwood, Alex D.}, title = {Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse}, 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 = {1329}, issn = {1866-8372}, doi = {10.25932/publishup-43120}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431200}, pages = {13}, year = {2015}, abstract = {Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.}, language = {en} } @misc{PajoroMadrigalMuinoetal.2014, author = {Pajoro, Alice and Madrigal, Pedro and Mui{\~n}o, Jose M. and Matus, Jos{\´e} Tom{\´a}s and Jin, Jian and Mecchia, Martin A. and Debernardi, Juan M. and Palatnik, Javier F. and Balazadeh, Salma and Arif, Muhammad and {\´O}'Maoil{\´e}idigh, Diarmuid S. and Wellmer, Frank and Krajewski, Pawel and Riechmann, Jos{\´e}-Luis and Angenent, Gerco C. and Kaufmann, Kerstin}, title = {Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {15}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-43113}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431139}, pages = {19}, year = {2014}, abstract = {Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.}, language = {en} } @misc{MeyerKustererLisecetal.2009, author = {Meyer, Rhonda Christiane and Kusterer, Barbara and Lisec, Jan and Steinfath, Matthias and Becher, Martina and Scharr, Hanno and Melchinger, Albrecht E. and Selbig, Joachim and Schurr, Ulrich and Willmitzer, Lothar and Altmann, Thomas}, title = {QTL analysis of early stage heterosis for biomass in Arabidopsis}, 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 = {1330}, issn = {1866-8372}, doi = {10.25932/publishup-43127}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431272}, pages = {11}, year = {2009}, abstract = {The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44\% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99\% for dry weight and from -58 to 143\% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7\% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.}, language = {en} } @misc{SteinfathGaertnerLisecetal.2009, author = {Steinfath, Matthias and G{\"a}rtner, Tanja and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers}, 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 = {1324}, issn = {1866-8372}, doi = {10.25932/publishup-43111}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431115}, pages = {9}, year = {2009}, abstract = {A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80\% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.}, language = {en} } @phdthesis{Courtin2023, author = {Courtin, J{\´e}r{\´e}my}, title = {Biodiversity changes in Siberia between quaternary glacial and interglacial stages}, doi = {10.25932/publishup-59584}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-595847}, school = {Universit{\"a}t Potsdam}, pages = {vi, 199}, year = {2023}, abstract = {Der vom Menschen verursachte Klimawandel wirkt sich auf die biologische Vielfalt der Erde und damit auf die {\"O}kosysteme und ihre Leistungen aus. Die {\"O}kosysteme in den hohen Breitengraden sind aufgrund der verst{\"a}rkten Erw{\"a}rmung an den Polen noch st{\"a}rker betroffen als der Rest der n{\"o}rdlichen Hemisph{\"a}re. Dennoch ist es schwierig, die Dynamik von {\"O}kosystemen in den hohen Breitengraden vorherzusagen, da die Wechselwirkungen zwischen abiotischen und biotischen Komponenten sehr komplex sind. Da die Vergangenheit der Schl{\"u}ssel zur Zukunft ist, ist die Interpretation vergangener {\"o}kologischer Ver{\"a}nderungen m{\"o}glich, um laufende Prozesse besser zu verstehen. Im Quart{\"a}r durchlief das Pleistoz{\"a}n mehrere glaziale und interglaziale Phasen, welche die {\"O}kosysteme der Vergangenheit beeinflussten. W{\"a}hrend des letzten Glazials bedeckte die pleistoz{\"a}ne Steppentundra den gr{\"o}ßten Teil der unvergletscherten n{\"o}rdlichen Hemisph{\"a}re und verschwand parallel zum Aussterben der Megafauna am {\"U}bergang zum Holoz{\"a}n (vor etwa 11 700 Jahren). Der Ursprung des R{\"u}ckgangs der Steppentundra ist nicht gut erforscht, und die Kenntnis {\"u}ber die Mechanismen, die zu den Ver{\"a}nderungen in den vergangenen Lebensgemeinschaften und {\"O}kosystemen gef{\"u}hrt haben, ist von hoher Priorit{\"a}t, da sie wahrscheinlich mit denen vergleichbar sind, die sich auf moderne {\"O}kosysteme auswirken. Durch die Entnahme von See- oder Permafrostkernsedimenten kann die vergangene Artenvielfalt an den {\"U}berg{\"a}ngen zwischen Eis- und Zwischeneiszeiten untersucht werden. Sibirien und Beringia waren der Ursprung der Ausbreitung der Steppentundra, weshalb die Untersuchung dieses Gebiets hohe Priorit{\"a}t hat. Bis vor kurzem waren Makrofossilien und Pollen die g{\"a}ngigsten Methoden. Sie dienen der Rekonstruktion vergangener Ver{\"a}nderungen in der Zusammensetzung der Bev{\"o}lkerung, haben aber ihre Grenzen und Schw{\"a}chen. Seit Ende des 20. Jahrhunderts kann auch sediment{\"a}re alte DNA (sedaDNA) untersucht werden. Mein Hauptziel war es, durch den Einsatz von sedaDNA-Ans{\"a}tzen wissenschaftliche Beweise f{\"u}r Ver{\"a}nderungen in der Zusammensetzung und Vielfalt der {\"O}kosysteme der n{\"o}rdlichen Hemisph{\"a}re am {\"U}bergang zwischen den quart{\"a}ren Eiszeiten und Zwischeneiszeiten zu liefern. In dieser Arbeit liefere ich Momentaufnahmen ganzer alter {\"O}kosysteme und beschreibe die Ver{\"a}nderungen in der Zusammensetzung zwischen Quart{\"a}rglazialen und Interglazialen und best{\"a}tige die Vegetationszusammensetzung sowie die r{\"a}umlichen und zeitlichen Grenzen der pleistoz{\"a}nen Steppentundra. Ich stelle einen allgemeinen Verlust der Pflanzenvielfalt fest, wobei das Aussterben der Pflanzen parallel zum Aussterben der Megafauna verlief. Ich zeige auf, wie der Verlust der biotischen Widerstandsf{\"a}higkeit zum Zusammenbruch eines zuvor gut etablierten Systems f{\"u}hrte, und diskutiere meine Ergebnisse im Hinblick auf den laufenden Klimawandel. Mit weiteren Arbeiten zur Eingrenzung von Verzerrungen und Grenzen kann sedaDNA parallel zu den etablierteren Makrofossilien- und Pollenans{\"a}tzen verwendet werden oder diese sogar ersetzen, da meine Ergebnisse die Robustheit und das Potenzial von sedaDNA zur Beantwortung neuer pal{\"a}o{\"o}kologischer Fragen wie Ver{\"a}nderungen der Pflanzenvielfalt und -verluste belegen und Momentaufnahmen ganzer alter Biota liefern.}, language = {en} } @phdthesis{Derežanin2023, author = {Derežanin, Lorena}, title = {Contribution of structural variation to adaptive evolution of mammalian genomes}, doi = {10.25932/publishup-59144}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-591443}, school = {Universit{\"a}t Potsdam}, pages = {188}, year = {2023}, abstract = {Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward. The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation. In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants. Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable. Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints. The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.}, language = {en} } @misc{MooijTrolleJeppesenetal.2010, author = {Mooij, Wolf M. and Trolle, Dennis and Jeppesen, Erik and Arhonditsis, George B. and Belolipetsky, Pavel V. and Chitamwebwa, Deonatus B. R. and Degermendzhy, Andrey G. and DeAngelis, Donald L. and Domis, Lisette Nicole de Senerpont and Downing, Andrea S. and Elliott, J. Alex and Fragoso Jr., Carlos Ruberto and Gaedke, Ursula and Genova, Svetlana N. and Gulati, Ramesh D. and H{\aa}kanson, Lars and Hamilton, David P. and Hipsey, Matthew R. and 't Hoen, Jochem and H{\"u}lsmann, Stephan and Los, F. Hans and Makler-Pick, Vardit and Petzoldt, Thomas and Prokopkin, Igor G. and Rinke, Karsten and Schep, Sebastiaan A. and Tominaga, Koji and Van Dam, Anne A. and Van Nes, Egbert H. and Wells, Scott A. and Janse, Jan H.}, title = {Challenges and opportunities for integrating lake ecosystem modelling approaches}, 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 = {1326}, issn = {1866-8372}, doi = {10.25932/publishup-42983}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429839}, pages = {35}, year = {2010}, abstract = {A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.}, language = {en} } @phdthesis{Goethel2023, author = {G{\"o}thel, Markus}, title = {Entwicklung eines Verfahrens zur Generierung von spezifischen monoklonalen Antik{\"o}rpern gegen Mikroorganismen basierend auf in silico Epitopanalysen}, doi = {10.25932/publishup-58801}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-588017}, school = {Universit{\"a}t Potsdam}, pages = {XVI, 113}, year = {2023}, abstract = {Monoklonale Antik{\"o}rper (mAK) sind eines der wichtigsten Biomolek{\"u}le f{\"u}r die Umweltanalytik und die medizinische Diagnostik. F{\"u}r die Detektion von Mikroorganismen bilden sie die Grundlage f{\"u}r ein schnelles und pr{\"a}zises Testverfahren. Bis heute gibt es, aufgrund des hohen zeitlichen und materiellen Aufwandes und der unspezifischen Immunisierungsstrategien, nur wenige mAK, die spezifisch Mikroorganismen erkennen. Zu diesem Zweck sollte ein anwendbares Verfahren f{\"u}r die Generierung von mAK gegen Mikroorganismen entwickelt werden, welches anhand von Escherichia coli O157:H7 und Legionella pneumophila validiert wurde. In dieser Dissertation konnten neue Oberfl{\"a}chenstrukturen auf den Mikroorganismen mittels vergleichender Genomanalysen und in silico Epitopanalysen identifiziert werden. Diese wurden in das Virush{\"u}llprotein VP1 integriert und f{\"u}r eine gezielte Immunisierungsstrategie verwendet. F{\"u}r die Bestimmung antigenspezifischer antik{\"o}rperproduzierender Hybridome wurde ein Immunf{\"a}rbeprotokoll entwickelt und etabliert, um die Hybridome im Durchflusszytometer zu sortieren. In der vorliegenden Studie konnten f{\"u}r E. coli O157:H7 insgesamt 53 potenzielle Proteinkandidaten und f{\"u}r L. pneumophila 38 Proteine mithilfe der bioinformatischen Analyse identifiziert werden. F{\"u}nf verschiedene potenzielle Epitope wurden f{\"u}r E. coli O157:H7 und drei verschiedenen f{\"u}r L. pneumophila ausgew{\"a}hlt und f{\"u}r die Immunisierung mit chim{\"a}ren VP1 verwendet. Alle Immunseren zeigten eine antigenspezifische Immunantwort. Aus den nachfolgend generierten Hybridomzellen konnten mehrere Antik{\"o}rperkandidaten gewonnen werden, welche in Charakterisierungsstudien eine starke Bindung zu E. coli O157:H7 bzw. L. pneumophila vorwiesen. Kreuzreaktivit{\"a}ten zu anderen relevanten Mikroorganismen konnten keine bzw. nur in geringem Maße festgestellt werden. Folglich konnte der hier beschriebene interdisziplin{\"a}re Ansatz zur Generierung spezifischer mAK gegen Mikroorganismen nachweislich spezifische mAK hervorbringen und ist als hocheffizienter Arbeitsablauf f{\"u}r die Herstellung von Antik{\"o}rpern gegen Mikroorganismen einsetzbar.}, language = {de} } @phdthesis{Gerling2022, author = {Gerling, Marten Tobias}, title = {A microfluidic system for high-precision image-based live cell sorting using dielectrophoretic forces}, doi = {10.25932/publishup-58742}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-587421}, school = {Universit{\"a}t Potsdam}, pages = {vii, 87, VI}, year = {2022}, abstract = {An important goal in biotechnology and (bio-) medical research is the isolation of single cells from a heterogeneous cell population. These specialised cells are of great interest for bioproduction, diagnostics, drug development, (cancer) therapy and research. To tackle emerging questions, an ever finer differentiation between target cells and non-target cells is required. This precise differentiation is a challenge for a growing number of available methods. Since the physiological properties of the cells are closely linked to their morphology, it is beneficial to include their appearance in the sorting decision. For established methods, this represents a non addressable parameter, requiring new methods for the identification and isolation of target cells. Consequently, a variety of new flow-based methods have been developed and presented in recent years utilising 2D imaging data to identify target cells within a sample. As these methods aim for high throughput, the devices developed typically require highly complex fluid handling techniques, making them expensive while offering limited image quality. In this work, a new continuous flow system for image-based cell sorting was developed that uses dielectrophoresis to precisely handle cells in a microchannel. Dielectrophoretic forces are exerted by inhomogeneous alternating electric fields on polarisable particles (here: cells). In the present system, the electric fields can be switched on and off precisely and quickly by a signal generator. In addition to the resulting simple and effective cell handling, the system is characterised by the outstanding quality of the image data generated and its compatibility with standard microscopes. These aspects result in low complexity, making it both affordable and user-friendly. With the developed cell sorting system, cells could be sorted reliably and efficiently according to their cytosolic staining as well as morphological properties at different optical magnifications. The achieved purity of the target cell population was up to 95\% and about 85\% of the sorted cells could be recovered from the system. Good agreement was achieved between the results obtained and theoretical considerations. The achieved throughput of the system was up to 12,000 cells per hour. Cell viability studies indicated a high biocompatibility of the system. The results presented demonstrate the potential of image-based cell sorting using dielectrophoresis. The outstanding image quality and highly precise yet gentle handling of the cells set the system apart from other technologies. This results in enormous potential for processing valuable and sensitive cell samples.}, language = {en} } @phdthesis{Leins2023, author = {Leins, Johannes A.}, title = {Combining model detail with large scales}, doi = {10.25932/publishup-58283}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582837}, school = {Universit{\"a}t Potsdam}, pages = {xv, 168}, year = {2023}, abstract = {The global climate crisis is significantly contributing to changing ecosystems, loss of biodiversity and is putting numerous species on the verge of extinction. In principle, many species are able to adapt to changing conditions or shift their habitats to more suitable regions. However, change is progressing faster than some species can adjust, or potential adaptation is blocked and disrupted by direct and indirect human action. Unsustainable anthropogenic land use in particular is one of the driving factors, besides global heating, for these ecologically critical developments. Precisely because land use is anthropogenic, it is also a factor that could be quickly and immediately corrected by human action. In this thesis, I therefore assess the impact of three climate change scenarios of increasing intensity in combination with differently scheduled mowing regimes on the long-term development and dispersal success of insects in Northwest German grasslands. The large marsh grasshopper (LMG, Stethophyma grossum, Linn{\´e} 1758) is used as a species of reference for the analyses. It inhabits wet meadows and marshes and has a limited, yet fairly good ability to disperse. Mowing and climate conditions affect the development and mortality of the LMG differently depending on its life stage. The specifically developed simulation model HiLEG (High-resolution Large Environmental Gradient) serves as a tool for investigating and projecting viability and dispersal success under different climate conditions and land use scenarios. It is a spatially explicit, stage- and cohort-based model that can be individually configured to represent the life cycle and characteristics of terrestrial insect species, as well as high-resolution environmental data and the occurrence of external disturbances. HiLEG is a freely available and adjustable software that can be used to support conservation planning in cultivated grasslands. In the three case studies of this thesis, I explore various aspects related to the structure of simulation models per se, their importance in conservation planning in general, and insights regarding the LMG in particular. It became apparent that the detailed resolution of model processes and components is crucial to project the long-term effect of spatially and temporally confined events. Taking into account conservation measures at the regional level has further proven relevant, especially in light of the climate crisis. I found that the LMG is benefiting from global warming in principle, but continues to be constrained by harmful mowing regimes. Land use measures could, however, be adapted in such a way that they allow the expansion and establishment of the LMG without overly affecting agricultural yields. Overall, simulation models like HiLEG can make an important contribution and add value to conservation planning and policy-making. Properly used, simulation results shed light on aspects that might be overlooked by subjective judgment and the experience of individual stakeholders. Even though it is in the nature of models that they are subject to limitations and only represent fragments of reality, this should not keep stakeholders from using them, as long as these limitations are clearly communicated. Similar to HiLEG, models could further be designed in such a way that not only the parameterization can be adjusted as required, but also the implementation itself can be improved and changed as desired. This openness and flexibility should become more widespread in the development of simulation models.}, language = {en} } @misc{MummSchefflerHermanussen2022, author = {Mumm, Rebekka and Scheffler, Christiane and Hermanussen, Michael}, title = {Locally structured correlation (LSC) plots describe inhomogeneity in normally distributed correlated bivariate variables}, 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 = {1319}, issn = {1866-8372}, doi = {10.25932/publishup-58877}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-588777}, pages = {6}, year = {2022}, abstract = {Background The association between bivariate variables may not necessarily be homogeneous throughout the whole range of the variables. We present a new technique to describe inhomogeneity in the association of bivariate variables. Methods We consider the correlation of two normally distributed random variables. The 45° diagonal through the origin of coordinates represents the line on which all points would lie if the two variables completely agreed. If the two variables do not completely agree, the points will scatter on both sides of the diagonal and form a cloud. In case of a high association between the variables, the band width of this cloud will be narrow, in case of a low association, the band width will be wide. The band width directly relates to the magnitude of the correlation coefficient. We then determine the Euclidean distances between the diagonal and each point of the bivariate correlation, and rotate the coordinate system clockwise by 45°. The standard deviation of all Euclidean distances, named "global standard deviation", reflects the band width of all points along the former diagonal. Calculating moving averages of the standard deviation along the former diagonal results in "locally structured standard deviations" and reflect patterns of "locally structured correlations (LSC)". LSC highlight inhomogeneity of bivariate correlations. We exemplify this technique by analyzing the association between body mass index (BMI) and hip circumference (HC) in 6313 healthy East German adults aged 18 to 70 years. Results The correlation between BMI and HC in healthy adults is not homogeneous. LSC is able to identify regions where the predictive power of the bivariate correlation between BMI and HC increases or decreases, and highlights in our example that slim people have a higher association between BMI and HC than obese people. Conclusion Locally structured correlations (LSC) identify regions of higher or lower than average correlation between two normally distributed variables.}, language = {en} } @phdthesis{KoikkarahAji2023, author = {Koikkarah Aji, Amit}, title = {Quantitative sub cellular characterization of Hantavirus structural proteins}, doi = {10.25932/publishup-58661}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-586612}, school = {Universit{\"a}t Potsdam}, pages = {101}, year = {2023}, abstract = {Hantaviruses (HVs) are a group of zoonotic viruses that infect human beings primarily through aerosol transmission of rodent excreta and urine samplings. HVs are classified geographically into: Old World HVs (OWHVs) that are found in Europe and Asia, and New World HVs (NWHVs) that are observed in the Americas. These different strains can cause severe hantavirus diseases with pronounced renal syndrome or severe cardiopulmonary system distress. HVs can be extremely lethal, with NWHV infections reaching up to 40 \% mortality rate. HVs are known to generate epidemic outbreaks in many parts of the world including Germany, which has seen periodic HV infections over the past decade. HV has a trisegmented genome. The small segment (S) encodes the nucleocapsid protein (NP), the middle segment (M) encodes the glycoproteins (GPs) Gn and Gc which forms up to tetramers and primarily monomers \\& dimers upon independent expression respectively and large segment (L) encodes RNA dependent RNA polymerase (RdRp). Interactions between these viral proteins are crucial in providing mechanistic insights into HV virion development. Despite best efforts, there continues to be lack of quantification of these associations in living cells. This is required in developing the mechanistic models for HV viral assembly. This dissertation focuses on three key questions pertaining to the initial steps of virion formation that primarily involves the GPs and NP. The research investigations in this work were completed using Fluorescence Correlation Spectroscopy (FCS) approaches. FCS is frequently used in assessing the biophysical features of bio-molecules including protein concentration and diffusion dynamics and circumvents the requirement of protein overexpression. FCS was primarily applied in this thesis to evaluate protein multimerization, at single cell resolution. The first question addressed which GP spike formation model proposed by Hepojoki et al.(2010) appropriately describes the evidence in living cells. A novel in cellulo assay was developed to evaluate the amount of fluorescently labelled and unlabeled GPs upon co-expression. The results clearly showed that Gn and Gc initially formed a heterodimeric Gn:Gc subunit. This sub-unit then multimerizes with congruent Gn:Gc subunits to generate the final GP spike. Based on these interactions, models describing the formation of GP complex (with multiple GP spike subunits) were additionally developed. HV GP assembly primarily takes place in the Golgi apparatus (GA) of infected cells. Interestingly, NWHV GPs are hypothesized to assemble at the plasma membrane (PM). This led to the second research question in this thesis, in which a systematic comparison between OWHV and NWHV GPs was conducted to validate this hypothesis. Surprisingly, GP localization at the PM was congruently observed with OWHV and NWHV GPs. Similar results were also discerned with OWHV and NWHV GP localization in the absence of cytoskeletal factors that regulate HV trafficking in cells. The final question focused on quantifying the NP-GP interactions and understanding their influence of NP and GP multimerization. Gc mutlimers were detected in the presence of NP and complimented by the presence of localized regions of high NP-Gc interactions in the perinuclear region of living cells. Gc-CT domain was shown to influence NP-Gc associations. Gn, on the other hand, formed up to tetrameric complexes, independent from the presence of NP. The results in this dissertation sheds light on the initial steps of HV virion formation by quantifying homo and heterotypic interactions involving NP and GPs, which otherwise are very difficult to perform. Finally, the in cellulo methodologies implemented in this work can be potentially extended to understand other key interactions involved in HV virus assembly.}, language = {en} } @misc{OmranianNikoloski2022, author = {Omranian, Sara and Nikoloski, Zoran}, title = {CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs}, 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 = {1315}, issn = {1866-8372}, doi = {10.25932/publishup-58686}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-586863}, pages = {12}, year = {2022}, abstract = {High-throughput proteomics approaches have resulted in large-scale protein-protein interaction (PPI) networks that have been employed for the prediction of protein complexes. However, PPI networks contain false-positive as well as false-negative PPIs that affect the protein complex prediction algorithms. To address this issue, here we propose an algorithm called CUBCO+ that: (1) employs GO semantic similarity to retain only biologically relevant interactions with a high similarity score, (2) based on link prediction approaches, scores the false-negative edges, and (3) incorporates the resulting scores to predict protein complexes. Through comprehensive analyses with PPIs from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we show that CUBCO+ performs as well as the approaches that predict protein complexes based on recently introduced graph partitions into biclique spanned subgraphs and outperforms the other state-of-the-art approaches. Moreover, we illustrate that in combination with GO semantic similarity, CUBCO+ enables us to predict more accurate protein complexes in 36\% of the cases in comparison to CUBCO as its predecessor.}, language = {en} } @misc{MendesFerreiraDammhahnEccard2022, author = {Mendes Ferreira, Clara and Dammhahn, Melanie and Eccard, Jana}, title = {Forager-mediated cascading effects on food resource species diversity}, 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 = {1312}, issn = {1866-8372}, doi = {10.25932/publishup-58509}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-585092}, pages = {13}, year = {2022}, abstract = {Perceived predation risk varies in space and time. Foraging in this landscape of fear alters forager-resource interactions via cascading nonconsumptive effects. Estimating these indirect effects is difficult in natural systems. Here, we applied a novel measure to quantify the diversity at giving-up density that allows to test how spatial variation in perceived predation risk modifies the diversity of multispecies resources at local and regional spatial levels. Furthermore, we evaluated whether the nonconsumptive effects on resource species diversity can be explained by the preferences of foragers for specific functional traits and by the forager species richness. We exposed rodents of a natural community to artificial food patches, each containing an initial multispecies resource community of eight species (10 items each) mixed in sand. We sampled 35 landscapes, each containing seven patches in a spatial array, to disentangle effects at local (patch) and landscape levels. We used vegetation height as a proxy for perceived predation risk. After a period of three nights, we counted how many and which resource species were left in each patch to measure giving-up density and resource diversity at the local level (alpha diversity) and the regional level (gamma diversity and beta diversity). Furthermore, we used wildlife cameras to identify foragers and assess their species richness. With increasing vegetation height, i.e., decreasing perceived predation risk, giving-up density, and local alpha and regional gamma diversity decreased, and patches became less similar within a landscape (beta diversity increased). Foragers consumed more of the bigger and most caloric resources. The higher the forager species richness, the lower the giving-up density, and alpha and gamma diversity. Overall, spatial variation of perceived predation risk of foragers had measurable cascading effects on local and regional resource species biodiversity, independent of the forager species. Thus, nonconsumptive predation effects modify forager-resource interactions and might act as an equalizing mechanism for species coexistence.}, language = {en} } @phdthesis{Pellegrino2022, author = {Pellegrino, Antonio}, title = {miRNA profiling for diagnosis of chronic pain in polyneuropathy}, doi = {10.25932/publishup-58385}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-583858}, school = {Universit{\"a}t Potsdam}, pages = {viii, 97, xi}, year = {2022}, abstract = {This dissertation aimed to determine differential expressed miRNAs in the context of chronic pain in polyneuropathy. For this purpose, patients with chronic painful polyneuropathy were compared with age matched healthy patients. Taken together, all miRNA pre library preparation quality controls were successful and none of the samples was identified as an outlier or excluded for library preparation. Pre sequencing quality control showed that library preparation worked for all samples as well as that all samples were free of adapter dimers after BluePippin size selection and reached the minimum molarity for further processing. Thus, all samples were subjected to sequencing. The sequencing control parameters were in their optimal range and resulted in valid sequencing results with strong sample to sample correlation for all samples. The resulting FASTQ file of each miRNA library was analyzed and used to perform a differential expression analysis. The differentially expressed and filtered miRNAs were subjected to miRDB to perform a target prediction. Three of those four miRNAs were downregulated: hsa-miR-3135b, hsa-miR-584-5p and hsa-miR-12136, while one was upregulated: hsa-miR-550a-3p. miRNA target prediction showed that chronic pain in polyneuropathy might be the result of a combination of miRNA mediated high blood flow/pressure and neural activity dysregulations/disbalances. Thus, leading to the promising conclusion that these four miRNAs could serve as potential biomarkers for the diagnosis of chronic pain in polyneuropathy. Since TRPV1 seems to be one of the major contributors of nociception and is associated with neuropathic pain, the influence of PKA phosphorylated ARMS on the sensitivity of TRPV1 as well as the part of AKAP79 during PKA phosphorylation of ARMS was characterized. Therefore, possible PKA-sites in the sequence of ARMS were identified. This revealed five canonical PKA-sites: S882, T903, S1251/52, S1439/40 and S1526/27. The single PKA-site mutants of ARMS revealed that PKA-mediated ARMS phosphorylation seems not to influence the interaction rate of TRPV1/ARMS. While phosphorylation of ARMST903 does not increase the interaction rate with TRPV1, ARMSS1526/27 is probably not phosphorylated and leads to an increased interaction rate. The calcium flux measurements indicated that the higher the interaction rate of TRPV1/ARMS, the lower the EC50 for capsaicin of TRPV1, independent of the PKA phosphorylation status of ARMS. In addition, the western blot analysis confirmed the previously observed TRPV1/ARMS interaction. More importantly, AKAP79 seems to be involved in the TRPV1/ARMS/PKA signaling complex. To overcome the problem of ARMS-mediated TRPV1 sensitization by interaction, ARMS was silenced by shRNA. ARMS silencing resulted in a restored TRPV1 desensitization without affecting the TRPV1 expression and therefore could be used as new topical therapeutic analgesic alternative to stop ARMS mediated TRPV1 sensitization.}, language = {en} } @misc{HeringHauptfleischKramerSchadtetal.2022, author = {Hering, Robert and Hauptfleisch, Morgan and Kramer-Schadt, Stephanie and Stiegler, Jonas and Blaum, Niels}, title = {Effects of fences and fence gaps on the movement behavior of three southern African antelope species}, 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 = {1308}, issn = {1866-8372}, doi = {10.25932/publishup-58267}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582672}, pages = {19}, year = {2022}, abstract = {Globally, migratory ungulates are affected by fences. While field observational studies reveal the amount of animal-fence interactions across taxa, GPS tracking-based studies uncover fence effects on movement patterns and habitat selection. However, studies on the direct effects of fences and fence gaps on movement behavior, especially based on high-frequency tracking data, are scarce. We used GPS tracking on three common African antelopes (Tragelaphus strepsiceros, Antidorcas marsupialis, and T. oryx) with movement strategies ranging from range residency to nomadism in a semi-arid, Namibian savanna traversed by wildlife-proof fences that elephants have regularly breached. We classified major forms of ungulate-fence interaction types on a seasonal and a daily scale. Furthermore, we recorded the distances and times spent at fences regarding the total individual space use. Based on this, we analyzed the direct effects of fences and fence gaps on the animals' movement behavior for the previously defined types of animal-fence interactions. Antelope-fence interactions peaked during the early hours of the day and during seasonal transitions when the limiting resource changed between water and forage. Major types of ungulate-fence interactions were quick, trace-like, or marked by halts. We found that the amount of time spent at fences was highest for nomadic eland. Migratory springbok adjusted their space use concerning fence gap positions. If the small home ranges of sedentary kudu included a fence, they frequently interacted with this fence. For springbok and eland, distance traveled along a fence declined with increasing utilization of a fence gap. All species reduced their speed in the proximity of a fence but often increased their speed when encountering the fence. Crossing a fence led to increased speeds for all species. We demonstrate that fence effects mainly occur during crucial foraging times (seasonal scale) and during times of directed movements (daily scale). Importantly, we provide evidence that fences directly alter antelope movement behaviors with negative implications for energy budgets and that persistent fence gaps can reduce the intensity of such alterations. Our findings help to guide future animal-fence studies and provide insights for wildlife fencing and fence gap planning.}, language = {en} } @phdthesis{Schlossarek2023, author = {Schlossarek, Dennis}, title = {Identification of dynamic protein-metabolite complexes in saccharomyces cerevisiae using co-fractionation mass spectrometry}, doi = {10.25932/publishup-58282}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582826}, school = {Universit{\"a}t Potsdam}, pages = {123}, year = {2023}, abstract = {Cells are built from a variety of macromolecules and metabolites. Both, the proteome and the metabolome are highly dynamic and responsive to environmental cues and developmental processes. But it is not their bare numbers, but their interactions that enable life. The protein-protein (PPI) and protein-metabolite interactions (PMI) facilitate and regulate all aspects of cell biology, from metabolism to mitosis. Therefore, the study of PPIs and PMIs and their dynamics in a cell-wide context is of great scientific interest. In this dissertation, I aim to chart a map of the dynamic PPIs and PMIs across metabolic and cellular transitions. As a model system, I study the shift from the fermentative to the respiratory growth, known as the diauxic shift, in the budding yeast Saccharomyces cerevisiae. To do so, I am applying a co-fractionation mass spectrometry (CF-MS) based method, dubbed protein metabolite interactions using size separation (PROMIS). PROMIS, as well as comparable methods, will be discussed in detail in chapter 1. Since PROMIS was developed originally for Arabidopsis thaliana, in chapter 2, I will describe the adaptation of PROMIS to S. cerevisiae. Here, the obtained results demonstrated a wealth of protein-metabolite interactions, and experimentally validated 225 previously predicted PMIs. Applying orthogonal, targeted approaches to validate the interactions of a proteogenic dipeptide, Ser-Leu, five novel protein-interactors were found. One of those proteins, phosphoglycerate kinase, is inhibited by Ser-Leu, placing the dipeptide at the regulation of glycolysis. In chapter 3, I am presenting PROMISed, a novel web-tool designed for the analysis of PROMIS- and other CF-MS-datasets. Starting with raw fractionation profiles, PROMISed enables data pre-processing, profile deconvolution, scores differences in fractionation profiles between experimental conditions, and ultimately charts interaction networks. PROMISed comes with a user-friendly graphic interface, and thus enables the routine analysis of CF-MS data by non-computational biologists. Finally, in chapter 4, I applied PROMIS in combination with the isothermal shift assay to the diauxic shift in S. cerevisiae to study changes in the PPI and PMI landscape across this metabolic transition. I found a major rewiring of protein-protein-metabolite complexes, exemplified by the disassembly of the proteasome in the respiratory phase, the loss of interaction of an enzyme involved in amino acid biosynthesis and its cofactor, as well as phase and structure specific interactions between dipeptides and enzymes of central carbon metabolism. In chapter 5, I am summarizing the presented results, and discuss a strategy to unravel the potential patterns of dipeptide accumulation and binding specificities. Lastly, I recapitulate recently postulated guidelines for CF-MS experiments, and give an outlook of protein interaction studies in the near future.}, language = {en} } @phdthesis{BysaniKondagari2023, author = {Bysani Kondagari, Viswanada Reddy}, title = {Engineering and evolution of saccharomyces cerevisiae for synthetic formatotrophic growth via the reductive glycine pathway}, doi = {10.25932/publishup-58222}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582222}, school = {Universit{\"a}t Potsdam}, pages = {124}, year = {2023}, abstract = {Increasing demand for food, healthcare, and transportation arising from the growing world population is accompanied by and driving global warming challenges due to the rise of the atmospheric CO2 concentration. Industrialization for human needs has been increasingly releasing CO2 into the atmosphere for the last century or more. In recent years, the possibility of recycling CO2 to stabilize the atmospheric CO2 concentration and combat rising temperatures has gained attention. Thus, using CO2 as the feedstock to address future world demands is the ultimate solution while controlling the rapid climate change. Valorizing CO2 to produce activated and stable one-carbon feedstocks like formate and methanol and further upgrading them to industrial microbial processes to replace unsustainable feedstocks would be crucial for a future biobased circular economy. However, not all microbes can grow on formate as a feedstock, and those microbes that can grow are not well established for industrial processes. S. cerevisiae is one of the industrially well-established microbes, and it is a significant contributor to bioprocess industries. However, it cannot grow on formate as a sole carbon and energy source. Thus, engineering S. cerevisiae to grow on formate could potentially pave the way to sustainable biomass and value-added chemicals production. The Reductive Glycine Pathway (RGP), designed as the aerobic twin of the anaerobic Reductive Acetyl-CoA pathway, is an efficient formate and CO2 assimilation pathway. The RGP comprises of the glycine synthesis module (Mis1p, Gcv1p, Gcv2p, Gcv3p, and Lpd1p), the glycine to serine conversion module (Shmtp), the pyruvate synthesis module (Cha1p), and the energy supply module (Fdh1p). The RGP requires formate and elevated CO2 levels to operate the glycine synthesis module. In this study, I established the RGP in the yeast system using growth-coupled selection strategies to achieve formate and CO2-dependent biomass formation in aerobic conditions. Firstly, I constructed serine biosensor strains by disrupting the native serine and glycine biosynthesis routes in the prototrophic S288c and FL100 yeast strains and insulated serine, glycine, and one-carbon metabolism from the central metabolic network. These strains cannot grow on glucose as the sole carbon source but require the supply of serine or glycine to complement the engineered auxotrophies. Using growth as a readout, I employed these strains as selection hosts to establish the RGP. Initially, to achieve this, I engineered different serine-hydroxymethyltransferases in the genome of serine biosensor strains for efficient glycine to serine conversion. Then, I implemented the glycine synthesis module of the RGP in these strains for the glycine and serine synthesis from formate and CO2. I successfully conducted Adaptive Laboratory Evolution (ALE) using these strains, which yielded a strain capable of glycine and serine biosynthesis from formate and CO2. Significant growth improvements from 0.0041 h-1 to 0.03695 h-1 were observed during ALE. To validate glycine and serine synthesis, I conducted carbon tracing experiments with 13C formate and 13CO2, confirming that more than 90\% of glycine and serine biosynthesis in the evolved strains occurs via the RGP. Interestingly, labeling data also revealed that 10-15\% of alanine was labelled, indicating pyruvate synthesis from the formate-derived serine using native serine deaminase (Cha1p) activity. Thus, RGP contributes to a small pyruvate pool which is converted to alanine without any selection pressure for pyruvate synthesis from formate. Hence, this data confirms the activity of all three modules of RGP even in the presence of glucose. Further, ALE in glucose limiting conditions did not improve pyruvate flux via the RGP. Growth characterization of these strains showed that the best growth rates were achieved in formate concentrations between 25 mM to 300 mM. Optimum growth required 5\% CO2, and dropped when the CO2 concentration was reduced from 5\% to 2.5\%. Whole-genome sequencing of these evolved strains revealed mutations in genes that encode Gdh1p, Pet9p, and Idh1p. These enzymes might influence intracellular NADPH, ATP, and NADH levels, indicating adjustment to meet the energy demand of the RGP. I reverse-engineered the GDH1 truncation mutation on unevolved serine biosensor strains and reproduced formate dependent growth. To elucidate the effect of the GDH1 mutation on formate assimilation, I reintroduced this mutation in the S288c strain and conducted carbon-tracing experiments to compared formate assimilation between WT and ∆gdh1 mutant strains. Comparatively, enhanced formate assimilation was recorded in the ∆gdh1 mutant strain. Although the 13C carbon tracing experiments confirmed the activity of all three modules of the RGP, the overall pyruvate flux via the RGP might be limited by the supply of reducing power. Hence, in a different approach, I overexpressed the formate dehydrogenase (Fdh1p) for energy supply and serine deaminase (Cha1p) for active pyruvate synthesis in the S288c parental strain and established growth on formate and serine without glucose in the medium. Further reengineering and evolution of this strain with a consistent energy, and formate-derived serine supply for pyruvate synthesis, is essential to achieve complete formatotrophic growth in the yeast system.}, language = {en} } @phdthesis{MartinezSeidel2023, author = {Martinez-Seidel, Federico}, title = {Ribosome Heterogeneity and Specialization during Temperature Acclimation in Plants}, doi = {10.25932/publishup-58072}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-580724}, school = {Universit{\"a}t Potsdam}, pages = {374}, year = {2023}, abstract = {Ribosomes decode mRNA to synthesize proteins. Ribosomes, once considered static, executing machines, are now viewed as dynamic modulators of translation. Increasingly detailed analyses of structural ribosome heterogeneity led to a paradigm shift toward ribosome specialization for selective translation. As sessile organisms, plants cannot escape harmful environments and evolved strategies to withstand. Plant cytosolic ribosomes are in some respects more diverse than those of other metazoans. This diversity may contribute to plant stress acclimation. The goal of this thesis was to determine whether plants use ribosome heterogeneity to regulate protein synthesis through specialized translation. I focused on temperature acclimation, specifically on shifts to low temperatures. During cold acclimation, Arabidopsis ceases growth for seven days while establishing the responses required to resume growth. Earlier results indicate that ribosome biogenesis is essential for cold acclimation. REIL mutants (reil-dkos) lacking a 60S maturation factor do not acclimate successfully and do not resume growth. Using these genotypes, I ascribed cold-induced defects of ribosome biogenesis to the assembly of the polypeptide exit tunnel (PET) by performing spatial statistics of rProtein changes mapped onto the plant 80S structure. I discovered that growth cessation and PET remodeling also occurs in barley, suggesting a general cold response in plants. Cold triggered PET remodeling is consistent with the function of Rei-1, a REIL homolog of yeast, which performs PET quality control. Using seminal data of ribosome specialization, I show that yeast remodels the tRNA entry site of ribosomes upon change of carbon sources and demonstrate that spatially constrained remodeling of ribosomes in metazoans may modulate protein synthesis. I argue that regional remodeling may be a form of ribosome specialization and show that heterogeneous cytosolic polysomes accumulate after cold acclimation, leading to shifts in the translational output that differs between wild-type and reil-dkos. I found that heterogeneous complexes consist of newly synthesized and reused proteins. I propose that tailored ribosome complexes enable free 60S subunits to select specific 48S initiation complexes for translation. Cold acclimated ribosomes through ribosome remodeling synthesize a novel proteome consistent with known mechanisms of cold acclimation. The main hypothesis arising from my thesis is that heterogeneous/ specialized ribosomes alter translation preferences, adjust the proteome and thereby activate plant programs for successful cold acclimation.}, language = {en} } @misc{OgunkolaGuiraudieCaprazFeronetal.2023, author = {Ogunkola, Moses Olalekan and Guiraudie-Capraz, Gaelle and F{\´e}ron, Fran{\c{c}}ois and Leimk{\"u}hler, Silke}, title = {The Human Mercaptopyruvate Sulfurtransferase TUM1 Is Involved in Moco Biosynthesis, Cytosolic tRNA Thiolation and Cellular Bioenergetics in Human Embryonic Kidney Cells}, 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 = {1307}, issn = {1866-8372}, doi = {10.25932/publishup-57958}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-579580}, pages = {23}, year = {2023}, abstract = {Sulfur is an important element that is incorporated into many biomolecules in humans. The incorporation and transfer of sulfur into biomolecules is, however, facilitated by a series of different sulfurtransferases. Among these sulfurtransferases is the human mercaptopyruvate sulfurtransferase (MPST) also designated as tRNA thiouridine modification protein (TUM1). The role of the human TUM1 protein has been suggested in a wide range of physiological processes in the cell among which are but not limited to involvement in Molybdenum cofactor (Moco) biosynthesis, cytosolic tRNA thiolation and generation of H2S as signaling molecule both in mitochondria and the cytosol. Previous interaction studies showed that TUM1 interacts with the L-cysteine desulfurase NFS1 and the Molybdenum cofactor biosynthesis protein 3 (MOCS3). Here, we show the roles of TUM1 in human cells using CRISPR/Cas9 genetically modified Human Embryonic Kidney cells. Here, we show that TUM1 is involved in the sulfur transfer for Molybdenum cofactor synthesis and tRNA thiomodification by spectrophotometric measurement of the activity of sulfite oxidase and liquid chromatography quantification of the level of sulfur-modified tRNA. Further, we show that TUM1 has a role in hydrogen sulfide production and cellular bioenergetics.}, language = {en} } @misc{MarggrafLindeckeVoigtetal.2023, author = {Marggraf, Lara Christin and Lindecke, Oliver and Voigt, Christian C. and Pētersons, Gunārs and Voigt-Heucke, Silke Luise}, title = {Nathusius' bats, Pipistrellus nathusii, bypass mating opportunities of their own species, but respond to foraging heterospecifics on migratory transit flights}, 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 = {1306}, issn = {1866-8372}, doi = {10.25932/publishup-57957}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-579574}, pages = {10}, year = {2023}, abstract = {In late summer, migratory bats of the temperate zone face the challenge of accomplishing two energy-demanding tasks almost at the same time: migration and mating. Both require information and involve search efforts, such as localizing prey or finding potential mates. In non-migrating bat species, playback studies showed that listening to vocalizations of other bats, both con-and heterospecifics, may help a recipient bat to find foraging patches and mating sites. However, we are still unaware of the degree to which migrating bats depend on con-or heterospecific vocalizations for identifying potential feeding or mating opportunities during nightly transit flights. Here, we investigated the vocal responses of Nathusius' pipistrelle bats, Pipistrellus nathusii, to simulated feeding and courtship aggregations at a coastal migration corridor. We presented migrating bats either feeding buzzes or courtship calls of their own or a heterospecific migratory species, the common noctule, Nyctalus noctula. We expected that during migratory transit flights, simulated feeding opportunities would be particularly attractive to bats, as well as simulated mating opportunities which may indicate suitable roosts for a stopover. However, we found that when compared to the natural silence of both pre-and post-playback phases, bats called indifferently during the playback of conspecific feeding sounds, whereas P. nathusii echolocation call activity increased during simulated feeding of N. noctula. In contrast, the call activity of P. nathusii decreased during the playback of conspecific courtship calls, while no response could be detected when heterospecific call types were broadcasted. Our results suggest that while on migratory transits, P. nathusii circumnavigate conspecific mating aggregations, possibly to save time or to reduce the risks associated with social interactions where aggression due to territoriality might be expected. This avoidance behavior could be a result of optimization strategies by P. nathusii when performing long-distance migratory flights, and it could also explain the lack of a response to simulated conspecific feeding. However, the observed increase of activity in response to simulated feeding of N. noctula, suggests that P. nathusii individuals may be eavesdropping on other aerial hawking insectivorous species during migration, especially if these occupy a slightly different foraging niche.}, language = {en} } @misc{KiemelGurkeParaskevopoulouetal.2022, author = {Kiemel, Katrin and Gurke, Marie and Paraskevopoulou, Sofia and Havenstein, Katja and Weithoff, Guntram and Tiedemann, Ralph}, title = {Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species}, 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 = {1305}, issn = {1866-8372}, doi = {10.25932/publishup-57863}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-578635}, pages = {14}, year = {2022}, abstract = {Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.}, language = {en} } @misc{BergholzSittelRistowetal.2022, author = {Bergholz, Kolja and Sittel, Lara-Pauline and Ristow, Michael and Jeltsch, Florian and Weiß, Lina}, title = {Pollinator guilds respond contrastingly at different scales to landscape parameters of land-use intensity}, 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 = {1298}, issn = {1866-8372}, doi = {10.25932/publishup-57730}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-577307}, pages = {11}, year = {2022}, abstract = {Land-use intensification is the main factor for the catastrophic decline of insect pollinators. However, land-use intensification includes multiple processes that act across various scales and should affect pollinator guilds differently depending on their ecology. We aimed to reveal how two main pollinator guilds, wild bees and hoverflies, respond to different land-use intensification measures, that is, arable field cover (AFC), landscape heterogeneity (LH), and functional flower composition of local plant communities as a measure of habitat quality. We sampled wild bees and hoverflies on 22 dry grassland sites within a highly intensified landscape (NE Germany) within three campaigns using pan traps. We estimated AFC and LH on consecutive radii (60-3000 m) around the dry grassland sites and estimated the local functional flower composition. Wild bee species richness and abundance was positively affected by LH and negatively by AFC at small scales (140-400 m). In contrast, hoverflies were positively affected by AFC and negatively by LH at larger scales (500-3000 m), where both landscape parameters were negatively correlated to each other. At small spatial scales, though, LH had a positive effect on hoverfly abundance. Functional flower diversity had no positive effect on pollinators, but conspicuous flowers seem to attract abundance of hoverflies. In conclusion, landscape parameters contrarily affect two pollinator guilds at different scales. The correlation of landscape parameters may influence the observed relationships between landscape parameters and pollinators. Hence, effects of land-use intensification seem to be highly landscape-specific.}, language = {en} } @misc{ParrySchlaegelTiedemannetal.2022, author = {Parry, Victor and Schl{\"a}gel, Ulrike E. and Tiedemann, Ralph and Weithoff, Guntram}, title = {Behavioural Responses of Defended and Undefended Prey to Their Predator}, 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 = {1302}, issn = {1866-8372}, doi = {10.25932/publishup-57759}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-577594}, pages = {14}, year = {2022}, abstract = {Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.}, language = {en} } @misc{StieglerLinsDammhahnetal.2022, author = {Stiegler, Jonas and Lins, Alisa and Dammhahn, Melanie and Kramer-Schadt, Stephanie and Ortmann, Sylvia and Blaum, Niels}, title = {Personality drives activity and space use in a mammalian herbivore}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1866-8372}, doi = {10.25932/publishup-57732}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-577327}, pages = {1 -- 12}, year = {2022}, abstract = {Background Animal personality has emerged as a key concept in behavioral ecology. While many studies have demonstrated the influence of personality traits on behavioral patterns, its quantification, especially in wild animal populations, remains a challenge. Only a few studies have established a link between personality and recurring movements within home ranges, although these small-scale movements are of key importance for identifying ecological interactions and forming individual niches. In this regard, differences in space use among individuals might reflect different exploration styles between behavioral types along the shy-bold continuum. Methods We assessed among-individual differences in behavior in the European hare (Lepus europaeus), a characteristic mammalian herbivore in agricultural landscapes using a standardized box emergence test for captive and wild hares. We determined an individuals' degree of boldness by measuring the latencies of behavioral responses in repeated emergence tests in captivity. During capture events of wild hares, we conducted a single emergence test and recorded behavioral responses proven to be stable over time in captive hares. Applying repeated novel environment tests in a near-natural enclosure, we further quantified aspects of exploration and activity in captive hares. Finally, we investigated whether and how this among-individual behavioral variation is related to general activity and space use in a wild hare population. Wild and captive hares were treated similarly and GPS-collared with internal accelerometers prior to release to the wild or the outdoor enclosure, respectively. General activity was quantified as overall dynamic body acceleration (ODBA) obtained from accelerometers. Finally, we tested whether boldness explained variation in (i) ODBA in both settings and (ii) variation in home ranges and core areas across different time scales of GPS-collared hares in a wild population. Results We found three behavioral responses to be consistent over time in captive hares. ODBA was positively related to boldness (i.e., short latencies to make first contact with the new environment) in both captive and wild hares. Space use in wild hares also varied with boldness, with shy individuals having smaller core areas and larger home ranges than bold conspecifics (yet in some of the parameter space, this association was just marginally significant). Conclusions Against our prediction, shy individuals occupied relatively large home ranges but with small core areas. We suggest that this space use pattern is due to them avoiding risky, and energy-demanding competition for valuable resources. Carefully validated, activity measurements (ODBA) from accelerometers provide a valuable tool to quantify aspects of animal personality along the shy-bold continuum remotely. Without directly observing—and possibly disturbing—focal individuals, this approach allows measuring variability in animal personality, especially in species that are difficult to assess with experiments. Considering that accelerometers are often already built into GPS units, we recommend activating them at least during the initial days of tracking to estimate individual variation in general activity and, if possible, match them with a simple novelty experiment. Furthermore, information on individual behavioral types will help to facilitate mechanistic understanding of processes that drive spatial and ecological dynamics in heterogeneous landscapes.}, language = {en} } @phdthesis{Steppert2022, author = {Steppert, Isabel}, title = {Entwicklung einer nichtinvasiven Diagnostikmethode zum Nachweis von Infektionserregern}, doi = {10.25932/publishup-57544}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-575441}, school = {Universit{\"a}t Potsdam}, pages = {XIV, 101, LVIII}, year = {2022}, abstract = {Die aktuelle COVID-19-Pandemie zeigt deutlich, wie sich Infektionskrankheiten weltweit verbreiten k{\"o}nnen. Neben Viruserkrankungen breiten sich auch multiresistente bakterielle Erreger weltweit aus. Dementsprechend besteht ein hoher Bedarf, durch fr{\"u}hzeitige Erkennung Erkrankte zu finden und Infektionswege zu unterbrechen. Herk{\"o}mmliche kulturelle Verfahren ben{\"o}tigen minimalinvasive bzw. invasive Proben und dauern f{\"u}r Screeningmaßnahmen zu lange. Deshalb werden schnelle, nichtinvasive Verfahren ben{\"o}tigt. Im klassischen Griechenland verließen sich die {\"A}rzte unter anderem auf ihren Geruchssinn, um Infektionen und andere Krankheiten zu differenzieren. Diese charakteristischen Ger{\"u}che sind fl{\"u}chtige organische Substanzen (VOC), die im Rahmen des Metabolismus eines Organismus entstehen. Tiere, die einen besseren Geruchssinn haben, werden trainiert, bestimmte Krankheitserreger am Geruch zu unterscheiden. Allerdings ist der Einsatz von Tieren im klinischen Alltag nicht praktikabel. Es bietet sich an, auf technischem Weg diese VOCs zu analysieren. Ein technisches Verfahren, diese VOCs zu unterscheiden, ist die Ionenmobilit{\"a}tsspektrometrie gekoppelt mit einer multikapillaren Gaschromatographies{\"a}ule (MCC-IMS). Hier zeigte sich, dass es sich bei dem Verfahren um eine schnelle, sensitive und verl{\"a}ssliche Methode handelt. Es ist bekannt, dass verschiedene Bakterien aufgrund des Metabolismus unterschiedliche VOCs und damit eigene spezifische Ger{\"u}che produzieren. Im ersten Schritt dieser Arbeit konnte gezeigt werden, dass die verschiedenen Bakterien in-vitro nach einer kurzen Inkubationszeitzeit von 90 Minuten anhand der VOCs differenziert werden k{\"o}nnen. Hier konnte analog zur Diagnose in biochemischen Testreihen eine hierarchische Klassifikation der Bakterien erfolgen. Im Gegensatz zu Bakterien haben Viren keinen eigenen Stoffwechsel. Ob virusinfizierte Zellen andere VOCs als nicht-infizierte Zellen freisetzen, wurde an Zellkulturen {\"u}berpr{\"u}ft. Hier konnte gezeigt werden, dass sich die Fingerprints der VOCs in Zellkulturen infizierter Zellen mit Respiratorischen Synzytial-Viren (RSV) von nicht-infizierten Zellen unterscheiden. Virusinfektionen im intakten Organismus unterscheiden sich von den Zellkulturen dadurch, dass hier neben Ver{\"a}nderungen im Zellstoffwechsel auch durch Abwehrmechanismen VOCs freigesetzt werden k{\"o}nnen. Zur {\"U}berpr{\"u}fung, inwiefern sich Infektionen im intakten Organismus ebenfalls anhand VOCs unterscheiden lassen, wurde bei Patienten mit und ohne Nachweis einer Influenza A Infektion als auch bei Patienten mit Verdacht auf SARS-CoV-2 (Schweres-akutes-Atemwegssyndrom-Coronavirus Typ 2) Infektion die Atemluft untersucht. Sowohl Influenza-infizierte als auch SARS-CoV-2 infizierte Patienten konnten untereinander und von nicht-infizierten Patienten mittels MCC-IMS Analyse der Atemluft unterschieden werden. Zusammenfassend erbringt die MCC-IMS ermutigende Resultate in der schnellen nichtinvasiven Erkennung von Infektionen sowohl in vitro als auch in vivo.}, language = {de} } @phdthesis{Drago2022, author = {Drago, Claudia}, title = {Microplastics in the environment: Assessing the ingestion and effect of microplastics on freshwater rotifers in an environmental scenario}, doi = {10.25932/publishup-57335}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-573356}, school = {Universit{\"a}t Potsdam}, pages = {xv, 116}, year = {2022}, abstract = {Microplastics in the environments are estimated to increase in the near future due to increasing consumption of plastic product and also due to further fragmentation in small pieces. The fate and effects of MP once released into the freshwater environment are still scarcely studied, compared to the marine environment. In order to understand possible effect and interaction of MPs in freshwater environment, planktonic zooplankton organisms are very useful for their crucial trophic role. In particular freshwater rotifers are one of the most abundant organisms and they are the interface between primary producers and secondary consumers. The aim of my thesis was to investigate the ingestion and the effect of MPs in rotifers from a more natural scenario and to individuate processes such as the aggregation of MPs, the food dilution effect and the increasing concentrations of MPs that could influence the final outcome of MPs in the environment. In fact, in a near natural scenario MPs interaction with bacteria and algae, aggregations together with the size and concentration are considered drivers of ingestion and effect. The aggregation of MPs makes smaller MPs more available for rotifers and larger MPs less ingested. The negative effect caused by the ingestion of MPs was modulated by their size but also by the quantity and the quality of food that cause variable responses. In fact, rotifers in the environment are subjected to food limitation and the presence of MPs could exacerbate this condition and decrease the population and the reproduction input. Finally, in a scenario incorporating an entire zooplanktonic community, MPs were ingested by most individuals taking into account their feeding mode but also the concentration of MPs, which was found to be essential for the availability of MPs. This study highlights the importance to investigate MPs from a more environmental perspective, this in fact could provide an alternative and realistic view of effect of MPs in the ecosystem.}, language = {en} } @misc{AgnePreickStraubeetal.2022, author = {Agne, Stefanie and Preick, Michaela and Straube, Nicolas and Hofreiter, Michael}, title = {Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set}, 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 = {1293}, issn = {1866-8372}, doi = {10.25932/publishup-57460}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-574600}, pages = {5}, year = {2022}, abstract = {A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84\% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50\% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.}, language = {en} } @misc{IlicicWoodhouseKarstenetal.2023, author = {Ilicic, Doris and Woodhouse, Jason and Karsten, Ulf and Zimmermann, Jonas and Wichard, Thomas and Quartino, Maria Liliana and Campana, Gabriela Laura and Livenets, Alexandra and Van den Wyngaert, Silke and Grossart, Hans-Peter}, title = {Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones}, 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 = {1290}, issn = {1866-8372}, doi = {10.25932/publishup-57289}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-572895}, pages = {14}, year = {2023}, abstract = {Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.}, language = {en} } @phdthesis{Tegtmeier2022, author = {Tegtmeier, Laura}, title = {Functional analysis of ENTH domain proteins}, doi = {10.25932/publishup-57004}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-570049}, school = {Universit{\"a}t Potsdam}, pages = {106}, year = {2022}, abstract = {In plant cells, subcellular transport of cargo proteins relies to a large extent on post-Golgi transport pathways, many of which are mediated by clathrin-coated vesicles (CCVs). Vesicle formation is facilitated by different factors like accessory proteins and adaptor protein complexes (APs), the latter serving as a bridge between cargo proteins and the coat protein clathrin. One type of accessory proteins is defined by a conserved EPSIN N-TERMINAL HOMOLOGY (ENTH) domain and interacts with APs and clathrin via motifs in the C-terminal part. In Arabidopsis thaliana, there are three closely related ENTH domain proteins (EPSIN1, 2 and 3) and one highly conserved but phylogenetically distant outlier, termed MODIFIED TRANSPORT TO THE VACUOLE1 (MTV1). In case of the trans-Golgi network (TGN) located MTV1, clathrin association and a role in vacuolar transport have been shown previously (Sauer et al. 2013). In contrast, for EPSIN1 and EPSIN2 limited functional and localization data were available; and EPSIN3 remained completely uncharacterized prior to this study (Song et al. 2006; Lee et al. 2007). The molecular details of ENTH domain proteins in plants are still unknown. In order to systematically characterize all four ENTH proteins in planta, we first investigated expression and subcellular localization by analysis of stable reporter lines under their endogenous promotors. Although all four genes are ubiquitously expressed, their subcellular distribution differs markedly. EPSIN1 and MTV1 are located at the TGN, whereas EPSIN2 and EPSIN3 are associated with the plasma membrane (PM) and the cell plate. To examine potential functional redundancy, we isolated knockout T-DNA mutant lines and created all higher order mutant combinations. The clearest evidence for functional redundancy was observed in the epsin1 mtv1 double mutant, which is a dwarf displaying overall growth reduction. These findings are in line with the TGN localization of both MTV1 and EPS1. In contrast, loss of EPSIN2 and EPSIN3 does not result in a growth phenotype compared to wild type, however, a triple knockout of EPSIN1, EPSIN2 and EPSIN3 shows partially sterile plants. We focused mainly on the epsin1 mtv1 double mutant and addressed the functional role of these two genes in clathrin-mediated vesicle transport by comprehensive molecular, biochemical, and genetic analyses. Our results demonstrate that EPSIN1 and MTV1 promote vacuolar transport and secretion of a subset of cargo. However, they do not seem to be involved in endocytosis and recycling. Importantly, employing high-resolution imaging, genetic and biochemical experiments probing the relationship of the AP complexes, we found that EPSIN1/AP1 and MTV1/AP4 define two spatially and molecularly distinct subdomains of the TGN. The AP4 complex is essential for MTV1 recruitment to the TGN, whereas EPSIN1 is independent of AP4 but presumably acts in an AP1-dependent framework. Our findings suggest that this ENTH/AP pairing preference is conserved between animals and plants.}, language = {en} } @phdthesis{Oberkofler2022, author = {Oberkofler, Vicky}, title = {Molecular basis of HS memory in Arabidopsis thaliana}, doi = {10.25932/publishup-56954}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569544}, school = {Universit{\"a}t Potsdam}, pages = {181}, year = {2022}, abstract = {Plants can be primed to survive the exposure to a severe heat stress (HS) by prior exposure to a mild HS. The information about the priming stimulus is maintained by the plant for several days. This maintenance of acquired thermotolerance, or HS memory, is genetically separable from the acquisition of thermotolerance itself and several specific regulatory factors have been identified in recent years. On the molecular level, HS memory correlates with two types of transcriptional memory, type I and type II, that characterize a partially overlapping subset of HS-inducible genes. Type I transcriptional memory or sustained induction refers to the sustained transcriptional induction above non-stressed expression levels of a gene for a prolonged time period after the end of the stress exposure. Type II transcriptional memory refers to an altered transcriptional response of a gene after repeated exposure to a stress of similar duration and intensity. In particular, enhanced re-induction refers to a transcriptional pattern in which a gene is induced to a significantly higher degree after the second stress exposure than after the first. This thesis describes the functional characterization of a novel positive transcriptional regulator of type I transcriptional memory, the heat shock transcription factor HSFA3, and compares it to HSFA2, a known positive regulator of type I and type II transcriptional memory. It investigates type I transcriptional memory and its dependence on HSFA2 and HSFA3 for the first time on a genome-wide level, and gives insight on the formation of heteromeric HSF complexes in response to HS. This thesis confirms the tight correlation between transcriptional memory and H3K4 hyper-methylation, reported here in a case study that aimed to reduce H3K4 hyper-methylation of the type II transcriptional memory gene APX2 by CRISPR/dCas9-mediated epigenome editing. Finally, this thesis gives insight into the requirements for a heat shock transcription factor to function as a positive regulator of transcriptional memory, both in terms of its expression profile and protein abundance after HS and the contribution of individual functional domains. In summary, this thesis contributes to a more detailed understanding of the molecular processes underlying transcriptional memory and therefore HS memory, in Arabidopsis thaliana.}, language = {en} } @phdthesis{Folikumah2022, author = {Folikumah, Makafui Yao}, title = {Stimuli-promoted in situ formation of hydrogels with thiol/thioester containing peptide precursors}, doi = {10.25932/publishup-56971}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569713}, school = {Universit{\"a}t Potsdam}, pages = {159}, year = {2022}, abstract = {Hydrogels are potential synthetic ECM-like substitutes since they provide functional and structural similarities compared to soft tissues. They can be prepared by crosslinking of macromolecules or by polymerizing suitable precursors. The crosslinks are not necessarily covalent bonds, but could also be formed by physical interactions such as π-π interactions, hydrophobic interactions, or H-bonding. On demand in situ forming hydrogels have garnered increased interest especially for biomedical applications over preformed gels due to the relative ease of in vivo delivery and filling of cavities. The thiol-Michael addition reaction provides a straightforward and robust strategy for in situ gel formation with its fast reaction kinetics and ability to proceed under physiological conditions. The incorporation of a trigger function into a crosslinking system becomes even more interesting since gelling can be controlled with stimulus of choice. The use of small molar mass crosslinker precursors with active groups orthogonal to thiol-Michael reaction type electrophile provides the opportunity to implement an on-demand in situ crosslinking without compromising the fast reaction kinetics. It was postulated that short peptide sequences due to the broad range structural-function relations available with the different constituent amino acids, can be exploited for the realisation of stimuli-promoted in situ covalent crosslinking and gelation applications. The advantages of this system over conventional polymer-polymer hydrogel systems are the ability tune and predict material property at the molecular level. The main aim of this work was to develop a simplified and biologically-friendly stimuli-promoted in situ crosslinking and hydrogelation system using peptide mimetics as latent crosslinkers. The approach aims at using a single thiodepsipeptide sequence to achieve separate pH- and enzyme-promoted gelation systems with little modification to the thiodepsipeptide sequence. The realization of this aim required the completion of three milestones. In the first place, after deciding on the thiol-Michael reaction as an effective in situ crosslinking strategy, a thiodepsipeptide, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH (TDP) with expected propensity towards pH-dependent thiol-thioester exchange (TTE) activation, was proposed as a suitable crosslinker precursor for pH-promoted gelation system. Prior to the synthesis of the proposed peptide-mimetic, knowledge of the thiol-Michael reactivity of the would-be activated thiol moiety SH-Leu, which is internally embedded in the thiodepsipeptide was required. In line with pKa requirements for a successful TTE, the reactivity of a more acidic thiol, SH-Phe was also investigated to aid the selection of the best thiol to be incorporated in the thioester bearing peptide based crosslinker precursor. Using 'pseudo' 2D-NMR investigations, it was found that only reactions involving SH-Leu yielded the expected thiol-Michael product, an observation that was attributed to the steric hindrance of the bulkier nature of SH-Phe. The fast reaction rates and complete acrylate/maleimide conversion obtained with SH-Leu at pH 7.2 and higher aided the direct elimination of SH-Phe as a potential thiol for the synthesis of the peptide mimetic. Based on the initial studies, for the pH-promoted gelation system, the proposed Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH was kept unmodified. The subtle difference in pKa values between SH-Leu (thioester thiol) and the terminal cysteamine thiol from theoretical conditions should be enough to effect a 'pseudo' intramolecular TTE. In polar protic solvents and under basic aqueous conditions, TDP successfully undergoes a 'pseudo' intramolecular TTE reaction to yield an α,ω-dithiol tripeptide, HSLeu-Leu-Gly-NEtSH. The pH dependence of thiolate ion generation by the cysteamine thiol aided the incorporation of the needed stimulus (pH) for the overall success of TTE (activation step) - thiol-Michael addition (crosslinking) strategy. Secondly, with potential biomedical applications in focus, the susceptibility of TDP, like other thioesters, to intermolecular TTE reaction was probed with a group of thiols of varying thiol pKa values, since biological milieu characteristically contain peptide/protein thiols. L-cysteine, which is a biologically relevant thiol, and a small molecular weight thiol, methylthioglycolate both with relatively similar thiol pKa, values, led to an increase concentration of the dithiol crosslinker when reacted with TDP. In the presence of acidic thiols (p-NTP and 4MBA), a decrease in the dithiol concentration was observed, an observation that can be attributed to the inability of the TTE tetrahedral intermediate to dissociate into exchange products and is in line with pKa requirements for successful TTE reaction. These results additionally makes TDP more attractive and the potentially the first crosslinker precursor for applications in biologically relevant media. Finally, the ability of TDP to promote pH-sensitive in situ gel formation was probed with maleimide functionalized 4-arm polyethylene glycol polymers in tris-buffered media of varying pHs. When a 1:1 thiol: maleimide molar ratio was used, TDP-PEG4MAL hydrogels formed within 3, 12 and 24 hours at pH values of 8.5, 8.0 and 7.5 respectively. However, gelation times of 3, 5 and 30 mins were observed for the same pH trend when the thiol: maleimide molar was increased to 2:1. A direct correlation of thiol content with G' of the gels at each pH could also be drawn by comparing gels with thiol: maleimide ratios of 1:1 to those with 2:1 thiol: maleimide mole ratios. This is supported by the fact that the storage modulus (G') is linearly dependent on the crosslinking density of the polymer. The values of initial G′ for all gels ranged between (200 - 5000 Pa), which falls in the range of elasticities of certain tissue microenvironments for example brain tissue 200 - 1000 Pa and adipose tissue (2500 - 3500 Pa). Knowledge so far gained from the study on the ability to design and tune the exchange reaction of thioester containing peptide mimetic will give those working in the field further insight into the development of new sequences tailored towards specific applications. TTE substrate design using peptide mimetic as presented in this work has revealed interesting new insights considering the state-of-the-art. Using the results obtained as reference, the strategy provides a possibility to extend the concept to the controlled delivery of active molecules needed for other robust and high yielding crosslinking reactions for biomedical applications. Application for this sequentially coupled functional system could be seen e.g. in the treatment of inflamed tissues associated with urinary tract like bladder infections for which pH levels above 7 were reported. By the inclusion of cell adhesion peptide motifs, the hydrogel network formed at this pH could act as a new support layer for the healing of damage epithelium as shown in interfacial gel formation experiments using TDP and PEG4MAL droplets. The versatility of the thiodepsipeptide sequence, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-(TDPo) was extended for the design and synthesis of a MMP-sensitive 4-arm PEG-TDPo conjugate. The purported cleavage of TDPo at the Gly-SLeu bond yields active thiol units for subsequent reaction of orthogonal Michael acceptor moieties. One of the advantages of stimuli-promoted in situ crosslinking systems using short peptides should be the ease of design of required peptide molecules due to the predictability of peptide functions their sequence structure. Consequently the functionalisation of a 4-arm PEG core with the collagenase active TDPo sequence yielded an MMP-sensitive 4-arm thiodepsipeptide-PEG conjugate (PEG4TDPo) substrate. Cleavage studies using thiol flourometric assay in the presence of MMPs -2 and -9 confirmed the susceptibility of PEG4TDPo towards these enzymes. The resulting time-dependent increase in fluorescence intensity in the presence of thiol assay signifies the successful cleavage of TDPo at the Gly-SLeu bond as expected. It was observed that the cleavage studies with thiol flourometric assay introduces a sigmoid non-Michaelis-Menten type kinetic profile, hence making it difficult to accurately determine the enzyme cycling parameters, kcat and KM . Gelation studies with PEG4MAL at 10 \% wt. concentrations revealed faster gelation with MMP-2 than MMP-9 with 28 and 40 min gelation times respectively. Possible contributions by hydrolytic cleavage of PEG4TDPo has resulted in the gelation of PEG4MAL blank samples but only after 60 minutes of reaction. From theoretical considerations, the simultaneous gelation reaction would be expected to more negatively impact the enzymatic than hydrolytic cleavage. The exact contributions from hydrolytic cleavage of PEG4TDPo would however require additional studies. In summary this new and simplified in situ crosslinking system using peptide-based crosslinker precursors with tuneable properties exhibited in situ crosslinking gelation kinetics on similar levels with already active dithiols reported. The advantageous on-demand functionality associated with its pH-sensitivity and physiological compatibility makes it a strong candidate worth further research as biomedical applications in general and on-demand material synthesis is concerned. Results from MMP-promoted gelation system unveils a simple but unexplored approach for in situ synthesis of covalently crosslinked soft materials, that could lead to the development of an alternative pathway in addressing cancer metastasis by making use of MMP overexpression as a trigger. This goal has so far not being reach with MMP inhibitors despite the extensive work this regard.}, language = {en} } @article{KathGaedkevanVelzen2022, author = {Kath, Nadja Jeanette and Gaedke, Ursula and van Velzen, Ellen}, title = {The double-edged sword of inducible defences: costs and benefits of maladaptive switching from the individual to the community level}, 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 = {1288}, issn = {1866-8372}, doi = {10.25932/publishup-57200}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-572006}, pages = {14}, year = {2022}, abstract = {Phenotypic plasticity can increase individual fitness when environmental conditions change over time. Inducible defences are a striking example, allowing species to react to fluctuating predation pressure by only expressing their costly defended phenotype under high predation risk. Previous theoretical investigations have focused on how this affects predator-prey dynamics, but the impact on competitive outcomes and broader community dynamics has received less attention. Here we use a small food web model, consisting of two competing plastic autotrophic species exploited by a shared consumer, to study how the speed of inducible defences across three trade-off constellations affects autotroph coexistence, biomasses across trophic levels, and temporal variability. Contrary to the intuitive idea that faster adaptation increases autotroph fitness, we found that higher switching rates reduced individual fitness as it consistently provoked more maladaptive switching towards undefended phenotypes under high predation pressure. This had an unexpected positive impact on the consumer, increasing consumer biomass and lowering total autotroph biomass. Additionally, maladaptive switching strongly reduced autotroph coexistence through an emerging source-sink dynamic between defended and undefended phenotypes. The striking impact of maladaptive switching on species and food web dynamics indicates that this mechanism may be of more critical importance than previously recognized.}, language = {en} } @misc{LiApriyantoFloresCastellanosetal.2022, author = {Li, Xiaoping and Apriyanto, Ardha and Flores Castellanos, Junio and Compart, Julia and Muntaha, Sidratul Nur and Fettke, J{\"o}rg}, title = {Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling}, 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 = {1286}, issn = {1866-8372}, doi = {10.25932/publishup-57125}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-571250}, pages = {16}, year = {2022}, abstract = {An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding.}, 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} } @misc{ReegStriglJeltsch2022, author = {Reeg, Jette and Strigl, Lea and Jeltsch, Florian}, title = {Agricultural buffer zone thresholds to safeguard functional bee diversity: Insights from a community modeling approach}, 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 = {1281}, issn = {1866-8372}, doi = {10.25932/publishup-57080}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-570800}, pages = {17}, year = {2022}, abstract = {Wild bee species are important pollinators in agricultural landscapes. However, population decline was reported over the last decades and is still ongoing. While agricultural intensification is a major driver of the rapid loss of pollinating species, transition zones between arable fields and forest or grassland patches, i.e., agricultural buffer zones, are frequently mentioned as suitable mitigation measures to support wild bee populations and other pollinator species. Despite the reported general positive effect, it remains unclear which amount of buffer zones is needed to ensure a sustainable and permanent impact for enhancing bee diversity and abundance. To address this question at a pollinator community level, we implemented a process-based, spatially explicit simulation model of functional bee diversity dynamics in an agricultural landscape. More specifically, we introduced a variable amount of agricultural buffer zones (ABZs) at the transition of arable to grassland, or arable to forest patches to analyze the impact on bee functional diversity and functional richness. We focused our study on solitary bees in a typical agricultural area in the Northeast of Germany. Our results showed positive effects with at least 25\% of virtually implemented agricultural buffer zones. However, higher amounts of ABZs of at least 75\% should be considered to ensure a sufficient increase in Shannon diversity and decrease in quasi-extinction risks. These high amounts of ABZs represent effective conservation measures to safeguard the stability of pollination services provided by solitary bee species. As the model structure can be easily adapted to other mobile species in agricultural landscapes, our community approach offers the chance to compare the effectiveness of conservation measures also for other pollinator communities in future.}, language = {en} } @phdthesis{Eckert2022, author = {Eckert, Silvia}, title = {Trait variation in changing environments: Assessing the role of DNA methylation in non-native plant species}, doi = {10.25932/publishup-56884}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-568844}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 134, CXXX}, year = {2022}, abstract = {The increasing introduction of non-native plant species may pose a threat to local biodiversity. However, the basis of successful plant invasion is not conclusively understood, especially since these plant species can adapt to the new range within a short period of time despite impoverished genetic diversity of the starting populations. In this context, DNA methylation is considered promising to explain successful adaptation mechanisms in the new habitat. DNA methylation is a heritable variation in gene expression without changing the underlying genetic information. Thus, DNA methylation is considered a so-called epigenetic mechanism, but has been studied in mainly clonally reproducing plant species or genetic model plants. An understanding of this epigenetic mechanism in the context of non-native, predominantly sexually reproducing plant species might help to expand knowledge in biodiversity research on the interaction between plants and their habitats and, based on this, may enable more precise measures in conservation biology. For my studies, I combined chemical DNA demethylation of field-collected seed material from predominantly sexually reproducing species and rearing offsping under common climatic conditions to examine DNA methylation in an ecological-evolutionary context. The contrast of chemically treated (demethylated) plants, whose variation in DNA methylation was artificially reduced, and untreated control plants of the same species allowed me to study the impact of this mechanism on adaptive trait differentiation and local adaptation. With this experimental background, I conducted three studies examining the effect of DNA methylation in non-native species along a climatic gradient and also between climatically divergent regions. The first study focused on adaptive trait differentiation in two invasive perennial goldenrod species, Solidago canadensis sensu latu and S. gigantea AITON, along a climate gradient of more than 1000 km in length in Central Europe. I found population differences in flowering timing, plant height, and biomass in the temporally longer-established S. canadensis, but only in the number of regrowing shoots for S. gigantea. While S. canadensis did not show any population structure, I was able to identify three genetic groups along this climatic gradient in S. gigantea. Surprisingly, demethylated plants of both species showed no change in the majority of traits studied. In the subsequent second study, I focused on the longer-established goldenrod species S. canadensis and used molecular analyses to infer spatial epigenetic and genetic population differences in the same specimens from the previous study. I found weak genetic but no epigenetic spatial variation between populations. Additionally, I was able to identify one genetic marker and one epigenetic marker putatively susceptible to selection. However, the results of this study reconfirmed that the epigenetic mechanism of DNA methylation appears to be hardly involved in adaptive processes within the new range in S. canadensis. Finally, I conducted a third study in which I reciprocally transplanted short-lived plant species between two climatically divergent regions in Germany to investigate local adaptation at the plant family level. For this purpose, I used four plant families (Amaranthaceae, Asteraceae, Plantaginaceae, Solanaceae) and here I additionally compared between non-native and native plant species. Seeds were transplanted to regions with a distance of more than 600 kilometers and had either a temperate-oceanic or a temperate-continental climate. In this study, some species were found to be maladapted to their own local conditions, both in non-native and native plant species alike. In demethylated individuals of the plant species studied, DNA methylation had inconsistent but species-specific effects on survival and biomass production. The results of this study highlight that DNA methylation did not make a substantial contribution to local adaptation in the non-native as well as native species studied. In summary, my work showed that DNA methylation plays a negligible role in both adaptive trait variation along climatic gradients and local adaptation in non-native plant species that either exhibit a high degree of genetic variation or rely mainly on sexual reproduction with low clonal propagation. I was able to show that the adaptive success of these non-native plant species can hardly be explained by DNA methylation, but could be a possible consequence of multiple introductions, dispersal corridors and meta-population dynamics. Similarly, my results illustrate that the use of plant species that do not predominantly reproduce clonally and are not model plants is essential to characterize the effect size of epigenetic mechanisms in an ecological-evolutionary context.}, language = {en} } @misc{SchloerHirschbergBenAmoretal.2022, author = {Schl{\"o}r, Anja and Hirschberg, Stefan and Ben Amor, Ghada and Meister, Toni Luise and Arora, Prerna and P{\"o}hlmann, Stefan and Hoffmann, Markus and Pf{\"a}nder, Stephanie and Eddin, Omar Kamal and Kamhieh-Milz, Julian and Hanack, Katja}, title = {SARS-CoV-2 neutralizing camelid heavy-chain-only antibodies as powerful tools for diagnostic and therapeutic applications}, 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 = {1280}, issn = {1866-8372}, doi = {10.25932/publishup-57012}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-570124}, pages = {14}, year = {2022}, abstract = {Introduction: The ongoing COVID-19 pandemic situation caused by SARS-CoV-2 and variants of concern such as B.1.617.2 (Delta) and recently, B.1.1.529 (Omicron) is posing multiple challenges to humanity. The rapid evolution of the virus requires adaptation of diagnostic and therapeutic applications. Objectives: In this study, we describe camelid heavy-chain-only antibodies (hcAb) as useful tools for novel in vitro diagnostic assays and for therapeutic applications due to their neutralizing capacity. Methods: Five antibody candidates were selected out of a na{\"i}ve camelid library by phage display and expressed as full length IgG2 antibodies. The antibodies were characterized by Western blot, enzyme-linked immunosorbent assays, surface plasmon resonance with regard to their specificity to the recombinant SARS-CoV-2 Spike protein and to SARS-CoV-2 virus-like particles. Neutralization assays were performed with authentic SARS-CoV-2 and pseudotyped viruses (wildtype and Omicron). Results: All antibodies efficiently detect recombinant SARS-CoV-2 Spike protein and SARS-CoV-2 virus-like particles in different ELISA setups. The best combination was shown with hcAb B10 as catcher antibody and HRP-conjugated hcAb A7.2 as the detection antibody. Further, four out of five antibodies potently neutralized authentic wildtype SARS-CoV-2 and particles pseudotyped with the SARS-CoV-2 Spike proteins of the wildtype and Omicron variant, sublineage BA.1 at concentrations between 0.1 and 0.35 ng/mL (ND50). Conclusion: Collectively, we report novel camelid hcAbs suitable for diagnostics and potential therapy.}, language = {en} } @misc{HeringHauptfleischJagoetal.2022, author = {Hering, Robert and Hauptfleisch, Morgan and Jago, Mark and Smith, Taylor and Kramer-Schadt, Stephanie and Stiegler, Jonas and Blaum, Niels}, title = {Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss}, 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 = {1278}, issn = {1866-8372}, doi = {10.25932/publishup-57008}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-570087}, pages = {18}, year = {2022}, abstract = {In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches.}, language = {en} } @misc{PawlakNoetzelDragoetal.2022, author = {Pawlak, Julia and Noetzel, Dominique Christian and Drago, Claudia and Weithoff, Guntram}, title = {Assessing the toxicity of polystyrene beads and silica particles on the microconsumer Brachionus calyciflorus at different timescales}, 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 = {1277}, issn = {1866-8372}, doi = {10.25932/publishup-56996}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569967}, pages = {1 -- 11}, year = {2022}, abstract = {Environmental pollution by microplastics has become a severe problem in terrestrial and aquatic ecosystems and, according to actual prognoses, problems will further increase in the future. Therefore, assessing and quantifying the risk for the biota is crucial. Standardized short-term toxicological procedures as well as methods quantifying potential toxic effects over the whole life span of an animal are required. We studied the effect of the microplastic polystyrene on the survival and reproduction of a common freshwater invertebrate, the rotifer Brachionus calyciflorus, at different timescales. We used pristine polystyrene spheres of 1, 3, and 6 µm diameter and fed them to the animals together with food algae in different ratios ranging from 0 to 50\% nonfood particles. As a particle control, we used silica to distinguish between a pure particle effect and a plastic effect. After 24 h, no toxic effect was found, neither with polystyrene nor with silica. After 96 h, a toxic effect was detectable for both particle types. The size of the particles played a negligible role. Studying the long-term effect by using life table experiments, we found a reduced reproduction when the animals were fed with 3 µm spheres together with similar-sized food algae. We conclude that the fitness reduction is mainly driven by the dilution of food by the nonfood particles rather than by a direct toxic effect.}, 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} } @phdthesis{Milles2022, author = {Milles, Alexander}, title = {Sources and consequences of intraspecific trait variation in movement behaviour}, doi = {10.25932/publishup-56501}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-565011}, school = {Universit{\"a}t Potsdam}, pages = {xvi, 225}, year = {2022}, abstract = {Variation in traits permeates and affects all levels of biological organisation, from within individuals to between species. Yet, intraspecific trait variation (ITV) is not sufficiently represented in many ecological theories. Instead, species averages are often assumed. Especially ITV in behaviour has only recently attracted more attention as its pervasiveness and magnitude became evident. The surge in interest in ITV in behaviour was accompanied by a methodological and technological leap in the field of movement ecology. Many aspects of behaviour become visible via movement, allowing us to observe inter-individual differences in fundamental processes such as foraging, mate searching, predation or migration. ITV in movement behaviour may result from within-individual variability and consistent, repeatable among-individual differences. Yet, questions on why such among-individual differences occur in the first place and how they are integrated with life-history have remained open. Furthermore, consequences of ITV, especially of among-individual differences in movement behaviour, on populations and species communities are not sufficiently understood. In my thesis, I approach timely questions on the sources and consequences of ITV, particularly, in movement behaviour. After outlining fundamental concepts and the current state of knowledge, I approach these questions by using agent-based models to integrate concepts from behavioural and movement ecology and to develop novel perspectives. Modern coexistence theory is a central pillar of community ecology, yet, insufficiently considers ITV in behaviour. In chapter 2, I model a competitive two-species system of ground-dwelling, central-place foragers to investigate the consequences of among-individual differences in movement behaviour on species coexistence. I show that the simulated among-individual differences, which matched with empirical data, reduce fitness differences betweem species, i.e. provide an equalising coexistence mechanism. Furthermore, I explain this result mechanistically and, thus, resolve an apparent ambiguity of the consequences of ITV on species coexistence described in previous studies. In chapter 3, I turn the focus to sources of among-individual differences in movement behaviour and their potential integration with life-history. The pace-of-life syndrome (POLS) theory predicts that the covariation between among-individual differences in behaviour and life-history is mediated by a trade-off between early and late reproduction. This theory has generated attention but is also currently scrutinised. In chapter 3, I present a model which supports a recent conceptual development that suggests fluctuating density-dependent selection as a cause of the POLS. Yet, I also identified processes that may alter the association between movement behaviour and life-history across levels of biological organization. ITV can buffer populations, i.e. reduce their extinction risk. For instance, among-individual differences can mediate portfolio effects or increase evolvability and, thereby, facilitate rapid evolution which can alleviate extinction risk. In chapter 4, I review ITV, environmental heterogeneity, and density-dependent processes which constitute local buffer mechanisms. In the light of habitat isolation, which reduces connectivity between populations, local buffer mechanisms may become more relevant compared to dispersal-related regional buffer mechanisms. In this chapter, I argue that capacities, latencies, and interactions of local buffer mechanisms should motivate more process-based and holistic integration of local buffer mechanisms in theoretical and empirical studies. Recent perspectives propose to apply principles from movement and community ecology to study filamentous fungi. It is an open question whether and how the arrangement and geometry of microstructures select for certain movement traits, and, thus, facilitate coexistence-stabilising niche partitioning. As a coauthor of chapter 5, I developed an agent-based model of hyphal tips navigating in soil-like microstructures along a gradient of soil porosity. By measuring network properties, we identified changes in the optimal movement behaviours along the gradient. Our findings suggest that the soil architecture facilitates niche partitioning. The core chapters are framed by a general introduction and discussion. In the general introduction, I outline fundamental concepts of movement ecology and describe theory and open questions on sources and consequences of ITV in movement behaviour. In the general discussion, I consolidate the findings of the core chapters and critically discuss their respective value and, if applicable, their impact. Furthermore, I emphasise promising avenues for further research.}, language = {en} } @misc{CzarneckaWeicheltRoedigeretal.2022, author = {Czarnecka, Malgorzata and Weichelt, Ulrike and R{\"o}diger, Stefan and Hanack, Katja}, title = {Novel Anti Double-Stranded Nucleic Acids Full-Length Recombinant Camelid Heavy-Chain Antibody for the Detection of miRNA}, 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-56914}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569142}, pages = {1 -- 18}, year = {2022}, abstract = {The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.}, language = {en} } @phdthesis{Heinsohn2022, author = {Heinsohn, Natascha}, title = {Development of a fiber-based sensor for the molecular detection of pathogens using Legionella as an example}, doi = {10.25932/publishup-56683}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-566833}, school = {Universit{\"a}t Potsdam}, pages = {X, 175}, year = {2022}, abstract = {Fiber-based microfluidics has undergone many innovative developments in recent years, with exciting examples of portable, cost-effective and easy-to-use detection systems already being used in diagnostic and analytical applications. In water samples, Legionella are a serious risk as human pathogens. Infection occurs through inhalation of aerosols containing Legionella cells and can cause severe pneumonia and may even be fatal. In case of Legionella contamination of water-bearing systems or Legionella infection, it is essential to find the source of the contamination as quickly as possible to prevent further infections. In drinking, industrial and wastewater monitoring, the culture-based method is still the most commonly used technique to detect Legionella contamination. In order to improve the laboratory-dependent determination, the long analysis times of 10-14 days as well as the inaccuracy of the measured values in colony forming units (CFU), new innovative ideas are needed. In all areas of application, for example in public, commercial or private facilities, rapid and precise analysis is required, ideally on site. In this PhD thesis, all necessary single steps for a rapid DNA-based detection of Legionella were developed and characterized on a fiber-based miniaturized platform. In the first step, a fast, simple and device-independent chemical lysis of the bacteria and extraction of genomic DNA was established. Subsequently, different materials were investigated with respect to their non-specific DNA retention. Glass fiber filters proved to be particularly suitable, as they allow recovery of the DNA sample from the fiber material in combination with dedicated buffers and exhibit low autofluorescence, which was important for fluorescence-based readout. A fiber-based electrophoresis unit was developed to migrate different oligonucleotides within a fiber matrix by application of an electric field. A particular advantage over lateral flow assays is the targeted movement, even after the fiber is saturated with liquid. For this purpose, the entire process of fiber selection, fiber chip patterning, combination with printed electrodes, and testing of retention and migration of different DNA samples (single-stranded, double-stranded and genomic DNA) was performed. DNA could be pulled across the fiber chip in an electric field of 24 V/cm within 5 minutes, remained intact and could be used for subsequent detection assays e.g., polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH). Fiber electrophoresis could also be used to separate DNA from other components e.g., proteins or cell lysates or to pull DNA through multiple layers of the glass microfiber. In this way, different fragments experienced a moderate, size-dependent separation. Furthermore, this arrangement offers the possibility that different detection reactions could take place in different layers at a later time. Electric current and potential measurements were collected to investigate the local distribution of the sample during migration. While an increase in current signal at high concentrations indicated the presence of DNA samples, initial experiments with methylene blue stained DNA showed a temporal sequence of signals, indicating sample migration along the chip. For the specific detection of a Legionella DNA, a FISH-based detection with a molecular beacon probe was tested on the glass microfiber. A specific region within the 16S rRNA gene of Legionella spp. served as a target. For this detection, suitable reaction conditions and a readout unit had to be set up first. Subsequently, the sensitivity of the probe was tested with the reverse complementary target sequence and the specificity with several DNA fragments that differed from the target sequence. Compared to other DNA sequences of similar length also found in Legionella pneumophila, only the target DNA was specifically detected on the glass microfiber. If a single base exchange is present or if two bases are changed, the probe can no longer distinguish between the DNA targets and non-targets. An analysis with this specificity can be achieved with other methods such as melting point determination, as was also briefly indicated here. The molecular beacon probe could be dried on the glass microfiber and stored at room temperature for more than three months, after which it was still capable of detecting the target sequence. Finally, the feasibility of fiber-based FISH detection for genomic Legionella DNA was tested. Without further processing, the probe was unable to detect its target sequence in the complex genomic DNA. However, after selecting and application of appropriate restriction enzymes, specific detection of Legionella DNA against other aquatic pathogens with similar fragment patterns as Acinetobacter haemolyticus was possible.}, language = {en} } @article{EckertHerdenStiftetal.2022, author = {Eckert, Silvia and Herden, Jasmin and Stift, Marc and Durka, Walter and Kleunen, Mark Van and Joshi, Jasmin Radha}, title = {Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {1866-8372}, doi = {10.25932/publishup-56675}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-566758}, pages = {1 -- 17}, year = {2022}, abstract = {Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.}, language = {en} } @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} } @phdthesis{Kuerschner2022, author = {K{\"u}rschner, Tobias}, title = {Disease transmission and persistence in dynamic landscapes}, doi = {10.25932/publishup-56468}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-564689}, school = {Universit{\"a}t Potsdam}, pages = {120, LXXIII}, year = {2022}, abstract = {Infectious diseases are an increasing threat to biodiversity and human health. Therefore, developing a general understanding of the drivers shaping host-pathogen dynamics is of key importance in both ecological and epidemiological research. Disease dynamics are driven by a variety of interacting processes such as individual host behaviour, spatiotemporal resource availability or pathogen traits like virulence and transmission. External drivers such as global change may modify the system conditions and, thus, the disease dynamics. Despite their importance, many of these drivers are often simplified and aggregated in epidemiological models and the interactions among multiple drivers are neglected. In my thesis, I investigate disease dynamics using a mechanistic approach that includes both bottom-up effects - from landscape dynamics to individual movement behaviour - as well as top-down effects - from pathogen virulence on host density and contact rates. To this end, I extended an established spatially explicit individual-based model that simulates epidemiological and ecological processes stochastically, to incorporate a dynamic resource landscape that can be shifted away from the timing of host population-dynamics (chapter 2). I also added the evolution of pathogen virulence along a theoretical virulence-transmission trade-off (chapter 3). In chapter 2, I focus on bottom-up effects, specifically how a temporal shift of resource availability away from the timing of biological events of host-species - as expected under global change - scales up to host-pathogen interactions and disease dynamics. My results show that the formation of temporary disease hotspots in combination with directed individual movement acted as key drivers for pathogen persistence even under highly unfavourable conditions for the host. Even with drivers like global change further increasing the likelihood of unfavourable interactions between host species and their environment, pathogens can continue to persist with heir hosts. In chapter 3, I demonstrate that the top-down effect caused by pathogen-associated mortality on its host population can be mitigated by selection for lower virulent pathogen strains when host densities are reduced through mismatches between seasonal resource availability and host life-history events. I chapter 4, I combined parts of both theoretical models into a new model that includes individual host movement decisions and the evolution of pathogenic virulence to simulate pathogen outbreaks in realistic landscapes. I was able to match simulated patterns of pathogen spread to observed patterns from long-term outbreak data of classical swine fever in wild boar in Northern Germany. The observed disease course was best explained by a simulated high virulent strain, whereas sampling schemes and vaccination campaigns could explain differences in the age-distribution of infected hosts. My model helps to understand and disentangle how the combination of individual decision making and evolution of virulence can act as important drivers of pathogen spread and persistence. As I show across the chapters of this thesis, the interplay of both bottom-up and top-down processes is a key driver of disease dynamics in spatially structured host populations, as they ultimately shape host densities and contact rates among moving individuals. My findings are an important step towards a paradigm shift in disease ecology away from simplified assumptions towards the inclusion of mechanisms, such as complex multi-trophic interactions, and their feedbacks on pathogen spread and disease persistence. The mechanisms presented here should be at the core of realistic predictive and preventive epidemiological models.}, language = {en} } @phdthesis{Nwosu2022, author = {Nwosu, Ebuka Canisius}, title = {Sedimentary DNA-based reconstruction of cyanobacterial communities from Lake Tiefer See, NE Germany, for the last 11,000 years}, doi = {10.25932/publishup-56359}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-563590}, school = {Universit{\"a}t Potsdam}, pages = {xxvi, 214}, year = {2022}, abstract = {Climate change and human-driven eutrophication promote the spread of harmful cyanobacteria blooms in lakes worldwide, which affects water quality and impairs the aquatic food chain. In recent times, sedimentary ancient DNA-based (sedaDNA) studies were used to probe how centuries of climate and environmental changes have affected cyanobacterial assemblages in temperate lakes. However, there is a lack of information on the consistency between sediment-deposited cyanobacteria communities versus those of the water column, and on the individual role of natural climatic changes versus human pressure on cyanobacteria community dynamics over multi-millennia time scales. Therefore, this thesis uses sedimentary ancient DNA of Lake Tiefer See in northeastern Germany to trace the deposition of cyanobacteria along the water column into the sediment, and to reconstruct cyanobacteria communities spanning the last 11,000 years using a set of molecular techniques including quantitative PCR, biomarkers, metabarcoding, and metagenome sequence analyses. The results of this thesis proved that cyanobacterial composition and species richness did not significantly differ among different water depths, sediment traps, and surface sediments. This means that the cyanobacterial community composition from the sediments reflects the water column communities. However, there is a skewed sediment deposition of different cyanobacteria groups because of DNA alteration and/or deterioration during transport along the water column to the sediment. Specifically, single filament taxa, such as Planktothrix, are poorly represented in sediments despite being abundant in the water column as shown by an additional study of the thesis on cyanobacteria seasonality. In contrast, aggregate-forming taxa, like Aphanizomenon, are relatively overrepresented in sediment although they are not abundant in the water column. These different deposition patterns of cyanobacteria taxa should be considered in future DNA-based paleolimnological investigations. The thesis also reveals a substantial increase in total cyanobacteria abundance during the Bronze Age which is not apparent in prior phases of the early to middle Holocene and is suggested to be caused by human farming, deforestation, and excessive nutrient addition to the lake. Not only cyanobacterial abundance was influenced by human activity but also cyanobacteria community composition differed significantly between phases of no, moderate, and intense human impact. The data presented in this thesis are the first on sedimentary cyanobacteria DNA since the early Holocene in a temperate lake. The results bring together archaeological, historical climatic, and limnological data with deep DNA-sequencing and paleoecology to reveal a legacy impact of human pressure on lake cyanobacteria populations dating back to approximately 4000 years.}, language = {en} }