@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} } @article{SchefflerBoginHermanussen2021, author = {Scheffler, Christiane and Bogin, Barry and Hermanussen, Michael}, title = {Catch-up growth is a better indicator of undernutrition than thresholds for stunting}, series = {Public health nutrition : PHN / The Nutrition Society}, volume = {24}, journal = {Public health nutrition : PHN / The Nutrition Society}, number = {1}, publisher = {Cambridge University Press}, address = {Cambridge ; New York, NY}, issn = {1475-2727}, doi = {10.1017/S1368980020003067}, pages = {52 -- 61}, year = {2021}, 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} } @article{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 = {Ecological applications}, volume = {31}, journal = {Ecological applications}, number = {1}, publisher = {Wiley Periodicals LLC}, address = {Washington DC}, issn = {1939-5582}, doi = {10.1002/eap.2216}, pages = {1 -- 22}, 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{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} } @article{LiPostlBoehmeretal.2022, author = {Li, Chenzhi and Postl, Alexander K. and B{\"o}hmer, Thomas and Cao, Xianyong and Dolman, Andrew M. and Herzschuh, Ulrike}, title = {Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)}, series = {Earth system science data : ESSD}, volume = {14}, journal = {Earth system science data : ESSD}, number = {3}, publisher = {Copernics Publications}, address = {Katlenburg-Lindau}, issn = {1866-3508}, doi = {10.5194/essd-14-1331-2022}, pages = {1331 -- 1343}, year = {2022}, abstract = {We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats. All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. The most common control points for the chronologies are radiocarbon dates (86.1 \%), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8\% of records), reservoir effect (4.9 \%), and sediment deposition discontinuity (4.4 \%). Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4\% of records could be improved according to our assessment. Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively.}, 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} } @article{OmranianAngeleskaNikoloski2021, author = {Omranian, Sara and Angeleska, Angela and Nikoloski, Zoran}, title = {Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient}, series = {Computational and structural biotechnology journal}, volume = {19}, journal = {Computational and structural biotechnology journal}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2001-0370}, doi = {10.1016/j.csbj.2021.09.014}, pages = {5255 -- 5263}, year = {2021}, abstract = {Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71\% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35\% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.}, language = {en} } @article{HampfNendelStreyetal.2021, author = {Hampf, Anna and Nendel, Claas and Strey, Simone and Strey, Robert}, title = {Biotic yield losses in the Southern Amazon, Brazil}, series = {Frontiers in plant science : FPLS}, volume = {12}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2021.621168}, pages = {16}, year = {2021}, abstract = {Pathogens and animal pests (P\&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P\&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P\&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P\&A, (2) map the spatial distribution of P\&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P\&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P\&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P\&A, whereas soybean is mainly affected by P\&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16\%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US\$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.}, language = {en} } @article{IrobBlaumBaldaufetal.2022, author = {Irob, Katja and Blaum, Niels and Baldauf, Selina and Kerger, Leon and Strohbach, Ben and Kanduvarisa, Angelina and Lohmann, Dirk and Tietjen, Britta}, title = {Browsing herbivores improve the state and functioning of savannas}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.8715}, pages = {19}, year = {2022}, abstract = {Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.}, language = {en} } @article{GhafarianWielandLuettschwageretal.2022, author = {Ghafarian, Fatemeh and Wieland, Ralf and L{\"u}ttschwager, Dietmar and Nendel, Claas}, title = {Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data}, series = {Environmental modelling \& software with environment data news}, volume = {156}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2022.105466}, pages = {11}, year = {2022}, abstract = {Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.}, language = {en} } @article{CasertaZhangYarmanetal.2021, author = {Caserta, Giorgio and Zhang, Xiaorong and Yarman, Aysu and Supala, Eszter and Wollenberger, Ulla and Gyurcs{\´a}nyi, R{\´o}bert E. and Zebger, Ingo and Scheller, Frieder W.}, title = {Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms}, series = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)}, volume = {381}, journal = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)}, publisher = {Elsevier}, address = {New York, NY [u.a.]}, issn = {0013-4686}, doi = {10.1016/j.electacta.2021.138236}, pages = {8}, year = {2021}, abstract = {Molecularly imprinted polymer (MIP) nanofilms have been successfully implemented for the recognition of different target molecules: however, the underlying mechanistic details remained vague. This paper provides new insights in the preparation and binding mechanism of electrosynthesized peptide-imprinted polymer nanofilms for selective recognition of the terminal pentapeptides of the beta-chains of human adult hemoglobin, HbA, and its glycated form HbA1c. To differentiate between peptides differing solely in a glucose adduct MIP nanofilms were prepared by a two-step hierarchical electrosynthesis that involves first the chemisorption of a cysteinyl derivative of the pentapeptide followed by electropolymerization of scopoletin. This approach was compared with a random single-step electrosynthesis using scopo-letin/pentapeptide mixtures. Electrochemical monitoring of the peptide binding to the MIP nanofilms by means of redox probe gating revealed a superior affinity of the hierarchical approach with a Kd value of 64.6 nM towards the related target. Changes in the electrosynthesized non-imprinted polymer and MIP nanofilms during chemical, electrochemical template removal and rebinding were substantiated in situ by monitoring the characteristic bands of both target peptides and polymer with surface enhanced infrared absorption spectroscopy. This rational approach led to MIPs with excellent selectivity and provided key mechanistic insights with respect to electrosynthesis, rebinding and stability of the formed MIPs.}, language = {en} } @article{MitzscherlingMacLeanLipusetal.2022, author = {Mitzscherling, Julia and MacLean, Joana and Lipus, Daniel and Bartholom{\"a}us, Alexander and Mangelsdorf, Kai and Lipski, Andr{\´e} and Roddatis, Vladimir and Liebner, Susanne and Wagner, Dirk}, title = {Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste}, series = {International journal of systematic and evolutionary microbiology}, volume = {72}, journal = {International journal of systematic and evolutionary microbiology}, number = {4}, publisher = {Microbiology Society}, address = {London}, issn = {1466-5026}, doi = {10.1099/ijsem.0.005319}, pages = {11}, year = {2022}, abstract = {Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1\% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6\%) and Nocardioides dubius KSL-104(T) (98.3\%). The genomic DNA G+C content of strain NGK65(T) was 68.2\%. Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9\% as well as digital DNA-DNA hybridization values between 22.5 and 19.7\%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).}, language = {en} } @article{HiltGrossartMcGinnisetal.2022, author = {Hilt, Sabine and Grossart, Hans-Peter and McGinnis, Daniel F. and Keppler, Frank}, title = {Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems}, series = {Limnology and oceanography}, journal = {Limnology and oceanography}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.12095}, pages = {13}, year = {2022}, abstract = {Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.}, language = {en} } @article{YarmanKurbanoğluZebgeretal.2021, author = {Yarman, Aysu and Kurbanoğlu, Sevin{\c{c}} and Zebger, Ingo and Scheller, Frieder W.}, title = {Simple and robust}, series = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers}, volume = {330}, journal = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0925-4005}, doi = {10.1016/j.snb.2020.129369}, pages = {12}, year = {2021}, abstract = {A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 \% of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering.}, language = {en} } @article{TranTamuraPhametal.2021, author = {Tran, V. Phuong and Tamura, Yui and Pham, Van-Cuong and Elhussiny, Mohamed Z. and Han, Guofeng and Sur Chowdhury, Vishwajit and Furuse, Mitsuhiro}, title = {Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status}, series = {Neuropeptides}, volume = {89}, journal = {Neuropeptides}, publisher = {Elsevier}, address = {New York, NY}, issn = {0143-4179}, doi = {10.1016/j.npep.2021.102169}, pages = {9}, year = {2021}, abstract = {The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions.}, language = {en} } @article{PanSarhanKochovskietal.2022, author = {Pan, Xuefeng and Sarhan, Radwan Mohamed and Kochovski, Zdravko and Chen, Guosong and Taubert, Andreas and Mei, Shilin and Lu, Yan}, title = {Template synthesis of dual-functional porous MoS2 nanoparticles with photothermal conversion and catalytic properties}, series = {Nanoscale}, volume = {14}, journal = {Nanoscale}, number = {18}, publisher = {RSC Publ. (Royal Society of Chemistry)}, address = {Cambridge}, issn = {2040-3372}, doi = {10.1039/d2nr01040b}, pages = {6888 -- 6901}, year = {2022}, abstract = {Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification. In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability. Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures). The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation. Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination. We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis.}, language = {en} } @article{HagemannConejeroStillfriedetal.2022, author = {Hagemann, Justus and Conejero, Carles and Stillfried, Milena and Mentaberre, Gregorio and Castillo-Contreras, Raquel and Fickel, J{\"o}rns and Lopez-Olvera, Jorge Ram{\´o}n}, title = {Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {833}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.155126}, pages = {10}, year = {2022}, abstract = {Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.}, language = {en} } @article{RalevskiApeltOlasetal.2022, author = {Ralevski, Alexandra and Apelt, Federico and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Rugarli, Elena I. and Kragler, Friedrich and Horvath, Tamas L.}, title = {Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice}, series = {Cellular and molecular life sciences}, volume = {79}, journal = {Cellular and molecular life sciences}, number = {6}, publisher = {Springer International Publishing AG}, address = {Cham (ZG)}, issn = {1420-682X}, doi = {10.1007/s00018-022-04382-3}, pages = {17}, year = {2022}, abstract = {Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.}, language = {en} } @article{WitzelAbuRishaAlbersetal.2020, author = {Witzel, Katja and Abu Risha, Marua and Albers, Philip and B{\"o}rnke, Frederik and Hanschen, Franziska S.}, title = {Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; B{\"o}rnke, Frederike; Hanschen, Franziska S. - Lausanne: Frontiers Media, 2019. - Frontiers in plant science : FPLS. - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552}, series = {Frontiers in plant science : FPLS}, volume = {11}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2020.00523}, pages = {2}, year = {2020}, 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} } @article{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 = {FEMS Microbiology Ecology}, volume = {96}, journal = {FEMS Microbiology Ecology}, number = {2}, publisher = {Oxford University Press}, address = {Oxford}, issn = {1574-6941}, doi = {10.1093/femsec/fiz200}, pages = {1 -- 8}, 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} } @article{KuerschnerSchererRadchuketal.2021, author = {K{\"u}rschner, Tobias and Scherer, C{\´e}dric and Radchuk, Viktoriia and Blaum, Niels and Kramer-Schadt, Stephanie}, title = {Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions}, series = {Ecology and evolution}, volume = {11}, journal = {Ecology and evolution}, number = {10}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.7478}, pages = {5728 -- 5741}, year = {2021}, abstract = {Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.}, language = {en} } @article{LeinsGrimmDrechsler2022, author = {Leins, Johannes A. and Grimm, Volker and Drechsler, Martin}, title = {Large-scale PVA modeling of insects in cultivated grasslands}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {7}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.9063}, pages = {17}, year = {2022}, abstract = {In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.}, language = {en} } @article{GhafarianWielandNendel2022, author = {Ghafarian, Fatemeh and Wieland, Ralf and Nendel, Claas}, title = {Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy}, series = {Water}, volume = {14}, journal = {Water}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2073-4441}, doi = {10.3390/w14030319}, pages = {16}, year = {2022}, abstract = {Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.}, 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} } @phdthesis{Kersting2024, author = {Kersting, Katerina}, title = {Development of a CRISPR/Cas gene editing technique for the coccolithophore Chrysotila carterae}, school = {Universit{\"a}t Potsdam}, pages = {137}, year = {2024}, language = {en} } @article{MillesDammhahnJeltschetal.2022, author = {Milles, Alexander Benedikt and Dammhahn, Melanie and Jeltsch, Florian and Schl{\"a}gel, Ulrike and Grimm, Volker}, title = {Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {199}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {4}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/718473}, pages = {E124 -- E139}, year = {2022}, abstract = {The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.}, 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} } @article{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 = {Aquatic Ecology}, volume = {54}, journal = {Aquatic Ecology}, number = {1}, publisher = {Springer Science}, address = {Dordrecht}, issn = {1573-5125}, doi = {10.1007/s10452-019-09745-w}, pages = {323 -- 336}, 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} } @article{StankeWengerBieretal.2022, author = {Stanke, Sandra and Wenger, Christian and Bier, Frank Fabian and H{\"o}lzel, Ralph}, title = {AC electrokinetic immobilization of influenza virus}, series = {Electrophoresis : microfluids \& proteomics}, volume = {43}, journal = {Electrophoresis : microfluids \& proteomics}, number = {12}, publisher = {Wiley-Blackwell}, address = {Weinheim}, issn = {0173-0835}, doi = {10.1002/elps.202100324}, pages = {1309 -- 1321}, year = {2022}, abstract = {The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.}, language = {en} } @article{TongNankarLiuetal.2022, author = {Tong, Hao and Nankar, Amol N. and Liu, Jintao and Todorova, Velichka and Ganeva, Daniela and Grozeva, Stanislava and Tringovska, Ivanka and Pasev, Gancho and Radeva-Ivanova, Vesela and Gechev, Tsanko and Kostova, Dimitrina and Nikoloski, Zoran}, title = {Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits}, series = {Horticulture research}, volume = {9}, journal = {Horticulture research}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {2052-7276}, doi = {10.1093/hr/uhac072}, pages = {11}, year = {2022}, abstract = {Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.}, 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} } @article{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 = {Scientific reports}, volume = {10}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-60506-4}, pages = {1 -- 15}, 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} } @article{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 = {Virus Evolution}, volume = {6}, journal = {Virus Evolution}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2057-1577}, doi = {10.1093/ve/vez061}, pages = {1 -- 10}, 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} } @article{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 = {Metabolites}, volume = {10}, journal = {Metabolites}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2218-1989}, doi = {10.3390/metabo10040148}, pages = {1 -- 18}, 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{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} }