@phdthesis{Wutke2016, author = {Wutke, Saskia}, title = {Tracing Changes in Space and Time}, school = {Universit{\"a}t Potsdam}, pages = {x, 84}, year = {2016}, abstract = {The horse is a fascinating animal symbolizing power, beauty, strength and grace. Among all the animal species domesticated the horse had the largest impact on the course of human history due to its importance for warfare and transportation. Studying the process of horse domestication contributes to the knowledge about the history of horses and even of our own species. Research based on molecular methods has increasingly focused on the genetic basis of horse domestication. Mitochondrial DNA (mtDNA) analyses of modern and ancient horses detected immense maternal diversity, probably due to many mares that contributed to the domestic population. However, mtDNA does not provide an informative phylogeographic structure. In contrast, Y chromosome analyses displayed almost complete uniformity in modern stallions but relatively high diversity in a few ancient horses. Further molecular markers that seem to be well suited to infer the domestication history of horses or genetic and phenotypic changes during this process are loci associated with phenotypic traits. This doctoral thesis consists of three different parts for which I analyzed various single nucleotide polymorphisms (SNPs) associated with coat color, locomotion or Y chromosomal variation of horses. These SNPs were genotyped in 350 ancient horses from the Chalcolithic (5,000 BC) to the Middle Ages (11th century). The distribution of the samples ranges from China to the Iberian Peninsula and Iceland. By applying multiplexed next-generation sequencing (NGS) I sequenced short amplicons covering the relevant positions: i) eight coat-color-associated mutations in six genes to deduce the coat color phenotype; ii) the so-called 'Gait-keeper' SNP in the DMRT3 gene to screen for the ability to amble; iii) 16 SNPs previously detected in ancient horses to infer the corresponding haplotype. Based on these data I investigated the occurrence and frequencies of alleles underlying the respective phenotypes as well as Y chromosome haplotypes at different times and regions. Also, selection coefficients for several Y chromosome lineages or phenotypes were estimated. Concerning coat color differences in ancient horses my work constitutes the most comprehensive study to date. I detected an increase of chestnut horses in the Middle Ages as well as differential selection for spotted and solid phenotypes over time which reflects changing human preferences. With regard to ambling horses, the corresponding allele was present in medieval English and Icelandic horses. Based on these results I argue that Norse settlers, who frequently invaded parts of Britain, brought ambling individuals to Iceland from the British Isles which can be regarded the origin of this trait. Moreover, these settlers appear to have selected for ambling in Icelandic horses. Relating to the third trait, the paternal diversity, these findings represent the largest ancient dataset of Y chromosome variation in non-humans. I proved the existence of several Y chromosome haplotypes in early domestic horses. The decline of Y chromosome variation coincides with the movement of nomadic peoples from the Eurasian steppes and later with different breeding practices in the Roman period. In conclusion, positive selection was estimated for several phenotypes/lineages in different regions or times which indicates that these were preferred by humans. Furthermore, I could successfully infer the distribution and dispersal of horses in association with human movements and actions. Thereby, a better understanding of the influence of people on the changing appearance and genetic diversity of domestic horses could be gained. My results also emphasize the close relationship of ancient genetics and archeology or history and that only in combination well-founded conclusions can be reached.}, language = {en} } @article{FagesHanghojKhanetal.2019, author = {Fages, Antoine and Hanghoj, Kristian and Khan, Naveed and Gaunitz, Charleen and Seguin-Orlando, Andaine and Leonardi, Michela and Constantz, Christian McCrory and Gamba, Cristina and Al-Rasheid, Khaled A. S. and Albizuri, Silvia and Alfarhan, Ahmed H. and Allentoft, Morten and Alquraishi, Saleh and Anthony, David and Baimukhanov, Nurbol and Barrett, James H. and Bayarsaikhan, Jamsranjav and Benecke, Norbert and Bernaldez-Sanchez, Eloisa and Berrocal-Rangel, Luis and Biglari, Fereidoun and Boessenkool, Sanne and Boldgiv, Bazartseren and Brem, Gottfried and Brown, Dorcas and Burger, Joachim and Crubezy, Eric and Daugnora, Linas and Davoudi, Hossein and Damgaard, Peter de Barros and de Chorro y de Villa-Ceballos, Maria de los Angeles and Deschler-Erb, Sabine and Detry, Cleia and Dill, Nadine and Oom, Maria do Mar and Dohr, Anna and Ellingvag, Sturla and Erdenebaatar, Diimaajav and Fathi, Homa and Felkel, Sabine and Fernandez-Rodriguez, Carlos and Garcia-Vinas, Esteban and Germonpre, Mietje and Granado, Jose D. and Hallsson, Jon H. and Hemmer, Helmut and Hofreiter, Michael and Kasparov, Aleksei and Khasanov, Mutalib and Khazaeli, Roya and Kosintsev, Pavel and Kristiansen, Kristian and Kubatbek, Tabaldiev and Kuderna, Lukas and Kuznetsov, Pavel and Laleh, Haeedeh and Leonard, Jennifer A. and Lhuillier, Johanna and von Lettow-Vorbeck, Corina Liesau and Logvin, Andrey and Lougas, Lembi and Ludwig, Arne and Luis, Cristina and Arruda, Ana Margarida and Marques-Bonet, Tomas and Silva, Raquel Matoso and Merz, Victor and Mijiddorj, Enkhbayar and Miller, Bryan K. and Monchalov, Oleg and Mohaseb, Fatemeh A. and Morales, Arturo and Nieto-Espinet, Ariadna and Nistelberger, Heidi and Onar, Vedat and Palsdottir, Albina H. and Pitulko, Vladimir and Pitskhelauri, Konstantin and Pruvost, Melanie and Sikanjic, Petra Rajic and Papesa, Anita Rapan and Roslyakova, Natalia and Sardari, Alireza and Sauer, Eberhard and Schafberg, Renate and Scheu, Amelie and Schibler, Jorg and Schlumbaum, Angela and Serrand, Nathalie and Serres-Armero, Aitor and Shapiro, Beth and Seno, Shiva Sheikhi and Shevnina, Irina and Shidrang, Sonia and Southon, John and Star, Bastiaan and Sykes, Naomi and Taheri, Kamal and Taylor, William and Teegen, Wolf-Rudiger and Vukicevic, Tajana Trbojevic and Trixl, Simon and Tumen, Dashzeveg and Undrakhbold, Sainbileg and Usmanova, Emma and Vahdati, Ali and Valenzuela-Lamas, Silvia and Viegas, Catarina and Wallner, Barbara and Weinstock, Jaco and Zaibert, Victor and Clavel, Benoit and Lepetz, Sebastien and Mashkour, Marjan and Helgason, Agnar and Stefansson, Kari and Barrey, Eric and Willerslev, Eske and Outram, Alan K. and Librado, Pablo and Orlando, Ludovic}, title = {Tracking five millennia of horse management with extensive ancient genome time series}, series = {Cell}, volume = {177}, journal = {Cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.03.049}, pages = {1419 -- 1435}, year = {2019}, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, language = {en} } @article{HilongaOtienoGhorbanietal.2018, author = {Hilonga, S. and Otieno, Joseph N. and Ghorbani, Abdolbaset and Pereus, D. and Kocyan, Alexander and de Boer, H.}, title = {Trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation}, series = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, volume = {122}, journal = {South African journal of botany : an international interdisciplinary journal for botanical sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0254-6299}, doi = {10.1016/j.sajb.2018.08.012}, pages = {214 -- 224}, year = {2018}, abstract = {In Tanzania, about 10\% of the reported 12,000 species of higher plants are estimated to be used as medicine for treating different human health problems. Most of the medicinal plants are collected from wild populations, but their trade and quantities are not properly recorded. Monitoring of trade in wild-harvested medicinal plants is challenging asmostmaterials are traded in various processed forms and most vendors practice informal trade. Yet, monitoring is important for conservation and sustainability. This study aims to assess the trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation. Semi-structured interviews were used to record frequency, volume of trade and uses of wild-harvested medicinal plants in Arusha, Dodoma, Mbeya, Morogoro and Mwanza regions. Relative frequency of citation and informant consensus factor were calculated for each species and mentioned use category. Forty vendors were interviewed, and 400 out of 522 collected market samples were identified to 162 species from herbarium-deposited collections. Plant parts with the largest volume of trade were roots (3818 kg), bark (1163 kg) and leaves (492 kg). The most frequently traded species were Zanthoxylum chalybaeum Engl., Albizia anthelmintica Brongn., Zanha africana (Radlk.) Exell, Warburgia stuhlmannii and Vachellia nilotica (L.) P.J.H. Hurter \& Mabb. The most popular medicinal plants in the markets are connected to local health problems including malaria, libido disorders or infertility. The high diversity of commercialized plants used for medicinal issues mainly relies on wild stock for local consumption and international trade, and this has significant implications for conservation concerns. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.}, language = {en} } @misc{GorochowskiIgnatovaBovenbergetal.2015, author = {Gorochowski, Thomas E. and Ignatova, Zoya and Bovenberg, Roel A. L. and Roubos, Johannes A.}, title = {Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {816}, issn = {1866-8372}, doi = {10.25932/publishup-44134}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441340}, pages = {13}, year = {2015}, abstract = {Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.}, language = {en} } @article{KlauschiesVasseurGaedke2016, author = {Klauschies, Toni and Vasseur, David A. and Gaedke, Ursula}, title = {Trait adaptation promotes species coexistence in diverse predator and prey communities}, series = {Ecology and evolution}, journal = {Ecology and evolution}, publisher = {John Wiley \& Sons, Inc.}, issn = {2045-7758}, doi = {10.1002/ece3.2172}, pages = {19}, year = {2016}, abstract = {Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator-prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to pre- vious studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.}, language = {en} } @misc{KlauschiesVasseurGaedke2016, author = {Klauschies, Toni and Vasseur, David A. and Gaedke, Ursula}, title = {Trait adaptation promotes species coexistence in diverse predator and prey communities}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-91498}, pages = {19}, year = {2016}, abstract = {Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator-prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to previous studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.}, language = {en} } @misc{BergholzKoberJeltschetal.2021, author = {Bergholz, Kolja and Kober, Klarissa and Jeltsch, Florian and Schmidt, Kristina and Weiß, Lina}, title = {Trait means or variance}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-51990}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-519905}, pages = {3357 -- 3365}, year = {2021}, abstract = {One of the few laws in ecology is that communities consist of few common and many rare taxa. Functional traits may help to identify the underlying mechanisms of this community pattern, since they correlate with different niche dimensions. However, comprehensive studies are missing that investigate the effects of species mean traits (niche position) and intraspecific trait variability (ITV, niche width) on species abundance. In this study, we investigated fragmented dry grasslands to reveal trait-occurrence relationships in plants at local and regional scales. We predicted that (a) at the local scale, species occurrence is highest for species with intermediate traits, (b) at the regional scale, habitat specialists have a lower species occurrence than generalists, and thus, traits associated with stress-tolerance have a negative effect on species occurrence, and (c) ITV increases species occurrence irrespective of the scale. We measured three plant functional traits (SLA = specific leaf area, LDMC = leaf dry matter content, plant height) at 21 local dry grassland communities (10 m × 10 m) and analyzed the effect of these traits and their variation on species occurrence. At the local scale, mean LDMC had a positive effect on species occurrence, indicating that stress-tolerant species are the most abundant rather than species with intermediate traits (hypothesis 1). We found limited support for lower specialist occurrence at the regional scale (hypothesis 2). Further, ITV of LDMC and plant height had a positive effect on local occurrence supporting hypothesis 3. In contrast, at the regional scale, plants with a higher ITV of plant height were less frequent. We found no evidence that the consideration of phylogenetic relationships in our analyses influenced our findings. In conclusion, both species mean traits (in particular LDMC) and ITV were differently related to species occurrence with respect to spatial scale. Therefore, our study underlines the strong scale-dependency of trait-abundance relationships.}, language = {en} } @article{BergholzKoberJeltschetal.2021, author = {Bergholz, Kolja and Kober, Klarissa and Jeltsch, Florian and Schmidt, Kristina and Weiß, Lina}, title = {Trait means or variance}, series = {Ecology and evolution}, volume = {11}, journal = {Ecology and evolution}, number = {7}, publisher = {John Wiley \& Sons, Inc.}, issn = {2045-7758}, doi = {10.1002/ece3.7287}, pages = {3357 -- 3365}, year = {2021}, abstract = {One of the few laws in ecology is that communities consist of few common and many rare taxa. Functional traits may help to identify the underlying mechanisms of this community pattern, since they correlate with different niche dimensions. However, comprehensive studies are missing that investigate the effects of species mean traits (niche position) and intraspecific trait variability (ITV, niche width) on species abundance. In this study, we investigated fragmented dry grasslands to reveal trait-occurrence relationships in plants at local and regional scales. We predicted that (a) at the local scale, species occurrence is highest for species with intermediate traits, (b) at the regional scale, habitat specialists have a lower species occurrence than generalists, and thus, traits associated with stress-tolerance have a negative effect on species occurrence, and (c) ITV increases species occurrence irrespective of the scale. We measured three plant functional traits (SLA = specific leaf area, LDMC = leaf dry matter content, plant height) at 21 local dry grassland communities (10 m × 10 m) and analyzed the effect of these traits and their variation on species occurrence. At the local scale, mean LDMC had a positive effect on species occurrence, indicating that stress-tolerant species are the most abundant rather than species with intermediate traits (hypothesis 1). We found limited support for lower specialist occurrence at the regional scale (hypothesis 2). Further, ITV of LDMC and plant height had a positive effect on local occurrence supporting hypothesis 3. In contrast, at the regional scale, plants with a higher ITV of plant height were less frequent. We found no evidence that the consideration of phylogenetic relationships in our analyses influenced our findings. In conclusion, both species mean traits (in particular LDMC) and ITV were differently related to species occurrence with respect to spatial scale. Therefore, our study underlines the strong scale-dependency of trait-abundance relationships.}, language = {en} } @phdthesis{Eckert2022, author = {Eckert, Silvia}, title = {Trait variation in changing environments: Assessing the role of DNA methylation in non-native plant species}, doi = {10.25932/publishup-56884}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-568844}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 134, CXXX}, year = {2022}, abstract = {The increasing introduction of non-native plant species may pose a threat to local biodiversity. However, the basis of successful plant invasion is not conclusively understood, especially since these plant species can adapt to the new range within a short period of time despite impoverished genetic diversity of the starting populations. In this context, DNA methylation is considered promising to explain successful adaptation mechanisms in the new habitat. DNA methylation is a heritable variation in gene expression without changing the underlying genetic information. Thus, DNA methylation is considered a so-called epigenetic mechanism, but has been studied in mainly clonally reproducing plant species or genetic model plants. An understanding of this epigenetic mechanism in the context of non-native, predominantly sexually reproducing plant species might help to expand knowledge in biodiversity research on the interaction between plants and their habitats and, based on this, may enable more precise measures in conservation biology. For my studies, I combined chemical DNA demethylation of field-collected seed material from predominantly sexually reproducing species and rearing offsping under common climatic conditions to examine DNA methylation in an ecological-evolutionary context. The contrast of chemically treated (demethylated) plants, whose variation in DNA methylation was artificially reduced, and untreated control plants of the same species allowed me to study the impact of this mechanism on adaptive trait differentiation and local adaptation. With this experimental background, I conducted three studies examining the effect of DNA methylation in non-native species along a climatic gradient and also between climatically divergent regions. The first study focused on adaptive trait differentiation in two invasive perennial goldenrod species, Solidago canadensis sensu latu and S. gigantea AITON, along a climate gradient of more than 1000 km in length in Central Europe. I found population differences in flowering timing, plant height, and biomass in the temporally longer-established S. canadensis, but only in the number of regrowing shoots for S. gigantea. While S. canadensis did not show any population structure, I was able to identify three genetic groups along this climatic gradient in S. gigantea. Surprisingly, demethylated plants of both species showed no change in the majority of traits studied. In the subsequent second study, I focused on the longer-established goldenrod species S. canadensis and used molecular analyses to infer spatial epigenetic and genetic population differences in the same specimens from the previous study. I found weak genetic but no epigenetic spatial variation between populations. Additionally, I was able to identify one genetic marker and one epigenetic marker putatively susceptible to selection. However, the results of this study reconfirmed that the epigenetic mechanism of DNA methylation appears to be hardly involved in adaptive processes within the new range in S. canadensis. Finally, I conducted a third study in which I reciprocally transplanted short-lived plant species between two climatically divergent regions in Germany to investigate local adaptation at the plant family level. For this purpose, I used four plant families (Amaranthaceae, Asteraceae, Plantaginaceae, Solanaceae) and here I additionally compared between non-native and native plant species. Seeds were transplanted to regions with a distance of more than 600 kilometers and had either a temperate-oceanic or a temperate-continental climate. In this study, some species were found to be maladapted to their own local conditions, both in non-native and native plant species alike. In demethylated individuals of the plant species studied, DNA methylation had inconsistent but species-specific effects on survival and biomass production. The results of this study highlight that DNA methylation did not make a substantial contribution to local adaptation in the non-native as well as native species studied. In summary, my work showed that DNA methylation plays a negligible role in both adaptive trait variation along climatic gradients and local adaptation in non-native plant species that either exhibit a high degree of genetic variation or rely mainly on sexual reproduction with low clonal propagation. I was able to show that the adaptive success of these non-native plant species can hardly be explained by DNA methylation, but could be a possible consequence of multiple introductions, dispersal corridors and meta-population dynamics. Similarly, my results illustrate that the use of plant species that do not predominantly reproduce clonally and are not model plants is essential to characterize the effect size of epigenetic mechanisms in an ecological-evolutionary context.}, language = {en} } @phdthesis{Bergholz2018, author = {Bergholz, Kolja}, title = {Trait-based understanding of plant species distributions along environmental gradients}, doi = {10.25932/publishup-42634}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426341}, school = {Universit{\"a}t Potsdam}, pages = {128}, year = {2018}, abstract = {For more than two centuries, plant ecologists have aimed to understand how environmental gradients and biotic interactions shape the distribution and co-occurrence of plant species. In recent years, functional trait-based approaches have been increasingly used to predict patterns of species co-occurrence and species distributions along environmental gradients (trait-environment relationships). Functional traits are measurable properties at the individual level that correlate well with important processes. Thus, they allow us to identify general patterns by synthesizing studies across specific taxonomic compositions, thereby fostering our understanding of the underlying processes of species assembly. However, the importance of specific processes have been shown to be highly dependent on the spatial scale under consideration. In particular, it remains uncertain which mechanisms drive species assembly and allow for plant species coexistence at smaller, more local spatial scales. Furthermore, there is still no consensus on how particular environmental gradients affect the trait composition of plant communities. For example, increasing drought because of climate change is predicted to be a main threat to plant diversity, although it remains unclear which traits of species respond to increasing aridity. Similarly, there is conflicting evidence of how soil fertilization affects the traits related to establishment ability (e.g., seed mass). In this cumulative dissertation, I present three empirical trait-based studies that investigate specific research questions in order to improve our understanding of species distributions along environmental gradients. In the first case study, I analyze how annual species assemble at the local scale and how environmental heterogeneity affects different facets of biodiversity—i.e. taxonomic, functional, and phylogenetic diversity—at different spatial scales. The study was conducted in a semi-arid environment at the transition zone between desert and Mediterranean ecosystems that features a sharp precipitation gradient (Israel). Different null model analyses revealed strong support for environmentally driven species assembly at the local scale, since species with similar traits tended to co-occur and shared high abundances within microsites (trait convergence). A phylogenetic approach, which assumes that closely related species are functionally more similar to each other than distantly related ones, partly supported these results. However, I observed that species abundances within microsites were, surprisingly, more evenly distributed across the phylogenetic tree than expected (phylogenetic overdispersion). Furthermore, I showed that environmental heterogeneity has a positive effect on diversity, which was higher on functional than on taxonomic diversity and increased with spatial scale. The results of this case study indicate that environmental heterogeneity may act as a stabilizing factor to maintain species diversity at local scales, since it influenced species distribution according to their traits and positively influenced diversity. All results were constant along the precipitation gradient. In the second case study (same study system as case study one), I explore the trait responses of two Mediterranean annuals (Geropogon hybridus and Crupina crupinastrum) along a precipitation gradient that is comparable to the maximum changes in precipitation predicted to occur by the end of this century (i.e., -30\%). The heterocarpic G. hybridus showed strong trends in seed traits, suggesting that dispersal ability increased with aridity. By contrast, the homocarpic C. crupinastrum showed only a decrease in plant height as aridity increased, while leaf traits of both species showed no consistent pattern along the precipitation gradient. Furthermore, variance decomposition of traits revealed that most of the trait variation observed in the study system was actually found within populations. I conclude that trait responses towards aridity are highly species-specific and that the amount of precipitation is not the most striking environmental factor at this particular scale. In the third case study, I assess how soil fertilization mediates—directly by increased nutrient addition and indirectly by increased competition—the effect of seed mass on establishment ability. For this experiment, I used 22 species differing in seed mass from dry grasslands in northeastern Germany and analyzed the interacting effects of seed mass with nutrient availability and competition on four key components of seedling establishment: seedling emergence, time of seedling emergence, seedling survival, and seedling growth. (Time of) seedling emergence was not affected by seed mass. However, I observed that the positive effect of seed mass on seedling survival is lowered under conditions of high nutrient availability, whereas the positive effect of seed mass on seedling growth was only reduced by competition. Based on these findings, I developed a conceptual model of how seed mass should change along a soil fertility gradient in order to reconcile conflicting findings from the literature. In this model, seed mass shows a U-shaped pattern along the soil fertility gradient as a result of changing nutrient availability and competition. Overall, the three case studies highlight the role of environmental factors on species distribution and co-occurrence. Moreover, the findings of this thesis indicate that spatial heterogeneity at local scales may act as a stabilizing factor that allows species with different traits to coexist. In the concluding discussion, I critically debate intraspecific trait variability in plant community ecology, the use of phylogenetic relationships and easily measured key functional traits as a proxy for species' niches. Finally, I offer my outlook for the future of functional plant community research.}, language = {en} } @article{KamranfarXueTohgeetal.2018, author = {Kamranfar, Iman and Xue, Gang-Ping and Tohge, Takayuki and Sedaghatmehr, Mastoureh and Fernie, Alisdair and Balazadeh, Salma and Mueller-Roeber, Bernd}, title = {Transcription factor RD26 is a key regulator of metabolic reprogramming during dark-induced senescence}, series = {New phytologist : international journal of plant science}, volume = {218}, journal = {New phytologist : international journal of plant science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.15127}, pages = {1543 -- 1557}, year = {2018}, abstract = {Leaf senescence is a key process in plants that culminates in the degradation of cellular constituents and massive reprogramming of metabolism for the recovery of nutrients from aged leaves for their reuse in newly developing sinks. We used molecular-biological and metabolomics approaches to identify NAC transcription factor (TF) RD26 as an important regulator of metabolic reprogramming in Arabidopsis thaliana. RD26 directly activates CHLOROPLAST VESICULATION (CV), encoding a protein crucial for chloroplast protein degradation, concomitant with an enhanced protein loss in RD26 over-expressors during senescence, but a reduced decline of protein in rd26 knockout mutants. RD26 also directly activates LKR/SDH involved in lysine catabolism, and PES1 important for phytol degradation. Metabolic profiling revealed reduced c-aminobutyric acid (GABA) in RD26 overexpressors, accompanied by the induction of respective catabolic genes. Degradation of lysine, phytol and GABA is instrumental for maintaining mitochondrial respiration in carbon-limiting conditions during senescence. RD26 also supports the degradation of starch and the accumulation of mono-and disaccharides during senescence by directly enhancing the expression of AMY1, SFP1 and SWEET15 involved in carbohydrate metabolism and transport. Collectively, during senescence RD26 acts by controlling the expression of genes across the entire spectrum of the cellular degradation hierarchy.}, language = {en} } @article{CanitzKirschbaumTiedemann2020, author = {Canitz, Julia and Kirschbaum, Frank and Tiedemann, Ralph}, title = {Transcriptome-wide single nucleotide polymorphisms related to electric organ discharge differentiation among African weakly electric fish species}, series = {PLoS one}, volume = {15}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {San Francisco, California, US}, issn = {1932-6203}, doi = {10.1371/journal.pone.0240812}, pages = {21}, year = {2020}, abstract = {African weakly electric fish of the mormyrid genus Campylomormyrus generate pulse-type electric organ discharges (EODs) for orientation and communication. Their pulse durations are species-specific and elongated EODs are a derived trait. So far, differential gene expression among tissue-specific transcriptomes across species with different pulses and point mutations in single ion channel genes indicate a relation of pulse duration and electrocyte geometry/excitability. However, a comprehensive assessment of expressed Single Nucleotide Polymorphisms (SNPs) throughout the entire transcriptome of African weakly electric fish, with the potential to identify further genes influencing EOD duration, is still lacking. This is of particular value, as discharge duration is likely based on multiple cellular mechanisms and various genes. Here we provide the first transcriptome-wide SNP analysis of African weakly electric fish species (genus Campylomormyrus) differing by EOD duration to identify candidate genes and cellular mechanisms potentially involved in the determination of an elongated discharge of C. tshokwe. Non-synonymous substitutions specific to C. tshokwe were found in 27 candidate genes with inferred positive selection among Campylomormyrus species. These candidate genes had mainly functions linked to transcriptional regulation, cell proliferation and cell differentiation. Further, by comparing gene annotations between C. compressirostris (ancestral short EOD) and C. tshokwe (derived elongated EOD), we identified 27 GO terms and 2 KEGG pathway categories for which C. tshokwe significantly more frequently exhibited a species-specific expressed substitution than C. compressirostris. The results indicate that transcriptional regulation as well cell proliferation and differentiation take part in the determination of elongated pulse durations in C. tshokwe. Those cellular processes are pivotal for tissue morphogenesis and might determine the shape of electric organs supporting the observed correlation between electrocyte geometry/tissue structure and discharge duration. The inferred expressed SNPs and their functional implications are a valuable resource for future investigations on EOD durations.}, language = {en} } @article{ApriyantoCompartFettke2023, author = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg}, title = {Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield}, series = {Frontiers in plant science}, volume = {14}, journal = {Frontiers in plant science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2023.1220237}, pages = {13}, year = {2023}, abstract = {The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.}, language = {en} } @phdthesis{Soja2014, author = {Soja, Aleksandra Maria}, title = {Transcriptomic and metabolomic analysis of Arabidopsis thaliana during abiotic stress}, pages = {134}, year = {2014}, language = {en} } @article{ApriyantoAjambang2022, author = {Apriyanto, Ardha and Ajambang, Walter}, title = {Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress}, series = {Data in Brief}, volume = {41}, journal = {Data in Brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2022.107914}, pages = {6}, year = {2022}, abstract = {Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.}, language = {en} } @phdthesis{Loiacono2017, author = {Loiacono, Filomena Vanessa}, title = {Transfer of chloroplast RNA editing events between species}, school = {Universit{\"a}t Potsdam}, pages = {155}, year = {2017}, language = {en} } @misc{RadchukKramerSchadtGrimm2019, author = {Radchuk, Viktoriia and Kramer-Schadt, Stephanie and Grimm, Volker}, title = {Transferability of mechanistic ecological models is about emergence}, series = {Trends in ecology and evolution}, volume = {34}, journal = {Trends in ecology and evolution}, number = {6}, publisher = {Elsevier}, address = {London}, issn = {0169-5347}, doi = {10.1016/j.tree.2019.01.010}, pages = {487 -- 488}, year = {2019}, language = {en} } @article{KirchlerKonigorskiNordenetal.2022, author = {Kirchler, Matthias and Konigorski, Stefan and Norden, Matthias and Meltendorf, Christian and Kloft, Marius and Schurmann, Claudia and Lippert, Christoph}, title = {transferGWAS}, series = {Bioinformatics}, volume = {38}, journal = {Bioinformatics}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btac369}, pages = {3621 -- 3628}, year = {2022}, abstract = {Motivation: Medical images can provide rich information about diseases and their biology. However, investigating their association with genetic variation requires non-standard methods. We propose transferGWAS, a novel approach to perform genome-wide association studies directly on full medical images. First, we learn semantically meaningful representations of the images based on a transfer learning task, during which a deep neural network is trained on independent but similar data. Then, we perform genetic association tests with these representations. Results: We validate the type I error rates and power of transferGWAS in simulation studies of synthetic images. Then we apply transferGWAS in a genome-wide association study of retinal fundus images from the UK Biobank. This first-of-a-kind GWAS of full imaging data yielded 60 genomic regions associated with retinal fundus images, of which 7 are novel candidate loci for eye-related traits and diseases.}, language = {en} } @article{RojasJimenezFonvielleMaetal.2017, author = {Rojas-Jimenez, Keilor and Fonvielle, Jeremy Andre and Ma, Hua and Grossart, Hans-Peter}, title = {Transformation of humic substances by the freshwater Ascomycete Cladosporium sp.}, series = {Waterbird}, volume = {40}, journal = {Waterbird}, publisher = {Waterbird SOC}, address = {Washington}, issn = {1524-4695}, doi = {10.1002/lno.10545}, pages = {282 -- 288}, year = {2017}, abstract = {The ecological relevance of fungi in freshwater ecosystems is becoming increasingly evident, particularly in processing the extensive amounts of polymeric organic carbon such as cellulose, chitin, and humic substances (HS). We isolated several fungal strains from oligo-mesotrophic Lake Stechlin, Brandenburg, Germany, and analyzed their ability to degrade polymeric-like substrates. Using liquid chromatography-organic carbon detection, we determined the byproducts of HS transformation by the freshwater fungus Cladosporium sp. KR14. We demonstrate the ability of this fungus to degrade and simultaneously synthesize HS, and that transformation processes were intensified when iron, as indicator of the occurrence of Fenton reactions, was present in the medium. Furthermore, we showed that structural complexity of the HS produced changed with the availability of other polymeric substances in the medium. Our study highlights the contribution of freshwater Ascomycetes to the transformation of complex organic compounds. As such, it has important implications for understanding the ecological contribution of fungi to aquatic food webs and related biogeochemical cycles.}, language = {en} } @article{ZhengToenjesPikovskij2021, author = {Zheng, Chunming and T{\"o}njes, Ralf and Pikovskij, Arkadij}, title = {Transition to synchrony in a three-dimensional swarming model with helical trajectories}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {104}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {1}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.104.014216}, pages = {7}, year = {2021}, abstract = {We investigate the transition from incoherence to global collective motion in a three-dimensional swarming model of agents with helical trajectories, subject to noise and global coupling. Without noise this model was recently proposed as a generalization of the Kuramoto model and it was found that alignment of the velocities occurs discontinuously for arbitrarily small attractive coupling. Adding noise to the system resolves this singular limit and leads to a continuous transition, either to a directed collective motion or to center-of-mass rotations.}, language = {en} } @article{KerneckerFienitzNendeletal.2022, author = {Kernecker, Maria and Fienitz, Meike and Nendel, Claas and Paetzig, Marlene and Walzl, Karin Pirhofer and Raatz, Larissa and Schmidt, Martin and Wulf, Monika and Zscheischler, Jana}, title = {Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields}, series = {Ecological solutions and evidence}, volume = {3}, journal = {Ecological solutions and evidence}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {2688-8319}, doi = {10.1002/2688-8319.12122}, pages = {7}, year = {2022}, abstract = {Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.}, language = {en} } @article{SchulzeMakuchWagnerKounavesetal.2018, author = {Schulze-Makuch, Dirk and Wagner, Dirk and Kounaves, Samuel P. and Mangelsdorf, Kai and Devine, Kevin G. and de Vera, Jean-Pierre and Schmitt-Kopplin, Philippe and Grossart, Hans-Peter and Parro, Victor and Kaupenjohann, Martin and Galy, Albert and Schneider, Beate and Airo, Alessandro and Froesler, Jan and Davila, Alfonso F. and Arens, Felix L. and Caceres, Luis and Cornejo, Francisco Solis and Carrizo, Daniel and Dartnell, Lewis and DiRuggiero, Jocelyne and Flury, Markus and Ganzert, Lars and Gessner, Mark O. and Grathwohl, Peter and Guan, Lisa and Heinz, Jacob and Hess, Matthias and Keppler, Frank and Maus, Deborah and McKay, Christopher P. and Meckenstock, Rainer U. and Montgomery, Wren and Oberlin, Elizabeth A. and Probst, Alexander J. and Saenz, Johan S. and Sattler, Tobias and Schirmack, Janosch and Sephton, Mark A. and Schloter, Michael and Uhl, Jenny and Valenzuela, Bernardita and Vestergaard, Gisle and Woermer, Lars and Zamorano, Pedro}, title = {Transitory microbial habitat in the hyperarid Atacama Desert}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1714341115}, pages = {2670 -- 2675}, year = {2018}, language = {en} } @phdthesis{Vossenkuhl2015, author = {Vossenkuhl, Birgit}, title = {Transmission of MRSA along the meat supply chain}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-85918}, school = {Universit{\"a}t Potsdam}, pages = {141}, year = {2015}, abstract = {Methicillin-resistente Staphylococcus aureus (MRSA) z{\"a}hlen zu den bedeutendsten antibiotikaresistenten Pathogenen, die vor allem in Krankenh{\"a}usern aber auch außerhalb von Einrichtungen des Gesundheitswesens weit verbreitet sind. Seit einigen Jahren ist eine neue Generation von MRSA auf dem Vormarsch, die vor allem Nutztierbest{\"a}nde als neue Nische besiedelt. Diese sogenannten Nutztier-assoziierten MRSA wurden wiederholt bei wirtschaftlich bedeutenden Nutztieren sowie daraus gewonnenem Fleisch nachgewiesen. Im Rahmen der vorliegenden Arbeit wurde ein methodischer Ansatz verfolgt, um die Hypothese einer m{\"o}glichen {\"U}bertragung von Nutztier-assoziierten MRSA entlang der Lebensmittelkette vom Tier auf dessen Fleisch zu best{\"a}tigen. Angepasst an die Unterschiede in den verf{\"u}gbaren Daten wurden daf{\"u}r zwei neue Konzepte erstellt. Zur Analyse der {\"U}bertragung von MRSA entlang der Schlachtkette wurde ein mathematisches Modell des Schweineschlachtprozesses entwickelt, welches dazu geeignet ist, den Verlauf der MRSA-Pr{\"a}valenz entlang der Schlachtkette zu quantifizieren sowie kritische Prozessschritte f{\"u}r eine MRSA-{\"U}bertragung zu identifizieren. Anhand von Pr{\"a}valenzdaten ist es dem Modell m{\"o}glich, die durchschnittlichen MRSA-Eliminations- und Kontaminationsraten jedes einzelnen Prozessschrittes zu sch{\"a}tzen, die anschließend in eine Monte-Carlo-Simulation einfließen. Im Ergebnis konnte gezeigt werden, dass es generell m{\"o}glich ist, die MRSA Pr{\"a}valenz im Laufe des Schlachtprozesses auf ein niedriges finales Niveau zwischen 0,15 bis 1,15\% zu reduzieren. Vor allem das Br{\"u}hen und Abfl{\"a}mmen der Schlachtk{\"o}rper wurden als kritische Prozesse im Hinblick auf eine MRSA-Dekontamination identifiziert. In Deutschland werden regelm{\"a}ßig MRSA-Pr{\"a}valenz und Typisierungsdaten auf allen Stufen der Lebensmittelkette verschiedener Nutztiere erfasst. Um die MRSA-Daten dieser Querschnittstudie hinsichtlich einer m{\"o}glichen {\"U}bertragung entlang der Kette zu analysieren, wurde ein neuer statistischer Ansatz entwickelt. Hierf{\"u}r wurde eine Chi-Quadrat-Statistik mit der Berechnung des Czekanowski-{\"A}hnlichkeitsindex kombiniert, um Unterschiede in der Verteilung stammspezifischer Eigenschaften zwischen MRSA aus dem Stall, von Karkassen nach der Schlachtung und aus Fleisch im Einzelhandel zu quantifizieren. Die Methode wurde am Beispiel der Putenfleischkette implementiert und zudem bei der Analyse der Kalbfleischkette angewendet. Die durchgehend hohen {\"A}hnlichkeitswerte zwischen den einzelnen Proben weisen auf eine m{\"o}gliche {\"U}bertragung von MRSA entlang der Lebensmittelkette hin. Die erarbeiteten Methoden sind nicht spezifisch bez{\"u}glich Prozessketten und Pathogenen. Sie bieten somit einen großen Anwendungsbereich und erweitern das Methodenspektrum zur Bewertung bakterieller {\"U}bertragungswege.}, language = {en} } @article{XiongStibollerGlabonjatetal.2020, author = {Xiong, Chan and Stiboller, Michael and Glabonjat, Ronald A. and Rieger, Jaqueline and Paton, Lhiam and Francesconi, Kevin A.}, title = {Transport of arsenolipids to the milk of a nursing mother after consuming salmon fish}, series = {Journal of trace elements in medicine and biology}, volume = {61}, journal = {Journal of trace elements in medicine and biology}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {0946-672X}, doi = {10.1016/j.jtemb.2020.126502}, pages = {6}, year = {2020}, abstract = {Objective: We address two questions relevant to infants' exposure to potentially toxic arsenolipids, namely, are the arsenolipids naturally present in fish transported intact to a mother's milk, and what is the efficiency of this transport. Methods: We investigated the transport of arsenolipids and other arsenic species present in fish to mother's milk by analyzing the milk of a single nursing mother at 15 sampling times over a 3-day period after she had consumed a meal of salmon. Total arsenic values were obtained by elemental mass spectrometry, and arsenic species were measured by HPLC coupled to both elemental and molecular mass spectrometry. Results: Total arsenic increased from background levels (0.1 mu g As kg(-1)) to a peak value of 1.72 lig As kg(-1) eight hours after the fish meal. The pattern for arsenolipids was similar to that of total arsenic, increasing from undetectable background levels (< 0.01 mu g As kg(-1)) to a peak after eight hours of 0.45 mu g As kg(-1). Most of the remaining total arsenic in the milk was accounted for by arsenobetaine. The major arsenolipids in the salmon were arsenic hydrocarbons (AsHCs; 55 \% of total arsenolipids), and these compounds were also the dominant arsenolipids in the milk where they contributed over 90 \% of the total arsenolipids. Conclusions: Our study has shown that ca 2-3 \% of arsenic hydrocarbons, natural constituents of fish, can be directly transferred unchanged to the milk of a nursing mother. In view of the potential neurotoxicity of AsHCs, the effects of these compounds on the brain developmental stage of infants need to be investigated.}, language = {en} } @phdthesis{Duensing2013, author = {Duensing, Nina}, title = {Transport processes in the arbuscular mycorrhizal symbiosis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-68210}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {The nutrient exchange between plant and fungus is the key element of the arbuscular mycorrhizal (AM) symbiosis. The fungus improves the plant's uptake of mineral nutrients, mainly phosphate, and water, while the plant provides the fungus with photosynthetically assimilated carbohydrates. Still, the knowledge about the mechanisms of the nutrient exchange between the symbiotic partners is very limited. Therefore, transport processes of both, the plant and the fungal partner, are investigated in this study. In order to enhance the understanding of the molecular basis underlying this tight interaction between the roots of Medicago truncatula and the AM fungus Rhizophagus irregularis, genes involved in transport processes of both symbiotic partners are analysed here. The AM-specific regulation and cell-specific expression of potential transporter genes of M. truncatula that were found to be specifically regulated in arbuscule-containing cells and in non-arbusculated cells of mycorrhizal roots was confirmed. A model for the carbon allocation in mycorrhizal roots is suggested, in which carbohydrates are mobilized in non-arbusculated cells and symplastically provided to the arbuscule-containing cells. New insights into the mechanisms of the carbohydrate allocation were gained by the analysis of hexose/H+ symporter MtHxt1 which is regulated in distinct cells of mycorrhizal roots. Metabolite profiling of leaves and roots of a knock-out mutant, hxt1, showed that it indeed does have an impact on the carbohydrate balance in the course of the symbiosis throughout the whole plant, and on the interaction with the fungal partner. The primary metabolite profile of M. truncatula was shown to be altered significantly in response to mycorrhizal colonization. Additionally, molecular mechanisms determining the progress of the interaction in the fungal partner of the AM symbiosis were investigated. The R. irregularis transcriptome in planta and in extraradical tissues gave new insight into genes that are differentially expressed in these two fungal tissues. Over 3200 fungal transcripts with a significantly altered expression level in laser capture microdissection-collected arbuscules compared to extraradical tissues were identified. Among them, six previously unknown specifically regulated potential transporter genes were found. These are likely to play a role in the nutrient exchange between plant and fungus. While the substrates of three potential MFS transporters are as yet unknown, two potential sugar transporters are might play a role in the carbohydrate flow towards the fungal partner. In summary, this study provides new insights into transport processes between plant and fungus in the course of the AM symbiosis, analysing M. truncatula on the transcript and metabolite level, and provides a dataset of the R. irregularis transcriptome in planta, providing a high amount of new information for future works.}, language = {en} } @misc{VanBelProostVanNesteetal.2013, author = {Van Bel, Michiel and Proost, Sebastian and Van Neste, Christophe and Deforce, Dieter and Van de Peer, Yves and Vandepoele, Klaas}, title = {TRAPID}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {900}, issn = {1866-8372}, doi = {10.25932/publishup-43640}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436409}, pages = {12}, year = {2013}, abstract = {Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.}, language = {en} } @article{ApanasewiczGrothScheffleretal.2020, author = {Apanasewicz, Anna and Groth, Detlef and Scheffler, Christiane and Hermanussen, Michael and Piosek, Magdalena and Wychowaniec, Patrycja and Babiszewska, Magdalena and Barbarska, Olga and Ziomkiewicz, Anna}, title = {Traumatized women's infants are bigger than children of mothers without traumas}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger}, volume = {77}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger}, number = {5}, publisher = {Schweizerbart science publishers}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2020/1285}, pages = {359 -- 374}, year = {2020}, abstract = {Life history theory predicts that experiencing stress during the early period of life will result in accelerated growth and earlier maturation. Indeed, animal and some human studies documented a faster pace of growth in the offspring of stressed mothers. Recent advances in epigenetics suggest that the effects of early developmental stress might be passed across the generations. However, evidence for such intergenerational transmission is scarce, at least in humans. Here we report the results of the study investigating the association between childhood trauma in mothers and physical growth in their children during the first months of life. Anthropometric and psychological data were collected from 99 mothers and their exclusively breastfed children at the age of 5 months. The mothers completed the Early Life Stress Questionnaire to assess childhood trauma. The questionnaire includes questions about the most traumatic events that they had experienced before the age of 12 years. Infant growth was evaluated based on the anthropometric measurements of weight, length, and head circumference. Also, to control for the size of maternal investment, the composition of breast milk samples taken at the time of infant anthropometric measurements was investigated. The children of mothers with higher early life stress tended to have higher weight and bigger head circumference. The association between infant anthropometrics and early maternal stress was not affected by breast milk composition, suggesting that the effect of maternal stress on infant growth was independent of the size of maternal investment. Our results demonstrate that early maternal trauma may affect the pace of growth in the offspring and, in consequence, lead to a faster life history strategy. This effect might be explained via changes in offspring epigenetics.}, language = {en} } @phdthesis{Kindermann2024, author = {Kindermann, Liana}, title = {Trees, shrubs, and land-use change}, doi = {10.25932/publishup-64894}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-648943}, school = {Universit{\"a}t Potsdam}, pages = {X, 186}, year = {2024}, abstract = {The global drylands cover nearly half of the terrestrial surface and are home to more than two billion people. In many drylands, ongoing land-use change transforms near-natural savanna vegetation to agricultural land to increase food production. In Southern Africa, these heterogenous savanna ecosystems are also recognized as habitats of many protected animal species, such as elephant, lion and large herds of diverse herbivores, which are of great value for the tourism industry. Here, subsistence farmers and livestock herder communities often live in close proximity to nature conservation areas. Although these land-use transformations are different regarding the future they aspire to, both processes, nature conservation with large herbivores and agricultural intensification, have in common, that they change the vegetation structure of savanna ecosystems, usually leading to destruction of trees, shrubs and the woody biomass they consist of. Such changes in woody vegetation cover and biomass are often regarded as forms of land degradation and forest loss. Global forest conservation approaches and international programs aim to stop degradation processes, also to conserve the carbon bound within wood from volatilization into earth's atmosphere. In search for mitigation options against global climate change savannas are increasingly discussed as potential carbon sinks. Savannas, however, are not forests, in that they are naturally shaped by and adapted to disturbances, such as wildfires and herbivory. Unlike in forests, disturbances are necessary for stable, functioning savanna ecosystems and prevent these ecosystems from forming closed forest stands. Their consequently lower levels of carbon storage in woody vegetation have long been the reason for savannas to be overlooked as a potential carbon sink but recently the question was raised if carbon sequestration programs (such as REDD+) could also be applied to savanna ecosystems. However, heterogenous vegetation structure and chronic disturbances hamper the quantification of carbon stocks in savannas, and current procedures of carbon storage estimation entail high uncertainties due to methodological obstacles. It is therefore challenging to assess how future land-use changes such as agricultural intensification or increasing wildlife densities will impact the carbon storage balance of African drylands. In this thesis, I address the research gap of accurately quantifying carbon storage in vegetation and soils of disturbance-prone savanna ecosystems. I further analyse relevant drivers for both ecosystem compartments and their implications for future carbon storage under land-use change. Moreover, I show that in savannas different carbon storage pools vary in their persistence to disturbance, causing carbon bound in shrub vegetation to be most likely to experience severe losses under land-use change while soil organic carbon stored in subsoils is least likely to be impacted by land-use change in the future. I start with summarizing conventional approaches to carbon storage assessment and where and for which reasons they fail to accurately estimated savanna ecosystem carbon storage. Furthermore, I outline which future-making processes drive land-use change in Southern Africa along two pathways of land-use transformation and how these are likely to influence carbon storage. In the following chapters, I propose a new method of carbon storage estimation which is adapted to the specific conditions of disturbance-prone ecosystems and demonstrate the advantages of this approach in relation to existing forestry methods. Specifically, I highlight sources for previous over- and underestimation of savanna carbon stocks which the proposed methodology resolves. In the following chapters, I apply the new method to analyse impacts of land-use change on carbon storage in woody vegetation in conjunction with the soil compartment. With this interdisciplinary approach, I can demonstrate that indeed both, agricultural intensification and nature conservation with large herbivores, reduce woody carbon storage above- and belowground, but partly sequesters this carbon into the soil organic carbon stock. I then quantify whole-ecosystem carbon storage in different ecosystem compartments (above- and belowground woody carbon in shrubs and trees, respectively, as well as topsoil and subsoil organic carbon) of two savanna vegetation types (scrub savanna and savanna woodland). Moreover, in a space-for-time substitution I analyse how land-use changes impact carbon storage in each compartment and in the whole ecosystem. Carbon storage compartments are found to differ in their persistence to land-use change with carbon bound in shrub biomass being least persistent to future changes and subsoil organic carbon being most stable under changing land-use. I then explore which individual land-use change effects act as drivers of carbon storage through Generalized Additive Models (GAMs) and uncover non-linear effects, especially of elephant browsing, with implications for future carbon storage. In the last chapter, I discuss my findings in the larger context of this thesis and discuss relevant implications for land-use change and future-making decisions in rural Africa.}, language = {en} } @article{GomulaNowakSzczepanskaHermanussenetal.2020, author = {Gomula, Aleksandra and Nowak-Szczepanska, Natalia and Hermanussen, Michael and Scheffler, Christiane and Koziel, Slawomir}, title = {Trends in growth and developmental tempo in boys aged 7 to 18 years between 1966 and 2012 in Poland}, series = {American journal of human biology : the official journal of the Human Biology Council}, volume = {33}, journal = {American journal of human biology : the official journal of the Human Biology Council}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1042-0533}, doi = {10.1002/ajhb.23548}, pages = {7}, year = {2020}, abstract = {Objectives: To assess trends in growth in different developmental periods and trends in developmental tempo in Polish boys between 1966 and 2012. Methods: Data on 34 828 boys aged 7 to 18 years were collected during Polish Anthropological Surveys conducted in 1966, 1978, 1988, and 2012. Biological parameters, related to onset of adolescent growth spurt (OGS) and peak height velocity (PHV), were derived from a Preece-Baines 1 model (PB1). Childhood (height at 7 years of age), pre-adolescent (height at OGS) and adolescent growth (adult height minus height at OGS) were identified. Results: Positive secular trend between 1966 and 2012 in adult height accounted for, on average, 1.5 cm/decade, with varying intensity between the Surveys. Decline in both age at OGS and APHV between 1966 and 2012 (1.5 and 1.4 years, respectively) indicated an acceleration in developmental tempo, on average, by 0.3 year/decade. Increases in the contribution to the trend in adult height gained during growth in particular developmental periods between 1966 and 2012 were as followed-childhood: 0.6\%, pre-adolescent growth: -3.1\%, adolescent growth: 3.1\%. Conclusions: Secular trend in developmental tempo and growth among boys reflects changes in living conditions and socio-political aspirations in Poland during nearly 50 years. Acceleration in tempo is already visible at age at OGS, whereas the trend in adult height occurs largely during adolescence, pointing to different regulation of developmental tempo and growth in body height. This finding emphasizes the importance of extending public health intervention into children's growth up until adolescence.}, language = {en} } @article{MitrovaTadjoungWaffoKaufmannetal.2018, author = {Mitrova, Biljana and Tadjoung Waffo, Armel Franklin and Kaufmann, Paul and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke and Wollenberger, Ulla}, title = {Trimethylamine N-Oxide Electrochemical Biosensor with a Chimeric Enzyme}, series = {ChemElectroChem}, volume = {6}, journal = {ChemElectroChem}, number = {6}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2196-0216}, doi = {10.1002/celc.201801422}, pages = {1732 -- 1737}, year = {2018}, abstract = {For the first time, an enzyme-based electrochemical biosensor system for determination of trimethylamine N-oxide (TMAO) is described. It employs an active chimeric variant of TorA in combination with an enzymatically deoxygenating system and a low-potential mediator for effective regeneration of the enzyme and cathodic current generation. TMAO reductase (TorA) is a molybdoenzyme found in marine and most enterobacteria that specifically catalyzes the reduction of TMAO to trimethylamine (TMA). The chimeric TorA, named TorA-FDH, corresponds to the apoform of TorA from Escherichia coli reconstituted with the molybdenum cofactor from formate dehydrogenase (FDH). Each enzyme, TorA and TorA-FDH, was immobilized on the surface of a carbon electrode and protected with a dialysis membrane. The biosensor operates at an applied potential of -0.8V [vs. Ag/AgCl (1M KCl)] under ambient air conditions thanks to an additional enzymatic O-2-scavenger system. A comparison between the two enzymatic sensors revealed a much higher sensitivity for the biosensor with immobilized TorA-FDH. This biosensor exhibits a sensitivity of 14.16nA/M TMAO in a useful measuring range of 2-110M with a detection limit of LOD=2.96nM (S/N=3), and was similar for TMAO in buffer and in spiked serum samples. With a response time of 16 +/- 2 s, the biosensor is stable over prolonged daily measurements (n=20). This electrochemical biosensor provides suitable applications in detecting TMAO levels in human serum.}, language = {en} } @article{KaechDennisVorburger2021, author = {Kaech, Heidi and Dennis, Alice B. and Vorburger, Christoph}, title = {Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa}, series = {BMC genomics}, volume = {22}, journal = {BMC genomics}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-021-07742-8}, pages = {21}, year = {2021}, abstract = {Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.}, language = {en} } @misc{DammhahnGoodman2014, author = {Dammhahn, Melanie and Goodman, Steven M.}, title = {Trophic niche differentiation and microhabitat utilization revealed by stable isotope analyses in a dry-forest bat assemblage at Ankarana, northern Madagascar}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-41515}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415157}, pages = {97 -- 109}, year = {2014}, abstract = {Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measuredstable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4\% in delta N-15 and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3\% enriched over plants) and different insectivorous bats as secondary consumers (c. 4\% enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of delta C-13-delta N-15 bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.}, language = {en} } @article{MehnerAttermeyerBraunsetal.2022, author = {Mehner, Thomas and Attermeyer, Katrin and Brauns, Mario and Brothers, Soren and Hilt, Sabine and Scharnweber, Inga Kristin and Dorst, Renee Minavan and Vanni, Michael J. and Gaedke, Ursula}, title = {Trophic transfer efficiency in lakes}, series = {Ecosystems}, volume = {25}, journal = {Ecosystems}, number = {8}, publisher = {Springer}, address = {New York}, issn = {1432-9840}, doi = {10.1007/s10021-022-00776-3}, pages = {1628 -- 1652}, year = {2022}, abstract = {Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate. We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE. Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes. Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment. We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups. This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms. An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production. We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes.}, language = {en} } @article{KehlmaierBarlowHastingsetal.2017, author = {Kehlmaier, Christian and Barlow, Axel and Hastings, Alexander K. and Vamberger, Melita and Paijmans, Johanna L. A. and Steadman, David W. and Albury, Nancy A. and Franz, Richard and Hofreiter, Michael and Fritz, Uwe}, title = {Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum}, series = {Proceedings of the Royal Society of London : Series B, Biological sciences}, volume = {284}, journal = {Proceedings of the Royal Society of London : Series B, Biological sciences}, publisher = {The Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2016.2235}, pages = {8}, year = {2017}, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, language = {en} } @article{FrancoObregonCambriaGreutertetal.2018, author = {Franco-Obregon, Alfredo and Cambria, Elena and Greutert, Helen and Wernas, Timon and Hitzl, Wolfgang and Egli, Marcel and Sekiguchi, Miho and Boos, Norbert and Hausmann, Oliver and Ferguson, Stephen J. and Kobayashi, Hiroshi and W{\"u}rtz-Kozak, Karin}, title = {TRPC6 in simulated microgravity of intervertebral disc cells}, series = {European Spine Journal}, volume = {27}, journal = {European Spine Journal}, number = {10}, publisher = {Springer}, address = {New York}, issn = {0940-6719}, doi = {10.1007/s00586-018-5688-8}, pages = {2621 -- 2630}, year = {2018}, abstract = {Purpose Prolonged bed rest and microgravity in space cause intervertebral disc (IVD) degeneration. However, the underlying molecular mechanisms are not completely understood. Transient receptor potential canonical (TRPC) channels are implicated in mechanosensing of several tissues, but are poorly explored in IVDs. Methods Primary human IVD cells from surgical biopsies composed of both annulus fibrosus and nucleus pulposus (passage 1-2) were exposed to simulated microgravity and to the TRPC channel inhibitor SKF-96365 (SKF) for up to 5days. Proliferative capacity, cell cycle distribution, senescence and TRPC channel expression were analyzed. Results Both simulated microgravity and TRPC channel antagonism reduced the proliferative capacity of IVD cells and induced senescence. While significant changes in cell cycle distributions (reduction in G1 and accumulation in G2/M) were observed upon SKF treatment, the effect was small upon 3days of simulated microgravity. Finally, downregulation of TRPC6 was shown under simulated microgravity. Conclusions Simulated microgravity and TRPC channel inhibition both led to reduced proliferation and increased senescence. Furthermore, simulated microgravity reduced TRPC6 expression. IVD cell senescence and mechanotransduction may hence potentially be regulated by TRPC6 expression. This study thus reveals promising targets for future studies.}, language = {en} } @misc{LaraNitzeGrosseetal.2018, author = {Lara, Mark J. and Nitze, Ingmar and Große, Guido and McGuire, David}, title = {Tundra landform and vegetation productivity trend maps for the Arctic Coastal Plain of northern Alaska}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1035}, issn = {1866-8372}, doi = {10.25932/publishup-45987}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459875}, pages = {12}, year = {2018}, abstract = {Arctic tundra landscapes are composed of a complex mosaic of patterned ground features, varying in soil moisture, vegetation composition, and surface hydrology over small spatial scales (10-100 m). The importance of microtopography and associated geomorphic landforms in influencing ecosystem structure and function is well founded, however, spatial data products describing local to regional scale distribution of patterned ground or polygonal tundra geomorphology are largely unavailable. Thus, our understanding of local impacts on regional scale processes (e.g., carbon dynamics) may be limited. We produced two key spatiotemporal datasets spanning the Arctic Coastal Plain of northern Alaska (similar to 60,000 km(2)) to evaluate climate-geomorphological controls on arctic tundra productivity change, using (1) a novel 30m classification of polygonal tundra geomorphology and (2) decadal-trends in surface greenness using the Landsat archive (1999-2014). These datasets can be easily integrated and adapted in an array of local to regional applications such as (1) upscaling plot-level measurements (e.g., carbon/energy fluxes), (2) mapping of soils, vegetation, or permafrost, and/or (3) initializing ecosystem biogeochemistry, hydrology, and/or habitat modeling.}, language = {en} } @phdthesis{Sarlet2023, author = {Sarlet, Adrien}, title = {Tuning the viscoelasticity of Escherichia coli biofilms}, school = {Universit{\"a}t Potsdam}, pages = {143}, year = {2023}, abstract = {Biofilms are heterogeneous structures made of microorganisms embedded in a self-secreted extracellular matrix. Recently, biofilms have been studied as sustainable living materials with a focus on the tuning of their mechanical properties. One way of doing so is to use metal ions. In particular biofilms have been shown to stiffen in presence of some metal cations and to soften in presence of others. However, the specificity and the determinants of those interactions vary between species. While Escherichia coli is a widely studied model organism, little is known concerning the response of its biofilms to metal ions. In this work, we aimed at tuning the mechanics of E. coli biofilms by acting on the interplay between matrix composition and metal cations. To do so, we worked with E. coli strains producing a matrix composed of curli amyloid fibres or phosphoethanolamine-cellulose (pEtN-cellulose) fibres or both. The viscoelastic behaviour of the resulting biofilms was investigated with rheology after incubation with one of the following metal ion solutions: FeCl3, AlCl3, ZnCl2 and CaCl2 or ultrapure water. We observed that the strain producing both fibres stiffen by a factor of two when exposed to the trivalent metal cations Al(III) and Fe(III) while no such response is observed for the bivalent cations Zn(II) and Ca(II). Strains producing only one matrix component did not show any stiffening in response to either cation, but even a small softening. In order to investigate further the contribution of each matrix component to the mechanical properties, we introduced additional bacterial strains producing curli fibres in combination with non-modified cellulose, non-modified cellulose only or neither component. We measured biofilms produced by those different strains with rheology and without any solution. Since rheology does not preserve the architecture of the matrix, we compared those results to the mechanical properties of biofilms probed with the non-destructive microindentation. The microindentation results showed that biofilm stiffness is mainly determined by the presence of curli amyloid fibres in the matrix. However, this clear distinction between biofilm matrices containing or not containing curli is absent from the rheology results, i.e. following partial destruction of the matrix architecture. In addition, rheology also indicated a negative impact of curli on biofilm yield stress and flow stress. This suggests that curli fibres are more brittle and therefore more affected by the mechanical treatments. Finally, to examine the molecular interactions between the biofilms and the metal cations, we used Attenuated total reflectance - Fourier transform infrared spectroscopy (ATR-FTIR) to study the three E.coli strains producing a matrix composed of curli amyloid fibres, pEtN-cellulose fibres or both. We measured biofilms produced by those strains in presence of each of the aforementioned metal cation solutions or ultrapure water. We showed that the three strains cannot be distinguished based on their FTIR spectra and that metal cations seem to have a non-specific effect on bacterial membranes in absence of pEtN-cellulose. We subsequently conducted similar experiments on purified curli or pEtN-cellulose fibres. The spectra of the pEtN-cellulose fibres revealed a non-valence-specific interaction between metal cations and the phosphate of the pEtN-modification. Altogether, these results demonstrate that the mechanical properties of E. coli biofilms can be tuned via incubation with metal ions. While the mechanism involving curli fibres remains to be determined, metal cations seem to adsorb onto pEtN-cellulose and this is not valence-specific. This work also underlines the importance of matrix architecture to biofilm mechanics and emphasises the specificity of each matrix composition.}, language = {en} } @article{YildizLeimkuehler2021, author = {Yildiz, Tugba and Leimk{\"u}hler, Silke}, title = {TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli}, series = {Journal of bacteriology}, volume = {203}, journal = {Journal of bacteriology}, number = {7}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {1098-5530}, doi = {10.1128/JB.00659-20}, pages = {20}, year = {2021}, abstract = {To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.
IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.}, language = {en} } @article{KamaliLoriteWebberetal.2022, author = {Kamali, Bahareh and Lorite, Ignacio J. and Webber, Heidi A. and Rezaei, Ehsan Eyshi and Gabaldon-Leal, Clara and Nendel, Claas and Siebert, Stefan and Ramirez-Cuesta, Juan Miguel and Ewert, Frank and Ojeda, Jonathan J.}, title = {Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Macmillan Publishers Limited,}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-022-08056-9}, pages = {13}, year = {2022}, abstract = {This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability. Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields. The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017). By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29\% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66\%). However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses. Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale.}, language = {en} } @phdthesis{Ogden2022, author = {Ogden, Michael}, title = {Uncovering the interplay between nutrient availability and cellulose biosynthesis inhibitor activity}, school = {Universit{\"a}t Potsdam}, pages = {XI, 124}, year = {2022}, abstract = {All plant cells are surrounded by a dynamic, carbohydrate-rich extracellular matrix known as the cell wall. Nutrient availability affects cell wall composition via uncharacterized regulatory mechanisms, and cellulose deficient mutants develop a hypersensitive root response to growth on high concentrations of nitrate. Since cell walls account for the bulk of plant biomass, it is important to understand how nutrients regulate cell walls. This could provide important knowledge for directing fertilizer treatments and engineering plants with higher nutrient use efficiency. The direct effect of nitrate on cell wall synthesis was investigated through growth assays on varying concentrations of nitrate, measuring cellulose content of roots and shoots, and assessing cellulose synthase activity (CESA) using live cell imaging with spinning disk confocal microscopy. A forward genetic screen was developed to isolate mutants impaired in nutrient-mediated cell wall regulation, revealing that cellulose biosynthesis inhibitor (CBI) activity is modulated by nutrient availability. Various non-CESA mutants were isolated that displayed CBI resistance, with the majority of mutations causing perturbation of mitochondria-localized proteins. To investigate mitochondrial involvement, the CBI mechanism of action was investigated using a reverse genetic screen, a targeted pharmacological screen, and -omics approaches. The results generated suggest that CBI-induced cellulose inhibition is due to off-target effects. This provides the groundwork to investigate uncharacterized processes of CESA regulation and adds valuable knowledge to the understanding of CBI activity, which could be harnessed to develop new and improved herbicides.}, language = {en} } @article{LehmannEccardScheffleretal.2018, author = {Lehmann, Andreas and Eccard, Jana and Scheffler, Christiane and Kurvers, Ralf H. J. M. and Dammhahn, Melanie}, title = {Under pressure: human adolescents express a pace-of-life syndrome}, series = {Behavioral ecology and sociobiology}, volume = {72}, journal = {Behavioral ecology and sociobiology}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0340-5443}, doi = {10.1007/s00265-018-2465-y}, pages = {15}, year = {2018}, abstract = {The pace-of-life syndrome (POLS) hypothesis posits that life-history characteristics, among individual differences in behavior, and physiological traits have coevolved in response to environmental conditions. This hypothesis has generated much research interest because it provides testable predictions concerning the association between the slow-fast life-history continuum and behavioral and physiological traits. Although humans are among the most well-studied species and similar concepts exist in the human literature, the POLS hypothesis has not yet been directly applied to humans. Therefore, we aimed to (i) test predicted relationships between life history, physiology, and behavior in a human population and (ii) better integrate the POLS hypothesis with other similar concepts. Using data of a representative sample of German adolescents, we extracted maturation status for girls (menarche, n = 791) and boys (voice break, n = 486), and a set of health-related risk-taking behaviors and cardiovascular parameters. Maturation status and health-related risk behavior as well as maturation status and cardiovascular physiology covaried in boys and girls. Fast maturing boys and girls had higher blood pressure and expressed more risk-taking behavior than same-aged slow maturing boys and girls, supporting general predictions of the POLS hypothesis. Only some physiological and behavioral traits were positively correlated, suggesting that behavioral and physiological traits might mediate life-history trade-offs differently. Moreover, some aspects of POLS were sex-specific. Overall, the POLS hypothesis shares many similarities with other conceptual frameworks from the human literature and these concepts should be united more thoroughly to stimulate the study of POLS in humans and other animals. Significance statement The pace-of-life syndrome (POLS) hypothesis suggests that life history, behavioral and physiological traits have coevolved in response to environmental conditions. Here, we tested this link in a representative sample of German adolescents, using data from a large health survey (the KIGGs study) containing information on individual age and state of maturity for girls and boys, and a set of health-related risk-taking behaviors and cardiovascular parameters. We found that fast maturing girls and boys had overall higher blood pressure and expressed more risk-taking behavior than same-aged slow maturing girls and boys. Only some behavioral and physiological traits were positively correlated, suggesting that behavioral and physiological traits might mediate life-history trade-offs differently and not necessarily form a syndrome. Our results demonstrate a general link between life history, physiological and behavioral traits in humans, while simultaneously highlighting a more complex and rich set of relationships, since not all relationships followed predictions by the POLS hypothesis.}, language = {en} } @phdthesis{Schaefer2019, author = {Sch{\"a}fer, Merlin}, title = {Understanding and predicting global change impacts on migratory birds}, doi = {10.25932/publishup-43925}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439256}, school = {Universit{\"a}t Potsdam}, pages = {XIV, 153}, year = {2019}, abstract = {This is a publication-based dissertation comprising three original research stud-ies (one published, one submitted and one ready for submission; status March 2019). The dissertation introduces a generic computer model as a tool to investigate the behaviour and population dynamics of animals in cyclic environments. The model is further employed for analysing how migratory birds respond to various scenarios of altered food supply under global change. Here, ecological and evolutionary time-scales are considered, as well as the biological constraints and trade-offs the individual faces, which ultimately shape response dynamics at the population level. Further, the effect of fine-scale temporal patterns in re-source supply are studied, which is challenging to achieve experimentally. My findings predict population declines, altered behavioural timing and negative carry-over effects arising in migratory birds under global change. They thus stress the need for intensified research on how ecological mechanisms are affected by global change and for effective conservation measures for migratory birds. The open-source modelling software created for this dissertation can now be used for other taxa and related research questions. Overall, this thesis improves our mechanistic understanding of the impacts of global change on migratory birds as one prerequisite to comprehend ongoing global biodiversity loss. The research results are discussed in a broader ecological and scientific context in a concluding synthesis chapter.}, language = {en} } @phdthesis{Ullmann2018, author = {Ullmann, Wiebke}, title = {Understanding animal movement behaviour in dynamic agricultural landscapes}, doi = {10.25932/publishup-42715}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427153}, school = {Universit{\"a}t Potsdam}, pages = {vii, 183}, year = {2018}, abstract = {The movement of organisms has formed our planet like few other processes. Movements shape populations, communities, entire ecosystems, and guarantee fundamental ecosystem functions and services, like seed dispersal and pollination. Global, regional and local anthropogenic impacts influence animal movements across ecosystems all around the world. In particular, land-use modification, like habitat loss and fragmentation disrupt movements between habitats with profound consequences, from increased disease transmissions to reduced species richness and abundance. However, neither the influence of anthropogenic change on animal movement processes nor the resulting effects on ecosystems are well understood. Therefore, we need a coherent understanding of organismal movement processes and their underlying mechanisms to predict and prevent altered animal movements and their consequences for ecosystem functions. In this thesis I aim at understanding the influence of anthropogenically caused land-use change on animal movement processes and their underlying mechanisms. In particular, I am interested in the synergistic influence of large-scale landscape structure and fine-scale habitat features on basic-level movement behaviours (e.g. the daily amount of time spend running, foraging, and resting) and their emerging higher-level movements (home range formation). Based on my findings, I identify the likely consequences of altered animal movements that lead to the loss of species richness and abundances. The study system of my thesis are hares in agricultural landscapes. European brown hares (Lepus europaeus) are perfectly suited to study animal movements in agricultural landscapes, as hares are hermerophiles and prefer open habitats. They have historically thrived in agricultural landscapes, but their numbers are in decline. Agricultural areas are undergoing strong land-use changes due to increasing food demand and fast developing agricultural technologies. They are already the largest land-use class, covering 38\% of the world's terrestrial surface. To consider the relevance of a given landscape structure for animal movement behaviour I selected two differently structured agricultural landscapes - a simple landscape in Northern Germany with large fields and few landscape elements (e.g. hedges and tree stands), and a complex landscape in Southern Germany with small fields and many landscape elements. I applied GPS devices (hourly fixes) with internal high-resolution accelerometers (4 min samples) to track hares, receiving an almost continuous observation of the animals' behaviours via acceleration analyses. I used the spatial and behavioural information in combination with remote sensing data (normalized difference vegetation index, or NDVI, a proxy for resource availability), generating an almost complete idea of what the animal was doing when, why and where. Apart from landscape structure (represented by the two differently structured study areas), I specifically tested whether the following fine-scale habitat features influence animal movements: resource, agricultural management events, habitat diversity, and habitat structure. My results show that, irrespective of the movement process or mechanism and the type of fine-scale habitat features, landscape structure was the overarching variable influencing hare movement behaviour. High resource variability forces hares to enlarge their home ranges, but only in the simple and not in the complex landscape. Agricultural management events result in home range shifts in both landscapes, but force hares to increase their home ranges only in the simple landscape. Also the preference of habitat patches with low vegetation and the avoidance of high vegetation, was stronger in the simple landscape. High and dense crop fields restricted hare movements temporarily to very local and small habitat patch remnants. Such insuperable barriers can separate habitat patches that were previously connected by mobile links. Hence, the transport of nutrients and genetic material is temporarily disrupted. This mechanism is also working on a global scale, as human induced changes from habitat loss and fragmentation to expanding monocultures cause a reduction in animal movements worldwide. The mechanisms behind those findings show that higher-level movements, like increasing home ranges, emerge from underlying basic-level movements, like the behavioural modes. An increasing landscape simplicity first acts on the behavioural modes, i.e. hares run and forage more, but have less time to rest. Hence, the emergence of increased home range sizes in simple landscapes is based on an increased proportion of time running and foraging, largely due to longer travelling times between distant habitats and scarce resource items in the landscape. This relationship was especially strong during the reproductive phase, demonstrating the importance of high-quality habitat for reproduction and the need to keep up self-maintenance first, in low quality areas. These changes in movement behaviour may release a cascade of processes that start with more time being allocated to running and foraging, resulting into an increased energy expenditure and may lead to a decline in individual fitness. A decrease in individual fitness and reproductive output will ultimately affect population viability leading to local extinctions. In conclusion, I show that landscape structure has one of the most important effects on hare movement behaviour. Synergistic effects of landscape structure, and fine-scale habitat features, first affect and modify basic-level movement behaviours, that can scales up to altered higher-level movements and may even lead to the decline of species richness and abundances, and the disruption of ecosystem functions. Understanding the connection between movement mechanisms and processes can help to predict and prevent anthropogenically induced changes in movement behaviour. With regard to the paramount importance of landscape structure, I strongly recommend to decrease the size of agricultural fields and increase crop diversity. On the small-scale, conservation policies should assure the year round provision of areas with low vegetation height and high quality forage. This could be done by generating wildflower strips and additional (semi-) natural habitat patches. This will not only help to increase the populations of European brown hares and other farmland species, but also ensure and protects the continuity of mobile links and their intrinsic value for sustaining important ecosystem functions and services.}, language = {en} } @phdthesis{Teckentrup2019, author = {Teckentrup, Lisa}, title = {Understanding predator-prey interactions}, doi = {10.25932/publishup-43162}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431624}, school = {Universit{\"a}t Potsdam}, pages = {ix, 133}, year = {2019}, abstract = {Predators can have numerical and behavioral effects on prey animals. While numerical effects are well explored, the impact of behavioral effects is unclear. Furthermore, behavioral effects are generally either analyzed with a focus on single individuals or with a focus on consequences for other trophic levels. Thereby, the impact of fear on the level of prey communities is overlooked, despite potential consequences for conservation and nature management. In order to improve our understanding of predator-prey interactions, an assessment of the consequences of fear in shaping prey community structures is crucial. In this thesis, I evaluated how fear alters prey space use, community structure and composition, focusing on terrestrial mammals. By integrating landscapes of fear in an existing individual-based and spatially-explicit model, I simulated community assembly of prey animals via individual home range formation. The model comprises multiple hierarchical levels from individual home range behavior to patterns of prey community structure and composition. The mechanistic approach of the model allowed for the identification of underlying mechanism driving prey community responses under fear. My results show that fear modified prey space use and community patterns. Under fear, prey animals shifted their home ranges towards safer areas of the landscape. Furthermore, fear decreased the total biomass and the diversity of the prey community and reinforced shifts in community composition towards smaller animals. These effects could be mediated by an increasing availability of refuges in the landscape. Under landscape changes, such as habitat loss and fragmentation, fear intensified negative effects on prey communities. Prey communities in risky environments were subject to a non-proportional diversity loss of up to 30\% if fear was taken into account. Regarding habitat properties, I found that well-connected, large safe patches can reduce the negative consequences of habitat loss and fragmentation on prey communities. Including variation in risk perception between prey animals had consequences on prey space use. Animals with a high risk perception predominantly used safe areas of the landscape, while animals with a low risk perception preferred areas with a high food availability. On the community level, prey diversity was higher in heterogeneous landscapes of fear if individuals varied in their risk perception compared to scenarios in which all individuals had the same risk perception. Overall, my findings give a first, comprehensive assessment of the role of fear in shaping prey communities. The linkage between individual home range behavior and patterns at the community level allows for a mechanistic understanding of the underlying processes. My results underline the importance of the structure of the landscape of fear as a key driver of prey community responses, especially if the habitat is threatened by landscape changes. Furthermore, I show that individual landscapes of fear can improve our understanding of the consequences of trait variation on community structures. Regarding conservation and nature management, my results support calls for modern conservation approaches that go beyond single species and address the protection of biotic interactions.}, language = {en} } @article{GhoddousiVanCayzeeleNegahdaretal.2022, author = {Ghoddousi, Arash and Van Cayzeele, Corinna and Negahdar, Pegah and Soofi, Mahmood and Kh. Hamidi, Amirhossein and Bleyhl, Benjamin and Fandos, Guillermo and Khorozyan, Igor and Waltert, Matthias and Kuemmerle, Tobias}, title = {Understanding spatial patterns of poaching pressure using ranger logbook data to optimize future patrolling strategies}, series = {Ecological applications : a publication of the Ecological Society of America}, volume = {32}, journal = {Ecological applications : a publication of the Ecological Society of America}, number = {5}, publisher = {Wiley}, address = {Hoboken}, issn = {1051-0761}, doi = {10.1002/eap.2601}, pages = {13}, year = {2022}, abstract = {Poaching is driving many species toward extinction, and as a result, lowering poaching pressure is a conservation priority. This requires understanding where poaching pressure is high and which factors determine these spatial patterns. However, the cryptic and illegal nature of poaching makes this difficult. Ranger patrol data, typically recorded in protected area logbooks, contain information on patrolling efforts and poaching detection and should thus provide opportunities for a better understanding of poaching pressure. However, these data are seldom analyzed and rarely used to inform adaptive management strategies. We developed a novel approach to making use of analog logbook records to map poaching pressure and to test environmental criminology and predator-prey relationship hypotheses explaining poaching patterns. We showcase this approach for Golestan National Park in Iran, where poaching has substantially depleted ungulate populations. We digitized data from >4800 ranger patrols from 2014 to 2016 and used an occupancy modeling framework to relate poaching to (1) accessibility, (2) law enforcement, and (3) prey availability factors. Based on predicted poaching pressure and patrolling intensity, we provide suggestions for future patrol allocation strategies. Our results revealed a low probability (12\%) of poacher detection during patrols. Poaching distribution was best explained by prey availability, indicating that poachers target areas with high concentrations of ungulates. Poaching pressure was estimated to be high (>0.49) in 39\% of our study area. To alleviate poaching pressure, we recommend ramping up patrolling intensity in 12\% of the national park, which could be achievable by reducing excess patrols in about 20\% of the park. However, our results suggest that for 27\% of the park, it is necessary to improve patrolling quality to increase detection probability of poaching, for example, by closing temporal patrolling gaps or expanding informant networks. Our approach illustrates that analog ranger logbooks are an untapped resource for evidence-based and adaptive planning of protected area management. Using this wealth of data can open up new avenues to better understand poaching and its determinants, to expand effectiveness assessments to the past, and, more generally, to allow for strategic conservation planning in protected areas.}, language = {en} } @article{StoneNicenboimVasishthetal.2023, author = {Stone, Kate and Nicenboim, Bruno and Vasishth, Shravan and R{\"o}sler, Frank}, title = {Understanding the effects of constraint and predictability in ERP}, series = {Neurobiology of language}, volume = {4}, journal = {Neurobiology of language}, number = {2}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, issn = {2641-4368}, doi = {10.1162/nol_a_00094}, pages = {221 -- 256}, year = {2023}, abstract = {Intuitively, strongly constraining contexts should lead to stronger probabilistic representations of sentences in memory. Encountering unexpected words could therefore be expected to trigger costlier shifts in these representations than expected words. However, psycholinguistic measures commonly used to study probabilistic processing, such as the N400 event-related potential (ERP) component, are sensitive to word predictability but not to contextual constraint. Some research suggests that constraint-related processing cost may be measurable via an ERP positivity following the N400, known as the anterior post-N400 positivity (PNP). The PNP is argued to reflect update of a sentence representation and to be distinct from the posterior P600, which reflects conflict detection and reanalysis. However, constraint-related PNP findings are inconsistent. We sought to conceptually replicate Federmeier et al. (2007) and Kuperberg et al. (2020), who observed that the PNP, but not the N400 or the P600, was affected by constraint at unexpected but plausible words. Using a pre-registered design and statistical approach maximising power, we demonstrated a dissociated effect of predictability and constraint: strong evidence for predictability but not constraint in the N400 window, and strong evidence for constraint but not predictability in the later window. However, the constraint effect was consistent with a P600 and not a PNP, suggesting increased conflict between a strong representation and unexpected input rather than greater update of the representation. We conclude that either a simple strong/weak constraint design is not always sufficient to elicit the PNP, or that previous PNP constraint findings could be an artifact of smaller sample size.}, language = {en} } @phdthesis{Weiss2017, author = {Weiß, Lina}, title = {Understanding the emergence and maintenance of biodiversity in grasslands}, school = {Universit{\"a}t Potsdam}, pages = {153}, year = {2017}, language = {en} } @phdthesis{RodriguezCubillos2018, author = {Rodriguez Cubillos, Andres Eduardo}, title = {Understanding the impact of heterozygosity on metabolism, growth and hybrid necrosis within a local Arabidopsis thaliana collection site}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416758}, school = {Universit{\"a}t Potsdam}, pages = {106}, year = {2018}, abstract = {Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization's impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around T{\"u}bingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size. In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed. This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation.}, language = {en} } @article{KnebelNeebZahnetal.2018, author = {Knebel, Constanze and Neeb, Jannika and Zahn, Elisabeth and Schmidt, Flavia and Carazo, Alejandro and Holas, Ondej and Pavek, Petr and P{\"u}schel, Gerhard Paul and Zanger, Ulrich M. and S{\"u}ssmuth, Roderich and Lampen, Alfonso and Marx-Stoelting, Philip and Braeuning, Albert}, title = {Unexpected Effects of Propiconazole, Tebuconazole, and Their Mixture on the Receptors CAR and PXR in Human Liver Cells}, series = {Toxicological sciences}, volume = {163}, journal = {Toxicological sciences}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1096-6080}, doi = {10.1093/toxsci/kfy026}, pages = {170 -- 181}, year = {2018}, abstract = {Analyzing mixture toxicity requires an in-depth understanding of the mechanisms of action of its individual components. Substances with the same target organ, same toxic effect and same mode of action (MoA) are believed to cause additive effects, whereas substances with different MoAs are assumed to act independently. Here, we tested 2 triazole fungicides, propiconazole, and tebuconazole (Te), for individual and combined effects on liver toxicity-related endpoints. Both triazoles are proposed to belong to the same cumulative assessment group and are therefore thought to display similar and additive behavior. Our data show that Te is an antagonist of the constitutive androstane receptor (CAR) in rats and humans, while propiconazole is an agonist of this receptor. Both substances activate the pregnane X-receptor (PXR) and further induce mRNA expression of CYP3A4. CYP3A4 enzyme activity, however, is inhibited by propiconazole. For common targets of PXR and CAR, the activation of PXR by Te overrides CAR inhibition. In summary, propiconazole and Te affect different hepatotoxicity-relevant cellular targets and, depending on the individual endpoint analyzed, act via similar or dissimilar mechanisms. The use of molecular data based on research in human cell systems extends the picture to refine cumulative assessment group grouping and substantially contributes to the understanding of mixture effects of chemicals in biological systems.}, language = {en} } @article{PancraceIshidaBriandetal.2018, author = {Pancrace, Claire and Ishida, Keishi and Briand, Enora and Pichi, Douglas Gatte and Weiz, Annika R. and Guljarmow, Arthur and Scalvenzi, Thibault and Sassoon, Nathalie and Hertweck, Christian and Dittmann, Elke and Gugger, Muriel}, title = {Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines}, series = {ACS chemical biology}, volume = {14}, journal = {ACS chemical biology}, number = {1}, publisher = {American Chemical Society}, address = {Washington}, issn = {1554-8929}, doi = {10.1021/acschembio.8b00918}, pages = {67 -- 75}, year = {2018}, abstract = {The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.}, language = {en} }