@article{FeddersMuenznerWeberetal.2021,
author = {Fedders, Ronja and Muenzner, Matthias and Weber, Pamela and Sommerfeld, Manuela and Knauer, Miriam and Kedziora, Sarah and Kast, Naomi and Heidenreich, Steffi and Raila, Jens and Weger, Stefan and Henze, Andrea and Schupp, Michael},
title = {Liver-secreted RBP4 does not impair glucose homeostasis in mice},
series = {The journal of biological chemistry},
volume = {293},
journal = {The journal of biological chemistry},
number = {39},
publisher = {American Society for Biochemistry and Molecular Biology},
address = {Bethesda},
issn = {1083-351X},
doi = {10.1074/jbc.RA118.004294},
pages = {15269 -- 15276},
year = {2021},
abstract = {Retinol-binding protein 4 (RBP4) is the major transport protein for retinol in blood. Recent evidence from genetic mouse models shows that circulating RBP4 derives exclusively from hepatocytes. Because RBP4 is elevated in obesity and associates with the development of glucose intolerance and insulin resistance, we tested whether a liver-specific overexpression of RBP4 in mice impairs glucose homeostasis. We used adeno-associated viruses (AAV) that contain a highly liver-specific promoter to drive expression of murine RBP4 in livers of adult mice. The resulting increase in serum RBP4 levels in these mice was comparable with elevated levels that were reported in obesity. Surprisingly, we found that increasing circulating RBP4 had no effect on glucose homeostasis. Also during a high-fat diet challenge, elevated levels of RBP4 in the circulation failed to aggravate the worsening of systemic parameters of glucose and energy homeostasis. These findings show that liver-secreted RBP4 does not impair glucose homeostasis. We conclude that a modest increase of its circulating levels in mice, as observed in the obese, insulin-resistant state, is unlikely to be a causative factor for impaired glucose homeostasis.},
language = {en}
}
@article{WojcikCeulemansGaedke2021,
author = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
title = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
series = {Ecology and Evolution},
volume = {11},
journal = {Ecology and Evolution},
number = {22},
publisher = {John Wiley \& Sons, Inc.},
address = {Hoboken (New Jersey)},
issn = {2045-7758},
doi = {10.1002/ece3.8214},
pages = {15639 -- 15663},
year = {2021},
abstract = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
language = {en}
}
@phdthesis{Ting2021,
author = {Ting, Michael Kien Yin},
title = {Circadian-regulated dynamics of translation in Arabidopsis thaliana},
school = {Universit{\"a}t Potsdam},
pages = {130},
year = {2021},
language = {en}
}
@phdthesis{Brunacci2021,
author = {Brunacci, Nadia},
title = {Oligodepsipeptides as matrix for drug delivery systems and submicron particulate carriers},
school = {Universit{\"a}t Potsdam},
year = {2021},
language = {en}
}
@article{GarridoLeimkuehler2021,
author = {Garrido, Claudia and Leimk{\"u}hler, Silke},
title = {The inactivation of human aldehyde oxidase 1 by hydrogen peroxide and superoxide},
series = {Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics},
volume = {49},
journal = {Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics},
number = {9},
publisher = {American Society for Pharmacology and Experimental Therapeutics},
address = {Bethesda},
issn = {1521-009X},
doi = {10.1124/dmd.121.000549},
pages = {729 -- 735},
year = {2021},
abstract = {Mammalian aldehyde oxidases (AOX) are molybdo-flavoenzymes of pharmacological and pathophysiologic relevance that are involved in phase I drug metabolism and, as a product of their enzymatic activity, are also involved in the generation of reactive oxygen species. So far, the physiologic role of aldehyde oxidase 1 in the human body remains unknown. The human enzyme hAOX1 is characterized by a broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into their corresponding carboxylic acids, and hydroxylating various heteroaromatic rings. The enzyme uses oxygen as terminal electron acceptor to produce hydrogen peroxide and superoxide during turnover. Since hAOX1 and, in particular, some natural variants produce not only H2O2 but also high amounts of superoxide, we investigated the effect of both ROS molecules on the enzymatic activity of hAOX1 in more detail. We compared hAOX1 to the high-O-2(.-)-producing natural variant L438V for their time-dependent inactivation with H2O2/O-2(.-) during substrate turnover. We show that the inactivation of the hAOX1 wild-type enzyme is mainly based on the production of hydrogen peroxide, whereas for the variant L438V, both hydrogen peroxide and superoxide contribute to the time-dependent inactivation of the enzyme during turnover. Further, the level of inactivation was revealed to be substrate-dependent: using substrates with higher turnover numbers resulted in a faster inactivation of the enzymes. Analysis of the inactivation site of the enzyme identified a loss of the terminal sulfido ligand at the molybdenum active site by the produced ROS during turnover.},
language = {en}
}
@article{CeulemansGuillGaedke2021,
author = {Ceulemans, Ruben and Guill, Christian and Gaedke, Ursula},
title = {Top predators govern multitrophic diversity effects in tritrophic food webs},
series = {Ecology : a publication of the Ecological Society of America},
volume = {102},
journal = {Ecology : a publication of the Ecological Society of America},
number = {7},
publisher = {Wiley},
address = {Hoboken},
issn = {0012-9658},
doi = {10.1002/ecy.3379},
pages = {16},
year = {2021},
abstract = {It is well known that functional diversity strongly affects ecosystem functioning. However, even in rather simple model communities consisting of only two or, at best, three trophic levels, the relationship between multitrophic functional diversity and ecosystem functioning appears difficult to generalize, because of its high contextuality. In this study, we considered several differently structured tritrophic food webs, in which the amount of functional diversity was varied independently on each trophic level. To achieve generalizable results, largely independent of parametrization, we examined the outcomes of 128,000 parameter combinations sampled from ecologically plausible intervals, with each tested for 200 randomly sampled initial conditions. Analysis of our data was done by training a random forest model. This method enables the identification of complex patterns in the data through partial dependence graphs, and the comparison of the relative influence of model parameters, including the degree of diversity, on food-web properties. We found that bottom-up and top-down effects cascade simultaneously throughout the food web, intimately linking the effects of functional diversity of any trophic level to the amount of diversity of other trophic levels, which may explain the difficulty in unifying results from previous studies. Strikingly, only with high diversity throughout the whole food web, different interactions synergize to ensure efficient exploitation of the available nutrients and efficient biomass transfer to higher trophic levels, ultimately leading to a high biomass and production on the top level. The temporal variation of biomass showed a more complex pattern with increasing multitrophic diversity: while the system initially became less variable, eventually the temporal variation rose again because of the increasingly complex dynamical patterns. Importantly, top predator diversity and food-web parameters affecting the top trophic level were of highest importance to determine the biomass and temporal variability of any trophic level. Overall, our study reveals that the mechanisms by which diversity influences ecosystem functioning are affected by every part of the food web, hampering the extrapolation of insights from simple monotrophic or bitrophic systems to complex natural food webs.},
language = {en}
}
@article{SauerGrebe2021,
author = {Sauer, Michael and Grebe, Markus},
title = {Plant cell biology},
series = {Current biology : CB},
volume = {31},
journal = {Current biology : CB},
number = {9},
publisher = {Cell Press},
address = {Cambridge},
issn = {0960-9822},
doi = {10.1016/j.cub.2021.03.070},
pages = {R449 -- R451},
year = {2021},
abstract = {PIN-FORMED (PIN) polar protein localization directs transport of the growth and developmental regulator auxin in plants. Once established after cytokinesis, PIN polarity requires maintenance. Now, direct interactions between PIN, MAB4/MEL and PID proteins suggest self-reinforced maintenance of PIN polarity through limiting lateral diffusion.},
language = {en}
}
@phdthesis{Tung2021,
author = {Tung, Wing Tai},
title = {Polymeric fibrous scaffold on macro/microscale towards tissue regeneration},
school = {Universit{\"a}t Potsdam},
year = {2021},
language = {en}
}
@article{StarkBachGuill2021,
author = {Stark, Markus and Bach, Moritz and Guill, Christian},
title = {Patch isolation and periodic environmental disturbances have idiosyncratic effects on local and regional population variabilities in meta-food chains},
series = {Theoretical ecology},
volume = {14},
journal = {Theoretical ecology},
number = {3},
publisher = {Springer},
address = {Dordrecht},
issn = {1874-1738},
doi = {10.1007/s12080-021-00510-0},
pages = {489 -- 500},
year = {2021},
abstract = {While habitat loss is a known key driver of biodiversity decline, the impact of other landscape properties, such as patch isolation, is far less clear. When patch isolation is low, species may benefit from a broader range of foraging opportunities, but are at the same time adversely affected by higher predation pressure from mobile predators. Although previous approaches have successfully linked such effects to biodiversity, their impact on local and metapopulation dynamics has largely been ignored. Since population dynamics may also be affected by environmental disturbances that temporally change the degree of patch isolation, such as periodic changes in habitat availability, accurate assessment of its link with isolation is highly challenging. To analyze the effect of patch isolation on the population dynamics on different spatial scales, we simulate a three-species meta-food chain on complex networks of habitat patches and assess the average variability of local populations and metapopulations, as well as the level of synchronization among patches. To evaluate the impact of periodic environmental disturbances, we contrast simulations of static landscapes with simulations of dynamic landscapes in which 30 percent of the patches periodically become unavailable as habitat. We find that increasing mean patch isolation often leads to more asynchronous population dynamics, depending on the parameterization of the food chain. However, local population variability also increases due to indirect effects of increased dispersal mortality at high mean patch isolation, consequently destabilizing metapopulation dynamics and increasing extinction risk. In dynamic landscapes, periodic changes of patch availability on a timescale much slower than ecological interactions often fully synchronize the dynamics. Further, these changes not only increase the variability of local populations and metapopulations, but also mostly overrule the effects of mean patch isolation. This may explain the often small and inconclusive impact of mean patch isolation in natural ecosystems.},
language = {en}
}
@article{GuillHuelsemannKlauschies2021,
author = {Guill, Christian and H{\"u}lsemann, Janne and Klauschies, Toni},
title = {Self-organised pattern formation increases local diversity in metacommunities},
series = {Ecology letters},
volume = {24},
journal = {Ecology letters},
number = {12},
publisher = {Wiley-Blackwell},
address = {Oxford},
issn = {1461-023X},
doi = {10.1111/ele.13880},
pages = {2624 -- 2634},
year = {2021},
abstract = {Self-organised formation of spatial patterns is known from a variety of different ecosystems, yet little is known about how these patterns affect the diversity of communities. Here, we use a food chain model in which autotroph diversity is described by a continuous distribution of a trait that affects both growth and defence against heterotrophs. On isolated patches, diversity is always lost over time due to stabilising selection, and the local communities settle on one of two alternative stable community states that are characterised by a dominance of either defended or undefended species. In a metacommunity context, dispersal can destabilise these states and complex spatio-temporal patterns in the species' abundances emerge. The resulting biomass-trait feedback increases local diversity by an order of magnitude compared to scenarios without self-organised pattern formation, thereby maintaining the ability of communities to adapt to potential future changes in biotic or abiotic environmental conditions.},
language = {en}
}
@article{RomeroMujalliRochowKahletal.2021,
author = {Romero-Mujalli, Daniel and Rochow, Markus and Kahl, Sandra M. and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph},
title = {Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies},
series = {Ecology and Evolution},
volume = {11},
journal = {Ecology and Evolution},
number = {11},
publisher = {John Wiley \& Sons, Inc.},
address = {New Jersey},
issn = {2045-7758},
pages = {17},
year = {2021},
abstract = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.},
language = {en}
}
@article{CahsanWestburyParaskevopoulouetal.2021,
author = {Cahsan, Binia De and Westbury, Michael V. and Paraskevopoulou, Sofia and Drews, Hauke and Ott, Moritz and Gollmann, G{\"u}nter and Tiedemann, Ralph},
title = {Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian},
series = {Evolutionary Applications},
volume = {14},
journal = {Evolutionary Applications},
number = {6},
publisher = {John Wiley \& Sons, Inc.},
address = {New Jersey},
issn = {1752-4563},
pages = {12},
year = {2021},
abstract = {Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.},
language = {en}
}
@article{SpikesRodriguezSilvaBennettetal.2021,
author = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph},
title = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario},
series = {BMC Research Notes},
volume = {14},
journal = {BMC Research Notes},
publisher = {BMC Research Notes / Biomed Central},
address = {London},
issn = {1756-0500},
doi = {10.1186/s13104-021-05843-x},
pages = {1 -- 8},
year = {2021},
abstract = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.},
language = {en}
}
@article{KruegerFoersterTrauthetal.2021,
author = {Kr{\"u}ger, Johanna and Foerster, Verena Elisabeth and Trauth, Martin H. and Hofreiter, Michael and Tiedemann, Ralph},
title = {Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core},
series = {Frontiers in Earth Science},
journal = {Frontiers in Earth Science},
publisher = {Frontiers in Earth Science},
address = {Lausanne, Schweiz},
issn = {2296-6463},
doi = {10.3389/feart.2021.683010},
pages = {1 -- 20},
year = {2021},
abstract = {Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.},
language = {en}
}
@article{Trindade2021,
author = {Trindade, In{\^e}s},
title = {License to flower},
series = {Molecular plant},
volume = {14},
journal = {Molecular plant},
number = {5},
publisher = {Oxford Univ. Press},
address = {Oxford},
issn = {1674-2052},
doi = {10.1016/j.molp.2021.04.007},
pages = {719 -- 720},
year = {2021},
language = {en}
}
@article{GraefGrafeMeyeretal.2021,
author = {Gr{\"a}f, Ralph and Grafe, Marianne and Meyer, Irene and Mitic, Kristina and Pitzen, Valentin},
title = {The dictyostelium centrosome},
series = {Cells : open access journal},
volume = {10},
journal = {Cells : open access journal},
number = {10},
publisher = {MDPI},
address = {Basel},
issn = {2073-4409},
doi = {10.3390/cells10102657},
pages = {26},
year = {2021},
abstract = {The centrosome of Dictyostelium amoebae contains no centrioles and consists of a cylindrical layered core structure surrounded by a corona harboring microtubule-nucleating gamma-tubulin complexes. It is the major centrosomal model beyond animals and yeasts. Proteomics, protein interaction studies by BioID and superresolution microscopy methods led to considerable progress in our understanding of the composition, structure and function of this centrosome type. We discuss all currently known components of the Dictyostelium centrosome in comparison to other centrosomes of animals and yeasts.},
language = {en}
}
@phdthesis{Cadek2021,
author = {Cadek, Chris},
title = {Charakterisierung der Funktion von TusA-homologen Proteinen im Schwefelmetabolismus von Escherichia coli},
school = {Universit{\"a}t Potsdam},
pages = {X, 114, XVI},
year = {2021},
language = {de}
}
@article{RaatzPirhoferWalzlMuelleretal.2021,
author = {Raatz, Larissa and Pirhofer-Walzl, Karin and M{\"u}ller, Marina E.H. and Scherber, Christoph and Joshi, Jasmin Radha},
title = {Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?},
series = {Ecology and Evolution},
volume = {11},
journal = {Ecology and Evolution},
edition = {19},
publisher = {Wiley-Blackwell},
address = {Oxford},
issn = {1467-6435},
doi = {10.1002/ece3.8046},
pages = {13232 -- 13246},
year = {2021},
abstract = {Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices.},
language = {en}
}
@article{Trindade2021,
author = {Trindade, In{\^e}s},
title = {A drop of immunity},
series = {Molecular plant},
volume = {14},
journal = {Molecular plant},
number = {9},
publisher = {Oxford Univ. Press},
address = {Oxford},
issn = {1674-2052},
doi = {10.1016/j.molp.2021.07.022},
pages = {1437 -- 1438},
year = {2021},
language = {en}
}
@article{PetrovićWendler2021,
author = {Petrović, Saša and Wendler, Petra},
title = {A RADD approach to probing AAA plus protein function},
series = {Nature structural \& molecular biology},
volume = {28},
journal = {Nature structural \& molecular biology},
number = {4},
publisher = {Nature Publishing Group},
address = {Berlin},
issn = {1545-9993},
doi = {10.1038/s41594-021-00579-5},
pages = {329 -- 330},
year = {2021},
abstract = {AAA+ proteins (ATPases associated with various cellular activities) catalyze the energy-dependent movement or rearrangement of macromolecules. A new study addresses the important question of how to design a selective chemical inhibitor for specific proteins in this diverse superfamily. The powerful chemical genetics approach adds to a growing toolbox of applications that allow dissection of the functions of distinct AAA+ proteins in vivo, facilitating the first steps toward effective drug development.},
language = {en}
}
@article{Leimkuehler2021,
author = {Leimk{\"u}hler, Silke},
title = {Transition metals in catalysis},
series = {Inorganics : open access journal},
volume = {9},
journal = {Inorganics : open access journal},
number = {1},
publisher = {MDPI},
address = {Basel},
issn = {2304-6740},
doi = {10.3390/inorganics9010006},
pages = {2},
year = {2021},
language = {en}
}
@phdthesis{Gibert2021,
author = {Gibert, Arthur},
title = {Influence of Amyloid Aggregates on the Trafficking and Signaling of GPCRs},
doi = {10.25932/publishup-50665},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-506659},
school = {Universit{\"a}t Potsdam},
pages = {100},
year = {2021},
abstract = {The prevalence of diseases associated with misfolded proteins increases with age. When cellular defense mechanisms become limited, misfolded proteins form aggregates and may also develop more stable cross-β structures ultimately forming amyloid aggregates. Amyloid aggregates are associated with neurodegenerative diseases such as Alzheimer's disease and Huntington's disease. The formation of amyloid deposits, their toxicity and cellular defense mechanisms have been intensively studied. However, surprisingly little is known about the effects of protein aggregates on cellular signal transduction. It is also not understood whether the presence of aggregation-prone, but still soluble proteins affect signal transduction. In this study, the still soluble aggregation-prone HttExon1Q74 and its amyloid aggregates were used to analyze the effect of amyloid aggregates on internalization and receptor activation of G protein-coupled receptors (GPCRs), the largest protein family of mammalian cell surface receptors involved in signal transduction. The aggregated HttExon1Q74, but not its soluble form, could inhibit ligand-induced clathrin-mediated endocytosis (CME) of various GPCRs. Most likely this inhibitory effect is based on a terminal sequestration of the HSC70 chaperone to the aggregates which is necessary for CME. Using the vasopressinV1a receptor (V1aR) and the corticotropin-releasing factor receptor 1 (CRF1R) as a model, it could be shown that the presence of HttExon1Q74 aggregates and the inhibition of ligand-induced CME leads to an accumulation of desensitized receptors at the plasma membrane. In turn, this disrupts Gq-mediated Ca2+ signaling and Gs-mediated cAMP signaling of the V1aR and the CRF1R respectively. In contrast to HttExon1Q74 amyloid aggregates, soluble HttExon1Q74 as well as amorphous aggregates did not inhibit GPCR internalization and signaling demonstrating that cellular signal transduction mechanisms are specifically impaired in response to the formation of amyloid aggregates. In addition, preliminary experiments could show that HttExon1Q74 aggregates provoke an increase in membrane expression of a protein from a structurally and functionally unrelated membrane protein family, namely the serotonin transporter SERT. As SERT is the main pharmacological target to treat depression this could shed light on this commonly occurring comorbidity in neurodegenerative diseases, in particular in early disease states.},
language = {en}
}
@phdthesis{Schaarschmidt2021,
author = {Schaarschmidt, Stephanie},
title = {Evaluation and application of omics approaches to characterize molecular responses to abiotic stresses in plants},
doi = {10.25932/publishup-50963},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-509630},
school = {Universit{\"a}t Potsdam},
pages = {viii, 117},
year = {2021},
abstract = {Aufgrund des globalen Klimawandels ist die Gew{\"a}hrleistung der Ern{\"a}hrungssicherheit f{\"u}r eine wachsende Weltbev{\"o}lkerung eine große Herausforderung. Insbesondere abiotische Stressoren wirken sich negativ auf Ernteertr{\"a}ge aus. Um klimaangepasste Nutzpflanzen zu entwickeln, ist ein umfassendes Verst{\"a}ndnis molekularer Ver{\"a}nderungen in der Reaktion auf unterschiedlich starke Umweltbelastungen erforderlich. Hochdurchsatz- oder "Omics"-Technologien k{\"o}nnen dazu beitragen, Schl{\"u}sselregulatoren und Wege abiotischer Stressreaktionen zu identifizieren. Zus{\"a}tzlich zur Gewinnung von Omics-Daten m{\"u}ssen auch Programme und statistische Analysen entwickelt und evaluiert werden, um zuverl{\"a}ssige biologische Ergebnisse zu erhalten. Ich habe diese Problemstellung in drei verschiedenen Studien behandelt und daf{\"u}r zwei Omics-Technologien benutzt. In der ersten Studie wurden Transkript-Daten von den beiden polymorphen Arabidopsis thaliana Akzessionen Col-0 und N14 verwendet, um sieben Programme hinsichtlich ihrer F{\"a}higkeit zur Positionierung und Quantifizierung von Illumina RNA Sequenz-Fragmenten („Reads") zu evaluieren. Zwischen 92\% und 99\% der Reads konnten an die Referenzsequenz positioniert werden und die ermittelten Verteilungen waren hoch korreliert f{\"u}r alle Programme. Bei der Durchf{\"u}hrung einer differentiellen Genexpressionsanalyse zwischen Pflanzen, die bei 20 °C oder 4 °C (K{\"a}lteakklimatisierung) exponiert wurden, ergab sich eine große paarweise {\"U}berlappung zwischen den Programmen. In der zweiten Studie habe ich die Transkriptome von zehn verschiedenen Oryza sativa (Reis) Kultivaren sequenziert. Daf{\"u}r wurde die PacBio Isoform Sequenzierungstechnologie benutzt. Die de novo Referenztranskriptome hatten zwischen 38.900 bis 54.500 hoch qualitative Isoformen pro Sorte. Die Isoformen wurden kollabiert, um die Sequenzredundanz zu verringern und danach evaluiert z.B. hinsichtlich des Vollst{\"a}ndigkeitsgrades (BUSCO), der Transkriptl{\"a}nge und der Anzahl einzigartiger Transkripte pro Genloci. F{\"u}r die hitze- und trockenheitstolerante Sorte N22 wurden ca. 650 einzigartige und neue Transkripte identifiziert, von denen 56 signifikant unterschiedlich in sich entwickelnden Samen unter kombiniertem Trocken- und Hitzestress exprimiert wurden. In der letzten Studie habe ich die Ver{\"a}nderungen in Metabolitprofilen von acht Reissorten gemessen und analysiert, die dem Stress hoher Nachttemperaturen (HNT) ausgesetzt waren und w{\"a}hrend der Trocken- und Regenzeit im Feld auf den Philippinen angebaut wurden. Es wurden jahreszeitlich bedingte Ver{\"a}nderungen im Metabolitspiegel sowie f{\"u}r agronomische Parameter identifiziert und m{\"o}gliche Stoffwechselwege, die einen Ertragsr{\"u}ckgang unter HNT-Bedingungen verursachen, vorgeschlagen. Zusammenfassend konnte ich zeigen, dass der Vergleich der RNA-seq Programme den Pflanzenwissenschaftler*innen helfen kann, sich f{\"u}r das richtige Werkzeug f{\"u}r ihre Daten zu entscheiden. Die de novo Transkriptom-Rekonstruktion von Reissorten ohne Genomsequenz bietet einen gezielten, kosteneffizienten Ansatz zur Identifizierung neuer Gene, die durch verschiedene Stressbedingungen reguliert werden unabh{\"a}ngig vom Organismus. Mit dem Metabolomik-Ansatz f{\"u}r HNT-Stress in Reis habe ich stress- und jahreszeitenspezifische Metabolite identifiziert, die in Zukunft als molekulare Marker f{\"u}r die Verbesserung von Nutzpflanzen verwendet werden k{\"o}nnten.},
language = {en}
}
@phdthesis{Moga2021,
author = {Moga, Akanksha},
title = {Reconstitution of molybdenum cofactor biosynthesis in giant vesicles},
doi = {10.25932/publishup-51016},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-510167},
school = {Universit{\"a}t Potsdam},
pages = {XIV, 148},
year = {2021},
abstract = {Bottom-up synthetic biology is used for the understanding of how a cell works. It is achieved through developing techniques to produce lipid-based vesicular structures as cellular mimics. The most common techniques used to produce cellular mimics or synthetic cells is through electroformation and swelling method. However, the abovementioned techniques cannot efficiently encapsulate macromolecules such as proteins, enzymes, DNA and even liposomes as synthetic organelles. This urges the need to develop new techniques that can circumvent this issue and make the artificial cell a reality where it is possible to imitate a eukaryotic cell through encapsulating macromolecules. In this thesis, the aim to construct a cell system using giant unilamellar vesicles (GUVs) to reconstitute the mitochondrial molybdenum cofactor biosynthetic pathway. This pathway is highly conserved among all life forms, and therefore is known for its biological significance in disorders induced through its malfunctioning. Furthermore, the pathway itself is a multi-step enzymatic reaction that takes place in different compartments. Initially, GTP in the mitochondrial matrix is converted to cPMP in the presence of cPMP synthase. Further, produced cPMP is transported across the membrane to the cytosol, to be converted by MPT synthase into MPT. This pathway provides a possibility to address the general challenges faced in the development of a synthetic cell, to encapsulate large biomolecules with good efficiency and greater control and to evaluate the enzymatic reactions involved in the process. For this purpose, the emulsion-based technique was developed and optimised to allow rapid production of GUVs (~18 min) with high encapsulation efficiency (80\%). This was made possible by optimizing various parameters such as density, type of oil, the impact of centrifugation speed/time, lipid concentration, pH, temperature, and emulsion droplet volume. Furthermore, the method was optimised in microtiter plates for direct experimentation and visualization after the GUV formation. Using this technique, the two steps - formation of cPMP from GTP and the formation of MPT from cPMP were encapsulated in different sets of GUVs to mimic the two compartments. Two independent fluorescence-based detection systems were established to confirm the successful encapsulation and conversion of the reactants. Alternatively, the enzymes produced using bacterial expression and measured. Following the successful encapsulation and evaluation of enzymatic reactions, cPMP transport across mitochondrial membrane has been mimicked using GUVs using a complex mitochondrial lipid composition. It was found that the cPMP interaction with the lipid bilayer results in transient pore-formation and leakage of internal contents. Overall, it can be concluded that in this thesis a novel technique has been optimised for fast production of functional synthetic cells. The individual enzymatic steps of the Moco biosynthetic pathway have successfully implemented and quantified within these cellular mimics.},
language = {en}
}
@phdthesis{Ceulemans2021,
author = {Ceulemans, Ruben},
title = {Diversity effects on ecosystem functions of tritrophic food webs},
doi = {10.25932/publishup-50325},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-503259},
school = {Universit{\"a}t Potsdam},
pages = {vii, 166},
year = {2021},
abstract = {There is a general consensus that diverse ecological communities are better equipped to adapt to changes in their environment, but our understanding of the mechanisms by which they do so remains incomplete. Accurately predicting how the global biodiversity crisis affects the functioning of ecosystems, and the services they provide, requires extensive knowledge about these mechanisms. Mathematical models of food webs have been successful in uncovering many aspects of the link between diversity and ecosystem functioning in small food web modules, containing at most two adaptive trophic levels. Meaningful extrapolation of this understanding to the functioning of natural food webs remains difficult, due to the presence of complex interactions that are not always accurately captured by bitrophic descriptions of food webs. In this dissertation, we expand this approach to tritrophic food web models by including the third trophic level. Using a functional trait approach, coexistence of all species is ensured using fitness-balancing trade-offs. For example, the defense-growth trade-off implies that species may be defended against predation, but this defense comes at the cost of a lower maximal growth rate. In these food webs, the functional diversity on a given trophic level can be varied by modifying the trait differences between the species on that level. In the first project, we find that functional diversity promotes high biomass on the top level, which, in turn, leads to a reduction in the temporal variability due to compensatory dynamical patterns governed by the top level. Next, these results are generalized by investigating the average behavior of tritrophic food webs, for wide intervals of all parameters describing species interactions in the food web. We find that the diversity on the top level is most important for determining the biomass and temporal variability of all other trophic levels, and show how biomass is only transferred efficiently to the top level when diversity is high everywhere in the food web. In the third project, we compare the response of a simple food chain against a nutrient pulse perturbation, to that of a food web with diversity on every trophic level. By joint consideration of the resistance, resilience, and elasticity, we uncover that the response is efficiently buffered when biomass on the top level is high, which is facilitated by functional diversity on every trophic level in the food web. Finally, in the fourth project, we show that even in a simple consumer-resource model without any diversity, top-down control on the intermediate level frequently causes the phase difference between the intermediate and basal level to deviate from the quarter-cycle lag rule. By adding a top predator, we show that these deviations become even more likely, and anti-phase cycles are often observed. The combined results of these projects show how the properties of the top trophic level, including its functional diversity, have a decisive influence on the functioning of tritrophic food webs from a mechanistic perspective. Because top species are often among the most vulnerable to extinction, our results emphasize the importance of their conservation in ecosystem management and restoration strategies.},
language = {en}
}
@phdthesis{Liu2021,
author = {Liu, Yue},
title = {Polymeric objects switchable between two shapes},
school = {Universit{\"a}t Potsdam},
pages = {xv, 73},
year = {2021},
abstract = {As the ongoing trend of developing smart materials that can reversibly switch geometry stimulated by environmental control addressed increasing attention in many research fields, especially for biomedical or soft robotic applications. Shape-memory polymers (SMPs), which can change shape, stiffness, size, and structure when exposed to an external stimulus, are intensively explored as encouraging material candidates for achieving multifunctionality, and for miniaturizing into micro-components to expand the applications. Besides, the geometrical design has gained growing attention for creating engineering applications, such as bi-stable mechanisms, and has the potential to be explored by implementing SMP for new functions. In this context, this thesis aimed to develop smart micro-/nano-objects based on SMP and explore new functions by geometrical design using SMP. Here, two types of stimuli-responsive objects capable of one-way temperature-memory effect (TME) or free-standing reversible actuation e.g., micro/nanofibers (i) and microcuboids (ii) at different aspects were explored. At first, it was hypothesized that the advanced atomic force microscopy (AFM) platform can be established to study individual polymeric micro-/nanofibers (i) in terms of incorporation and characterization of a reversible shape-memory actuation capability. Crystallizable material was chosen for preparing the fibers and the molecular alignment within the fibers among different diameters will influence the crystallization-induced elongation during cooling that determined the reversible effect. For the second type, microcuboids (ii), it was hypothesized that a programming and quantification approach can be developed to enable the realization and characterization of a one-way micro-TME and micro-shape-memory polymer actuation (SMPA) in microcuboids. The responsive temperature of one-way shape transformation can be tuned by programming temperature (Tp) and the separation temperature (Tsep) for post-programming can influence the actuation. Finally, a geometrical design with bi-stability was combined with SME to create new functions of shape actuation. It was hypothesized that the predicted bi-stable or mono-stable structures can be achieved with the aid of digital fabrication methods. Using shape-memory effect (SME), the alteration of bi-stable and mono-stable can initiate shape transformation with a larger magnitude and higher energy output. In the first part, the method to quantify the reversible SMPA of a single micro/nano crystallizable fiber with geometry change during the actuation was explored. Electrospinning was used to prepare poly (ε-caprolactone) (PCL) micro/nanofiber with different diameters, which were fixed by UV glue and crosslinked on the structured silicon wafer. Using AFM, the programming, as well as the observation of recovery and reversible displacement of the fiber, were performed by vertical three-point bending at the free suspended part. A plateau tip was chosen to achieve stable contact and longer working distance for performing larger deformation, enabling intensified reversible SMPA of single fibers. In this way, programming strains of 39 ± 1\% or 46 ± 1\% were realized for fiber with a diameter of 1 ± 0.2 µm and 300 ± 50 nm, which were bent at 80 °C and fixed at 10 °C. Values for the reversible elongation of εrev = 3.4 ± 0.1\% and 10.5 ± 0.1\% were obtained for a single micro and nanofiber respectively between 10 and 60 °C. The higher actuation effect observed for nanofiber demonstrated that the highly compact and oriented crystallites in nanofibers, which determined the pronounced εrev compared to the thick microfibers. Besides, a stable reversible actuation of a nanofiber can be tracked by AFM tip up to 10 cycles, indicating a sustainable application can be achieved on the fiber actuators. The findings obtained for cPCL micro-/nano-fibers will help design and evaluate the next generation polymeric microactuators or micromanipulators. The second part of the thesis studies the shape-memory effect (SME) of a single individual SMP micro-object by controlling deformation temperatures during programming and actuation temperatures during reversible change. In this work, microcuboids of crosslinked poly[ethylene-co-(vinyl acetate)] (cPEVA) elastomers with 18 wt\% vinyl acetate (VA) contents were successfully prepared by template-based replication from polydimethylsiloxane (PDMS) mold. The micro-TME and micro-SMPA were observed and studied based on micro-geometry change using optical microscopy (OM) and AFM. Different switching temperatures of shape recovery were achieved from 55 °C to 86 °C by tuning Tp from 55 °C to 100 °C, indicating a successful implementation of micro-TME on individual microcuboid. For micro-SMPA functionalization, microcuboids were deformed by compression at 100 °C and the change in single particle height was monitored during cyclic heating and cooling between various Tseps from 60 °C to 85 °C and 20 °C. The micro-SMPA on a single microcuboid was achieved with a reversible strain in the range of 2 to 7\%, whereby higher compression ratio CR and Tsep induced prominent reversible strain. The results achieved in this work demonstrated the successful functionalization of microcuboids with different SMEs by controlling temperatures during programming and actuation processes. Based on these achievements, such micro-objects can be further designed as on demand switchable microactuators or release systems with adjustable working temperatures. In the last part of the work, a new function of shape-memory polymeric bi-stable 3D structured film was designed and fabricated. The SME and geometrical design of compliant mechanics were merged to enable switching between bi-stable and mono-stable states, which generate snap movement that mimics the Venus flytrap. A truncated tetrahedron structure with a slope angle as a tunable parameter to alter the bi-stability was chosen for the study to combine with SME. It was anticipated that the structured film designed with a slope angle of 30° exhibited mono-stable behavior, and such a structure with a slope angle of 45° exhibited bi-stable behavior. Then the structured SMP film of designed mono-stable shape was successfully fabricated using soft lithography based on 3D printed master molds supported from digital manufacturing. The structured mold was also used in programming the SMP film into the structure with a higher slope angle to attain bi-stability. Finally, the switching between bi-stable and mono-stable states was successfully realized using SME, which introduces snapping movement triggered by heat. The implementation of compliant mechanisms by the SME increased the magnitude of thermally induced reconfiguration without additional external force. To sum up, the results of the thesis support the development of smart objects capable of one-way micro-TME, free-standing reversible actuation, or bi-stability mediated shape-memory reconfiguration. Electrospinning and template-based method were used for fabrication with good control of geometry and low size dispersity. Microscopy methods especially the AFM platform with decent sensitivity was developed for implementation as well as characterization of SME on individual micro-/nanoobjects. Implementation of bi-stability improves the shape transformation amplitude of thermally triggered SMP. These findings can give novel insights for designing polymer-based actuators or soft robotics.},
language = {en}
}
@article{SteppertSchoenfelderSchultzetal.2021,
author = {Steppert, Isabel and Sch{\"o}nfelder, Jessy and Schultz, Carolyn and Kuhlmeier, Dirk},
title = {Rapid in vitro differentiation of bacteria by ion mobility spectrometry},
series = {Applied Microbiology and Biotechnology},
volume = {105},
journal = {Applied Microbiology and Biotechnology},
number = {10},
publisher = {Springer},
address = {New York},
issn = {0175-7598},
doi = {10.1007/s00253-021-11315-w},
pages = {4297 -- 4307},
year = {2021},
abstract = {Rapid screening of infected people plays a crucial role in interrupting infection chains. However, the current methods for identification of bacteria are very tedious and labor intense. Fast on-site screening for pathogens based on volatile organic compounds (VOCs) by ion mobility spectrometry (IMS) could help to differentiate between healthy and potentially infected subjects. As a first step towards this, the feasibility of differentiating between seven different bacteria including resistant strains was assessed using IMS coupled to multicapillary columns (MCC-IMS). The headspace above bacterial cultures was directly drawn and analyzed by MCC-IMS after 90 min of incubation. A cluster analysis software and statistical methods were applied to select discriminative VOC clusters. As a result, 63 VOC clusters were identified, enabling the differentiation between all investigated bacterial strains using canonical discriminant analysis. These 63 clusters were reduced to 7 discriminative VOC clusters by constructing a hierarchical classification tree. Using this tree, all bacteria including resistant strains could be classified with an AUC of 1.0 by receiver-operating characteristic analysis. In conclusion, MCC-IMS is able to differentiate the tested bacterial species, even the non-resistant and their corresponding resistant strains, based on VOC patterns after 90 min of cultivation. Although this result is very promising, in vivo studies need to be performed to investigate if this technology is able to also classify clinical samples. With a short analysis time of 5 min, MCC-IMS is quite attractive for a rapid screening for possible infections in various locations from hospitals to airports. Key Points center dot Differentiation of bacteria by MCC-IMS is shown after 90-min cultivation. center dot Non-resistant and resistant strains can be distinguished. center dot Classification of bacteria is possible based on metabolic features.},
language = {en}
}
@article{StrongScherzCaldwell2021,
author = {Strong, Catherine R. C. and Scherz, Mark D. and Caldwell, Michael Wayne},
title = {Deconstructing the Gestalt},
series = {The anatomical record : AR ; advances in integrative anatomy and evolutionary biology ; an official publication of the American Association of Anatomists, AAA},
volume = {304},
journal = {The anatomical record : AR ; advances in integrative anatomy and evolutionary biology ; an official publication of the American Association of Anatomists, AAA},
number = {10},
publisher = {Wiley},
address = {Hoboken},
issn = {1932-8486},
doi = {10.1002/ar.24630},
pages = {2303 -- 2351},
year = {2021},
abstract = {Snakes-a subset of lizards-have traditionally been divided into two major groups based on feeding mechanics: "macrostomy," involving the ingestion of proportionally large prey items; and "microstomy," the lack of this ability. "Microstomy"-considered present in scolecophidian and early-diverging alethinophidian snakes-is generally viewed as a symplesiomorphy shared with non-snake lizards. However, this perspective of "microstomy" as plesiomorphic and morphologically homogenous fails to recognize the complexity of this condition and its evolution across "microstomatan" squamates. To challenge this problematic paradigm, we formalize a new framework for conceptualizing and testing the homology of overall character complexes, or "morphotypes," which underlies our re-assessment of "microstomy." Using micro-computed tomography (micro-CT) scans, we analyze the morphology of the jaws and suspensorium across purported "microstomatan" squamates (scolecophidians, early-diverging alethinophidians, and non-snake lizards) and demonstrate that key components of the jaw complex are not homologous at the level of primary character state identity across these taxa. Therefore, rather than treating "microstomy" as a uniform condition, we instead propose that non-snake lizards, early-diverging alethinophidians, anomalepidids, leptotyphlopids, and typhlopoids each exhibit a unique and nonhomologous jaw morphotype: "minimal-kinesis microstomy," "snout-shifting," "axle-brace maxillary raking," "mandibular raking," and "single-axle maxillary raking," respectively. The lack of synapomorphy among scolecophidians is inconsistent with the notion of scolecophidians representing an ancestral snake condition, and instead reflects a hypothesis of the independent evolution of fossoriality, miniaturization, and "microstomy" in each scolecophidian lineage. We ultimately emphasize that a rigorous approach to comparative anatomy is necessary in constructing evolutionary hypotheses that accurately reflect biological reality.},
language = {en}
}
@article{GuljamowBarchewitzGrosseetal.2021,
author = {Guljamow, Arthur and Barchewitz, Tino and Große, Rebecca and Timm, Stefan and Hagemann, Martin and Dittmann, Elke},
title = {Diel Variations of Extracellular Microcystin Influence the Subcellular Dynamics of RubisCO in Microcystis aeruginosa PCC 7806},
series = {Microorganisms : open access journal},
volume = {9},
journal = {Microorganisms : open access journal},
number = {6},
publisher = {MDPI},
address = {Basel},
issn = {2076-2607},
doi = {10.3390/microorganisms9061265},
pages = {14},
year = {2021},
abstract = {The ubiquitous freshwater cyanobacterium Microcystis is remarkably successful, showing a high tolerance against fluctuations in environmental conditions. It frequently forms dense blooms which can accumulate significant amounts of the hepatotoxin microcystin, which plays an extracellular role as an infochemical but also acts intracellularly by interacting with proteins of the carbon metabolism, notably with the CO2 fixing enzyme RubisCO. Here we demonstrate a direct link between external microcystin and its intracellular targets. Monitoring liquid cultures of Microcystis in a diel experiment revealed fluctuations in the extracellular microcystin content that correlate with an increase in the binding of microcystin to intracellular proteins. Concomitantly, reversible relocation of RubisCO from the cytoplasm to the cell's periphery was observed. These variations in RubisCO localization were especially pronounced with cultures grown at higher cell densities. We replicated these effects by adding microcystin externally to cultures grown under continuous light. Thus, we propose that microcystin may be part of a fast response to conditions of high light and low carbon that contribute to the metabolic flexibility and the success of Microcystis in the field.},
language = {en}
}
@misc{WojcikCeulemansGaedke2021,
author = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
title = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {1251},
issn = {1866-8372},
doi = {10.25932/publishup-55373},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-553730},
pages = {25},
year = {2021},
abstract = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
language = {en}
}
@misc{BornhorstAbdelilahSeyfried2021,
author = {Bornhorst, Dorothee and Abdelilah-Seyfried, Salim},
title = {Strong as a Hippo's Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
issn = {1866-8372},
doi = {10.25932/publishup-54873},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-548731},
pages = {1 -- 10},
year = {2021},
abstract = {The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology.},
language = {en}
}
@misc{SpikesRodriguezSilvaBennettetal.2021,
author = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph},
title = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
issn = {1866-8372},
doi = {10.25932/publishup-54888},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-548882},
pages = {1 -- 8},
year = {2021},
abstract = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.},
language = {en}
}
@misc{KruegerFoersterTrauthetal.2021,
author = {Kr{\"u}ger, Johanna and Foerster, Verena Elisabeth and Trauth, Martin H. and Hofreiter, Michael and Tiedemann, Ralph},
title = {Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
issn = {1866-8372},
doi = {10.25932/publishup-55007},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-550071},
pages = {1 -- 20},
year = {2021},
abstract = {Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.},
language = {en}
}
@article{RaatzPirhoferWalzlMuelleretal.2021,
author = {Raatz, Larissa and Pirhofer-Walzl, Karin and M{\"u}ller, Marina E.H. and Scherber, Christoph and Joshi, Jasmin Radha},
title = {Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
issn = {1866-8372},
doi = {10.25932/publishup-54962},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549622},
pages = {13232 -- 13246},
year = {2021},
abstract = {Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices.},
language = {en}
}
@misc{GuljamowBarchewitzGrosseetal.2021,
author = {Guljamow, Arthur and Barchewitz, Tino and Große, Rebecca and Timm, Stefan and Hagemann, Martin and Dittmann, Elke},
title = {Diel Variations of Extracellular Microcystin Influence the Subcellular Dynamics of RubisCO in Microcystis aeruginosa PCC 7806},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {1154},
issn = {1866-8372},
doi = {10.25932/publishup-52128},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-521287},
pages = {16},
year = {2021},
abstract = {The ubiquitous freshwater cyanobacterium Microcystis is remarkably successful, showing a high tolerance against fluctuations in environmental conditions. It frequently forms dense blooms which can accumulate significant amounts of the hepatotoxin microcystin, which plays an extracellular role as an infochemical but also acts intracellularly by interacting with proteins of the carbon metabolism, notably with the CO2 fixing enzyme RubisCO. Here we demonstrate a direct link between external microcystin and its intracellular targets. Monitoring liquid cultures of Microcystis in a diel experiment revealed fluctuations in the extracellular microcystin content that correlate with an increase in the binding of microcystin to intracellular proteins. Concomitantly, reversible relocation of RubisCO from the cytoplasm to the cell's periphery was observed. These variations in RubisCO localization were especially pronounced with cultures grown at higher cell densities. We replicated these effects by adding microcystin externally to cultures grown under continuous light. Thus, we propose that microcystin may be part of a fast response to conditions of high light and low carbon that contribute to the metabolic flexibility and the success of Microcystis in the field.},
language = {en}
}
@misc{RomeroMujalliRochowKahletal.2021,
author = {Romero-Mujalli, Daniel and Rochow, Markus and Kahl, Sandra M. and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph},
title = {Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies},
series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {1170},
issn = {1866-8372},
doi = {10.25932/publishup-52320},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523201},
pages = {19},
year = {2021},
abstract = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.},
language = {en}
}
@misc{CahsanWestburyParaskevopoulouetal.2021,
author = {Cahsan, Binia De and Westbury, Michael V. and Paraskevopoulou, Sofia and Drews, Hauke and Ott, Moritz and Gollmann, G{\"u}nter and Tiedemann, Ralph},
title = {Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian},
series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {6},
issn = {1866-8372},
doi = {10.25932/publishup-52314},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523140},
pages = {14},
year = {2021},
abstract = {Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.},
language = {en}
}
@phdthesis{Borghi2021,
author = {Borghi, Gian Luca},
title = {Evolution and diversity of photosynthetic metabolism in C3, C3-C4 intermediate and C4 plants},
doi = {10.25932/publishup-52220},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522200},
school = {Universit{\"a}t Potsdam},
pages = {163},
year = {2021},
abstract = {In C3 plants, CO2 diffuses into the leaf and is assimilated by the Calvin-Benson cycle in the mesophyll cells. It leaves Rubisco open to its side reaction with O2, resulting in a wasteful cycle known as photorespiration. A sharp fall in atmospheric CO2 levels about 30 million years ago have further increased the side reaction with O2. The pressure to reduce photorespiration led, in over 60 plant genera, to the evolution of a CO2-concentrating mechanism called C4 photosynthesis; in this mode, CO2 is initially incorporated into 4-carbon organic acids, which diffuse to the bundle sheath and are decarboxylated to provide CO2 to Rubisco. Some genera, like Flaveria, contain several species that represent different steps in this complex evolutionary process. However, the majority of terrestrial plant species did not evolve a CO2-concentrating mechanism and perform C3 photosynthesis. This thesis compares photosynthetic metabolism in several species with C3, C4 and intermediate modes of photosynthesis. Metabolite profiling and stable isotope labelling were performed to detect inter-specific differences changes in metabolite profile and, hence, how a pathway operates. The results obtained were subjected to integrative data analyses like hierarchical clustering and principal component analysis, and were deepened by correlation analyses to uncover specific metabolic features and reaction steps that were conserved or differed between species. The main findings are that Calvin-Benson cycle metabolite profiles differ between C3 and C4 species and between different C3 species, including a very different response to rising irradiance in Arabidopsis and rice. These findings confirm Calvin-Benson cycle operation diverged between C3 and C4 species and, most unexpectedly, even between different C3 species. Moreover, primary metabolic profiles supported the current C4 evolutionary model in the genus Flaveria and also provided new insights and opened up new questions. Metabolite profiles also point toward a progressive adjustment of the Calvin-Benson cycle during the evolution of C4 photosynthesis. Overall, this thesis point out the importance of a metabolite-centric approach to uncover underlying differences in species apparently sharing the same photosynthetic routes and as a valid method to investigate evolutionary transition between C3 and C4 photosynthesis.},
language = {en}
}
@phdthesis{Krumbholz2021,
author = {Krumbholz, Julia},
title = {Identification of chemical mediators that regulate the specialized metabolism in Nostoc punctiforme},
doi = {10.25932/publishup-54024},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-540240},
school = {Universit{\"a}t Potsdam},
pages = {xxiii, 187},
year = {2021},
abstract = {Specialized metabolites, so-called natural products, are produced by a variety of different organisms, including bacteria and fungi. Due to their wide range of different biological activities, including pharmaceutical relevant properties, microbial natural products are an important source for drug development. They are encoded by biosynthetic gene clusters (BGCs), which are a group of locally clustered genes. By screening genomic data for genes encoding typical core biosynthetic enzymes, modern bioinformatical approaches are able to predict a wide range of BGCs. To date, only a small fraction of the predicted BGCs have their associated products identified. The phylum of the cyanobacteria has been shown to be a prolific, but largely untapped source for natural products. Especially multicellular cyanobacterial genera, like Nostoc, harbor a high amount of BGCs in their genomes. A main goal of this study was to develop new concepts for the discovery of natural products in cyanobacteria. Due to its diverse setup of orphan BGCs and its amenability to genetic manipulation, Nostoc punctiforme PCC 73102 (N. punctiforme) appeared to be a promising candidate to be established as a model organism for natural product discovery in cyanobacteria. By utilizing a combination of genome-mining, bioactivity-screening, variations of culture conditions, as well as metabolic engineering, not only two new polyketides were discovered, but also first-time insights into the regulation of the specialized metabolism in N. punctiforme were gained during this study. The cultivation of N. punctiforme to very high densities by utilizing increasing light intensities and CO2 levels, led to an enhanced metabolite production, causing rather complex metabolite extracts. By utilizing a library of CFP reporter mutant strains, each strain reporting for one of the predicted BGCs, it was shown that eight out of 15 BGCs were upregulated under high density (HD) cultivation conditions. Furthermore, it could be demonstrated that the supernatant of an HD culture can increase the expression of four of the influenced BGCs, even under conventional cultivation conditions. This led to the hypothesis that a chemical mediator encoded by one of the affected BGCs is accumulating in the HD supernatant and is able to increase the expression of other BGCs as part of a cell-density dependent regulatory circuit. To identify which of the BGCs could be a main trigger of the presumed regulatory circuit, it was tried to activate four BGCs (pks1, pks2, ripp3, ripp4) selectively by overexpression of putative pathway-specific regulatory genes that were found inside the gene clusters. Transcriptional analysis of the mutants revealed that only the mutant strain targeting the pks1 BGC, called AraC_PKS1, was able to upregulate the expression of its associated BGC. From an RNA sequencing study of the AraC_PKS1 mutant strain, it was discovered that beside pks1, the orphan BGCs ripp3 and ripp4 were also upregulated in the mutant strain. Furthermore, it was observed that secondary metabolite production in the AraC_PKS1 mutant strain is further enhanced under high-light and high-CO2 cultivation conditions. The increased production of the pks1 regulator NvlA also had an impact on other regulatory factors, including sigma factors and the RNA chaperone Hfq. Analysis of the AraC_PKS1 cell and supernatant extracts led to the discovery of two novel polyketides, nostoclide and nostovalerolactone, both encoded by the pks1 BGC. Addition of the polyketides to N. punctiforme WT demonstrated that the pks1-derived compounds are able to partly reproduce the effects on secondary metabolite production found in the AraC_PKS1 mutant strain. This indicates that both compounds are acting as extracellular signaling factors as part of a regulatory network. Since not all transcriptional effects that were found in the AraC_PKS1 mutant strain could be reproduced by the pks1 products, it can be assumed that the regulator NvlA has a global effect and is not exclusively specific to the pks1 pathway. This study was the first to use a putative pathway specific regulator for the specific activation of BGC expression in cyanobacteria. This strategy did not only lead to the detection of two novel polyketides, it also gave first-time insights into the regulatory mechanism of the specialized metabolism in N. punctiforme. This study illustrates that understanding regulatory pathways can aid in the discovery of novel natural products. The findings of this study can guide the design of new screening strategies for bioactive compounds in cyanobacteria and help to develop high-titer production platforms for cyanobacterial natural products.},
language = {en}
}
@phdthesis{Hasnat2021,
author = {Hasnat, Muhammad Abrar},
title = {A-Type Carrier Proteins are involved in [4Fe-4S] Cluster insertion into the Radical S-adenosylmethionine (SAM) Protein MoaA and other molybdoenzymes},
doi = {10.25932/publishup-53079},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-530791},
school = {Universit{\"a}t Potsdam},
pages = {200},
year = {2021},
abstract = {Iron-sulfur clusters are essential enzyme cofactors. The most common and stable clusters are [2Fe-2S] and [4Fe-4S] that are found in nature. They are involved in crucial biological processes like respiration, gene regulation, protein translation, replication and DNA repair in prokaryotes and eukaryotes. In Escherichia coli, Fe-S clusters are essential for molybdenum cofactor (Moco) biosynthesis, which is a ubiquitous and highly conserved pathway. The first step of Moco biosynthesis is catalyzed by the MoaA protein to produce cyclic pyranopterin monophosphate (cPMP) from 5'GTP. MoaA is a [4Fe-4S] cluster containing radical S-adenosyl-L-methionine (SAM) enzyme. The focus of this study was to investigate Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions using E. coli as a model organism. Nitrate and TMAO respiration usually occur under anaerobic conditions, where oxygen is depleted. Under these conditions, E. coli uses nitrate and TMAO as terminal electron. Previous studies revealed that Fe-S cluster insertion is performed by Fe-S cluster carrier proteins. In E. coli, these proteins are known as A-type carrier proteins (ATC) by phylogenomic and genetic studies. So far, three of them have been characterized in detail in E. coli, namely IscA, SufA, and ErpA. This study shows that ErpA and IscA are involved in Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions. ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. SufA is not able to replace the functions of IscA or ErpA under nitrate respiratory conditions. Nitrate reductase is a molybdoenzyme that coordinates Moco and Fe-S clusters. Under nitrate respiratory conditions, the expression of nitrate reductase is significantly increased in E. coli. Nitrate reductase is encoded in narGHJI genes, the expression of which is regulated by the transcriptional regulator, fumarate and nitrate reduction (FNR). The activation of FNR under conditions of nitrate respiration requires one [4Fe-4S] cluster. In this part of the study, we analyzed the insertion of Fe-S cluster into FNR for the expression of narGHJI genes in E. coli. The results indicate that ErpA is essential for the FNR-dependent expression of the narGHJI genes, a role that can be replaced partially by IscA and SufA when they are produced sufficiently under the conditions tested. This observation suggests that ErpA is indirectly regulating nitrate reductase expression via inserting Fe-S clusters into FNR. Most molybdoenzymes are complex multi-subunit and multi-cofactor-containing enzymes that coordinate Fe-S clusters, which are functioning as electron transfer chains for catalysis. In E. coli, periplasmic aldehyde oxidoreductase (PaoAC) is a heterotrimeric molybdoenzyme that consists of flavin, two [2Fe-2S], one [4Fe-4S] cluster and Moco. In the last part of this study, we investigated the insertion of Fe-S clusters into E. coli periplasmic aldehyde oxidoreductase (PaoAC). The results show that SufA and ErpA are involved in inserting [4Fe-4S] and [2Fe-2S] clusters into PaoABC, respectively under aerobic respiratory conditions.},
language = {en}
}
@phdthesis{Dahmani2021,
author = {Dahmani, Ismail},
title = {Influenza A virus matrix protein M1},
doi = {10.25932/publishup-52740},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-527409},
school = {Universit{\"a}t Potsdam},
pages = {XI, 147},
year = {2021},
abstract = {Influenza A virus (IAV) is a pathogen responsible for severe seasonal epidemics threatening human and animal populations every year. During the viral assembly process in the infected cells, the plasma membrane (PM) has to bend in localized regions into a vesicle towards the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. M1 is the most abundant protein in IAV particles. It plays an important role in virus assembly and budding at the PM. M1 is recruited to the host cell membrane where it associates with lipids and other viral proteins. However, the details of M1 interactions with the cellular PM, as well as M1-mediated membrane bending at the budozone, have not been clarified. In this work, we used several experimental approaches to analyze M1-lipids and M1-M1 interactions. By performing SPR analysis, we quantified membrane association for full-length M1 and different genetically engineered M1 constructs (i.e., N- and C-terminally truncated constructs and a mutant of the polybasic region). This allowed us to obtain novel information on the protein regions mediating M1 binding to membranes. By using fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), and three-dimensional (3D) tomography (cryo-ET), we showed that M1 is indeed able to cause membrane deformation on vesicles containing negatively-charged lipids, in the absence of other viral components. Further, sFCS analysis proved that simple protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1-M1 interactions and multimer formation are required to alter the bilayer three-dimensional structure through the formation of a protein scaffold. Finally, to mimic the budding mechanism in cells that arise by the lateral organization of the virus membrane components on lipid raft domains, we created vesicles with lipid domains. Our results showed that local binding of M1 to spatial confined acidic lipids within membrane domains of vesicles led to local M1 inward curvature.},
language = {en}
}
@misc{MuenchAbdelilahSeyfried2021,
author = {M{\"u}nch, Juliane and Abdelilah-Seyfried, Salim},
title = {Sensing and Responding of Cardiomyocytes to Changes of Tissue Stiffness in the Diseased Heart},
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-54580},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-545805},
pages = {15},
year = {2021},
abstract = {Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology.},
language = {en}
}
@article{FloederYongKlauschiesetal.2021,
author = {Fl{\"o}der, Sabine and Yong, Joanne and Klauschies, Toni and Gaedke, Ursula and Poprick, Tobias and Brinkhoff, Thorsten and Moorthi, Stefanie},
title = {Intraspecific trait variation alters the outcome of competition in freshwater ciliates},
series = {Ecology and evolution},
volume = {11},
journal = {Ecology and evolution},
number = {15},
publisher = {Wiley},
address = {Hoboken},
issn = {2045-7758},
doi = {10.1002/ece3.7828},
pages = {10225 -- 10243},
year = {2021},
abstract = {Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The ciliates competed for the microalgae Cryptomonas sp. (Cry) and Navicula pelliculosa (Nav), and the bacteria present in the cultures over a period of 33 days. We used monoclonal Euplotes and three different Coleps clones (Col 1, Col 2, and Col 3) in the experiment that could be distinguished by a newly developed rDNA-based molecular assay based on the internal transcribed spacer (ITS) regions. While Euplotes feeds on Cry and on bacteria, the Coleps clones cannot survive on bacteria alone but feed on both Cry and Nav with clone-specific rates. Experimental treatments comprised two-species mixtures of Euplotes and one or all of the three different Coleps clones, respectively. We found intraspecific variation in the traits "selectivity" and "maximum ingestion rate" for the different algae to significantly affect the competitive outcome between the two ciliate species. As Nav quickly escaped top-down control and likely reached a state of low food quality, ciliate competition was strongly determined by the preference of different Coleps clones for Cry as opposed to feeding on Nav. In addition, the ability of Euplotes to use bacteria as an alternative food source strengthened its persistence once Cry was depleted. Hence, trait variation at both trophic levels codetermined the population dynamics and the outcome of species competition.},
language = {en}
}
@article{BaunachChowdhuryStallforthetal.2021,
author = {Baunach, Martin and Chowdhury, Somak and Stallforth, Pierre and Dittmann-Th{\"u}nemann, Elke},
title = {The landscape of recombination events that create nonribosomal peptide diversity},
series = {Molecular biology and evolution : MBE},
volume = {38},
journal = {Molecular biology and evolution : MBE},
number = {5},
publisher = {Oxford Univ. Press},
address = {Oxford},
issn = {0737-4038},
doi = {10.1093/molbev/msab015},
pages = {2116 -- 2130},
year = {2021},
abstract = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.},
language = {en}
}
@article{RuthsatzScherzVences2021,
author = {Ruthsatz, Katharina and Scherz, Mark D. and Vences, Miguel},
title = {Dissecting the tree of life},
series = {Zootaxa : an international journal of zootaxonomy ;},
volume = {5016},
journal = {Zootaxa : an international journal of zootaxonomy ;},
number = {3},
publisher = {Magnolia Press},
address = {Auckland},
issn = {1175-5326},
doi = {10.11646/zootaxa.5016.3.10},
pages = {448 -- 450},
year = {2021},
language = {en}
}
@article{SchneebergerEccard2021,
author = {Schneeberger, Karin and Eccard, Jana},
title = {Experience of social density during early life is associated with attraction to conspecific odour in the common vole (Microtus arvalis)},
series = {Ethology : international journal of behavioural biology},
volume = {127},
journal = {Ethology : international journal of behavioural biology},
number = {10},
publisher = {Wiley-Blackwell},
address = {Berlin},
issn = {0179-1613},
doi = {10.1111/eth.13211},
pages = {908 -- 913},
year = {2021},
abstract = {Social organisation in species with fluctuating population sizes can change with density. Therefore, information on (future) density obtained during early life stages may be associated with social behaviour. Olfactory cues may carry important social information. We investigated whether early life experience of different experimental densities was subsequently associated with differences in attraction to adult conspecific odours. We used common voles (Microtus arvalis), a rodent species undergoing extreme density fluctuations. We found that individuals originating from high experimental density populations kept in large outdoor enclosures invested more time in inspecting conspecific olfactory cues than individuals from low-density populations. Generally, voles from both treatments spent more time with the olfactory cues than expected by chance and did not differ in their latency to approach the odour samples. Our findings indicate either that early experience affects odour sensitivity or that animals evaluate the social information contained in conspecific odours differently, depending on their early life experience of conspecific density.},
language = {en}
}
@article{MalchowBocediPalmeretal.2021,
author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
title = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes},
series = {Ecography},
volume = {44},
journal = {Ecography},
number = {10},
publisher = {John Wiley \& Sons, Inc.},
address = {New Jersey},
issn = {1600-0587},
pages = {10},
year = {2021},
abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
language = {en}
}
@misc{MalchowBocediPalmeretal.2021,
author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
title = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes},
series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {10},
issn = {1866-8372},
doi = {10.25932/publishup-52397},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523979},
pages = {12},
year = {2021},
abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
language = {en}
}
@article{KoekerAkcaalanDittmannetal.2021,
author = {K{\"o}ker, Latife and Ak{\c{c}}aalan, Reyhan and Dittmann, Elke and Albay, Meri{\c{c}}},
title = {Depth profiles of protein-bound microcystin in K{\"u}{\c{c}}{\"u}k{\c{c}}ekmece Lagoon},
series = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
volume = {198},
journal = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
publisher = {Elsevier},
address = {Oxford},
issn = {0041-0101},
doi = {10.1016/j.toxicon.2021.05.005},
pages = {156 -- 163},
year = {2021},
abstract = {Microcystis is the most commonly found toxic cyanobacterial genus around the world and has a negative impact on the ecosystem. As a predominant producer of the potent hepatotoxin microcystin (MC), the genus causes outbreaks in freshwaters worldwide. Standard analytical methods that are used for the detection of microcystin variants can only measure the free form of microcystin in cells. Since microcystin was found as free and proteinbound forms in the cells, a significant proportion of microcystin is underestimated with analytical methods. The aim of the study was to measure protein-bound microcystins and determine the environmental factors that affect the binding of microcystin to proteins. Samples were taken at depths of surface, 1 m, 5 m, 10 m, 15 m, and 18 m in Kucukcekmece Lagoon to analyze depth profiles of two different microcystin forms from June to September 2012 at regular monthly intervals. Our findings suggest that the most important parameter affecting proteinbound microcystin at surface water is high light. Due to favorable environmental conditions such as temperature, light, and physicochemical parameters, the higher microcystin contents, both free and protein-bound MCs, were found in summer periods.},
language = {en}
}
@article{MuenchAbdelilahSeyfried2021,
author = {M{\"u}nch, Juliane and Abdelilah-Seyfried, Salim},
title = {Sensing and responding of cardiomyocytes to changes of tissue stiffness in the diseased heart},
series = {Frontiers in cell developmental biology},
volume = {9},
journal = {Frontiers in cell developmental biology},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {2296-634X},
doi = {10.3389/fcell.2021.642840},
pages = {13},
year = {2021},
abstract = {Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology.},
language = {en}
}
@article{BornhorstAbdelilahSeyfried2021,
author = {Bornhorst, Dorothee and Abdelilah-Seyfried, Salim},
title = {Strong as a Hippo's Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development},
series = {Frontiers in Cell and Developmental Biology},
volume = {9},
journal = {Frontiers in Cell and Developmental Biology},
publisher = {Frontiers Media},
address = {Lausanne, Schweiz},
issn = {2296-634X},
doi = {10.3389/fcell.2021.731101},
pages = {1 -- 10},
year = {2021},
abstract = {The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology.},
language = {en}
}
@article{EilersKleineEckertetal.2021,
author = {Eilers, Elisabeth Johanna and Kleine, Sandra and Eckert, Silvia and Waldherr, Simon and M{\"u}ller, Caroline},
title = {Flower production, headspace volatiles, pollen nutrients, and florivory in tanacetum vulgare chemotypes},
series = {Frontiers in plant science : FPLS},
volume = {11},
journal = {Frontiers in plant science : FPLS},
publisher = {Frontiers Media},
address = {Lausanne},
issn = {1664-462X},
doi = {10.3389/fpls.2020.611877},
pages = {17},
year = {2021},
abstract = {Floral volatiles and reward traits are major drivers for the behavior of mutualistic as well as antagonistic flower visitors, i.e., pollinators and florivores. These floral traits differ tremendously between species, but intraspecific differences and their consequences on organism interactions remain largely unknown. Floral volatile compounds, such as terpenoids, function as cues to advertise rewards to pollinators, but should at the same time also repel florivores. The reward composition, e.g., protein and lipid contents in pollen, differs between individuals of distinct plant families. Whether the nutritional value of rewards within the same plant species is linked to their chemotypes, which differ in their pattern of specialized metabolites, has yet not been investigated. In the present study, we compared Tanacetum vulgare plants of five terpenoid chemotypes with regard to flower production, floral headspace volatiles, pollen macronutrient and terpenoid content, and floral attractiveness to florivorous beetles. Our analyses revealed remarkable differences between the chemotypes in the amount and diameter of flower heads, duration of bloom period, and pollen nutritional quality. The floral headspace composition of pollen-producing mature flowers, but not of premature flowers, was correlated to that of pollen and leaves in the same plant individual. For two chemotypes, florivorous beetles discriminated between the scent of mature and premature flower heads and preferred the latter. In semi-field experiments, the abundance of florivorous beetles and flower tissue miners differed between T. vulgare chemotypes. Moreover, the scent environment affected the choice and beetles were more abundant in homogenous plots composed of one single chemotype than in plots with different neighboring chemotypes. In conclusion, flower production, floral metabolic composition and pollen quality varied to a remarkable extend within the species T. vulgare, and the attractiveness of floral scent differed also intra-individually with floral ontogeny. We found evidence for a trade-off between pollen lipid content and pollen amount on a per-plant-level. Our study highlights that chemotypes which are more susceptible to florivory are less attacked when they grow in the neighborhood of other chemotypes and thus gain a benefit from high overall chemodiversity.},
language = {en}
}
@article{SteppertSteppertSterlaccietal.2021,
author = {Steppert, Claus and Steppert, Isabel and Sterlacci, William and Bollinger, Thomas},
title = {Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath},
series = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
volume = {15},
journal = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
number = {2},
publisher = {IOP Publ. Ltd.},
address = {Bristol},
issn = {1752-7163},
doi = {10.1088/1752-7163/abe5ca},
pages = {8},
year = {2021},
abstract = {There is an urgent need for screening of patients with a communicable viral disease to cut infection chains. Recently, we demonstrated that ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is able to identify influenza-A infections in patients' breath. With a decreasing influenza epidemic and upcoming SARS-CoV-2 infections we proceeded further and analyzed patients with suspected SARS-CoV-2 infections. In this study, the nasal breath of 75 patients (34 male, 41 female, aged 64.4 +/- 15.4 years) was investigated by MCC-IMS for viral infections. Fourteen were positively diagnosed with influenza-A infection and sixteen with SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) of nasopharyngeal swabs. In one patient RT-PCR was highly suspicious of SARS-CoV-2 but initially inconclusive. The remaining 44 patients served as controls. Breath fingerprints for specific infections were assessed by a combination of cluster analysis and multivariate statistics. There were no significant differences in gender or age according to the groups. In the cross validation of the discriminant analysis 72 of the 74 clearly defined patients could be correctly classified to the respective group. Even the inconclusive patient could be mapped to the SARS-CoV-2 group by applying the discrimination functions. Conclusion: SARS-CoV-2 infection and influenza-A infection can be detected with the help of MCC-IMS in breath in this pilot study. As this method provides a fast non-invasive diagnosis it should be further developed in a larger cohort for screening of communicable viral diseases. A validation study is ongoing during the second wave of COVID-19. Trial registration: ClinicalTrial.gov, NCT04282135 Registered 20 February 2020-Retrospectively registered,},
language = {en}
}
@article{ApriyantoTambunan2021,
author = {Apriyanto, Ardha and Tambunan, Van Basten},
title = {Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil},
series = {Data in Brief},
volume = {34},
journal = {Data in Brief},
publisher = {Elsevier},
address = {Amsterdam},
issn = {2352-3409},
doi = {10.1016/j.dib.2021.106745},
pages = {7},
year = {2021},
abstract = {Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is an essential insect pollinator in oil palm plantations. Recently, researches have been undertaken to improve pollination efficiency using this species. A fundamental understanding of the genes related to this pollinator behavior is necessary to achieve this goal. Here, we present the draft genome sequence, annotation, and simple sequence repeat (SSR) marker data for this pollinator. In total, 34.97 Gb of sequence data from one male individual (monoisolate) were obtained using Illumina short-read platform NextSeq 500. The draft genome assembly was found to be 269.79 Mb and about 59.9\% of completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 26.566 genes. Also, a total of 281.668 putative SSR markers were identified. This draft genome sequence is a valuable resource for understanding the population genetics, phylogenetics, dispersal patterns, and behavior of this species.},
language = {en}
}
@article{LiYangSunetal.2021,
author = {Li, Xiaoxiao and Yang, Wei and Sun, Tao and Gaedke, Ursula},
title = {Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed},
series = {Marine biology : international journal on life in oceans and coastal waters},
volume = {168},
journal = {Marine biology : international journal on life in oceans and coastal waters},
number = {5},
publisher = {Springer},
address = {Berlin ; Heidelberg},
issn = {0025-3162},
doi = {10.1007/s00227-021-03878-z},
pages = {17},
year = {2021},
abstract = {Seagrass beds are important habitats in coastal areas but increasingly decline in area and quality, thus conservation measures are urgently needed. Quantitative food webs, describing the biomass distribution and energy fluxes among trophic groups, reveal structural and functional aspects of ecosystems. Their knowledge can improve ecological conservation. For the recently discovered large warm-temperate seagrass (Zostera japonica) habitat in China's Yellow River Delta wetland, we used delta C-13 and delta N-15 measurements and a Bayesian isotope mixing model to construct its food web diagram with quantitative estimations of consumer diet compositions, comprising detritus and 14 living trophic groups from primary producers to fish. We then estimated the quantitative food web fluxes based on biomass measurements and calculated corresponding ecosystem functions. Pelagic producers were significantly C-13-depleted compared to benthic sources. Consumers (except zooplankton) were increasingly C-13-depleted with increasing trophic positions even though the consumed benthic production surpassed the pelagic one. Bivalves dominated consumer biomasses and fluxes and were the first to connect the pelagic and benthic pathways, whereas zooplankton and gastropods were specialized on the two pathways, respectively. We found flat biomass and production pyramids indicating low trophic transfer efficiencies. Generally, the energetic structure of the quantitative food web was consistent with the stable isotope analysis, and the estimated net primary production and most estimated production to biomass ratios of the trophic groups fell within literature ranges. This study provides a systematical understanding of the quantitative trophic ecology of a seagrass bed and facilitates synergistic knowledge on management, conservation, and restoration.},
language = {en}
}
@article{WarmtFenzelHenkeletal.2021,
author = {Warmt, Christian and Fenzel, Carolin Kornelia and Henkel, J{\"o}rg and Bier, Frank Fabian},
title = {Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes},
series = {Scientific reports},
volume = {11},
journal = {Scientific reports},
number = {1},
publisher = {Macmillan Publishers Limited, part of Springer Nature},
address = {[London]},
issn = {2045-2322},
doi = {10.1038/s41598-021-99774-z},
pages = {9},
year = {2021},
abstract = {In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1\% Cy5-dUTP and 99\% unlabelled dTTP we were able to detect the bla(CTX-M15) gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.},
language = {en}
}
@article{MazzaGuenther2021,
author = {Mazza, Valeria and G{\"u}nther, Anja},
title = {City mice and country mice},
series = {Animal behaviour},
volume = {172},
journal = {Animal behaviour},
publisher = {Elsevier},
address = {Amsterdam},
issn = {0003-3472},
doi = {10.1016/j.anbehav.2020.12.007},
pages = {197 -- 210},
year = {2021},
abstract = {The ability to produce innovative behaviour is a key determinant in the successful coping with environmental challenges and changes. The expansion of human-altered environments presents wildlife with multiple novel situations in which innovativeness could be beneficial. A better understanding of the drivers of within-species variation in innovation propensity and its consequences will provide insights into the traits enabling animals to thrive in the face of human-induced rapid environmental change. We compared problem-solving performance of 31 striped field mice, Apodemus agrarius, originating from rural or urban environments in a battery of eight foraging extraction tasks. We tested whether differences in problem-solving performance were mediated by the extent and duration of the animal's exploration of the experimental set-ups, the time required to solve the tasks, and their persistence. In addition, we tested the influence of the diversity of motor responses, as well as of behavioural traits boldness and activity on problem-solving performance. Urban individuals were better problem solvers despite rural individuals approaching faster and interacting longer with the test set-ups. Participation rates and time required to solve a task did not differ between rural and urban individuals. However, in case of failure to solve a task, rural mice were more persistent. The best predictors of solving success, aside from the area of origin, were the time spent exploring the set-ups and boldness, while activity and diversity of motor responses did not explain it. Problem-solving ability could thus be a contributing factor to the successful coping with the rapid and recent expansion of human-altered environments.},
language = {en}
}
@phdthesis{Woehlecke2021,
author = {Woehlecke, Sandra},
title = {Das erweiterte Fachwissen f{\"u}r den schulischen Kontext als Leitlinie f{\"u}r eine additive fachliche Lehrveranstaltung im Lehramtsstudium Biologie},
doi = {10.25932/publishup-52120},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-521209},
school = {Universit{\"a}t Potsdam},
pages = {304},
year = {2021},
abstract = {Das Fachwissen von Lehrkr{\"a}ften weist f{\"u}r die Auspr{\"a}gung fachdidaktischer Expertise eine hohe Bedeutung auf. Welche Merkmale universit{\"a}re Lehrveranstaltungen aufweisen sollten, um Lehramtsstudierenden ein berufsspezifisches Fachwissen zu vermitteln, ist jedoch {\"u}berwiegend noch unklar. Innerhalb des Projekts PSI-Potsdam wurde auf theoretischer Grundlage das fach{\"u}bergreifende Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext entwickelt. Als Ansatz zur Verbesserung des Biologie-Lehramtsstudiums diente dieses Modell als Konzeptionsgrundlage f{\"u}r eine additive Lehrveranstaltung. Hierbei werden Lerngelegenheiten geboten, um das universit{\"a}r erworbene Fachwissen {\"u}ber zellbiologische Inhalte auf schulische Kontexte anzuwenden, z.B. durch die Dekonstruktion und anschließende Rekonstruktion von schulischen Lerntexten. Die Wirkung des Seminars wurde in mehreren Zyklen im Forschungsformat der Fachdidaktischen Entwicklungsforschung beforscht. Eine der zentralen Forschungsfragen lautet dabei: Wie kann eine Lerngelegenheit f{\"u}r Lehramtsstudierende der Biologie gestaltet sein, um ein erweitertes Fachwissen f{\"u}r den schulischen Kontext f{\"u}r den zellbiologischen Themenbereich „Struktur und Funktion der Biomembran" zu f{\"o}rdern? Anhand fall{\"u}bergreifender Analysen (n = 29) wird im empirischen Teil aufgezeigt, welche Einstellungen zum Lehramtsstudium in der Stichprobe bestehen. Als ein wichtiges Ergebnis kann hierbei herausgestellt werden, dass sich das Fachinteresse hinsichtlich schulisch und universit{\"a}r vermittelter Inhalte bei den untersuchten Studierenden auffallend unterscheidet, wobei dem Schulwissen ein deutlich h{\"o}heres Interesse entgegengebracht wird. Die Berufsrelevanz fachlicher Inhalte wird seitens der Studierenden h{\"a}ufig am Schulwissen festgemacht. Innerhalb konkreter Einzelfallanalysen (n = 6) wird anhand von Lernpfaden dargestellt, wie sich {\"u}ber mehrere Design-Experimente hinweg fachliche Konzepte entwickelt haben. Bei der Beschreibung wird vor allem auf Schl{\"u}sselstellen und H{\"u}rden im Lernprozess fokussiert. Aus diesen Ergebnissen folgend werden vorgenommene Iterationen f{\"u}r die einzelnen Zyklen beschrieben, die ebenfalls anhand der iterativen Entwicklung der Design-Prinzipien dargelegt werden. Es konnte gezeigt werden, dass die Schl{\"u}sselstellen sehr individuell aufgrund der subjektiv fokussierten Inhalte zu Tage treten. Meist treten sie jedoch im Zusammenhang mit der Verkn{\"u}pfung verschiedener fachlicher Konzepte oder durch kooperative Aufschl{\"u}sselungen von Konzepten auf. Fachliche H{\"u}rden konnten hingegen in Form von fachlich unangemessenen Vorstellungen fall{\"u}bergreifend identifiziert werden. Dies betrifft unter anderem die Vorstellung der Biomembran als Wand, die mit den Vorstellungen einer Schutzfunktion und einer formgebenden Funktion der Biomembran einhergeht. Weiterhin wird beleuchtet, wie das erweiterte Fachwissen f{\"u}r den schulischen Kontext zur Bearbeitung der Lernaufgaben angewendet wurde. Es hat sich gezeigt, dass sich bestimmte Lerngelegenheiten eigenen, um bestimmte Facetten des erweiterten Fachwissens zu f{\"o}rdern. Insgesamt scheint das Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext {\"a}ußerst geeignet zu sein, um anhand der Facetten und deren Beschreibungen Lerngelegenheiten oder Gestaltungsprinzipien f{\"u}r diese zu konzipieren. F{\"u}r das untersuchte Lehr-Lernarrangement haben sich kleinere Adaptationen des Modells als sinnvoll erwiesen. Hinsichtlich der Methodologie konnten Ableitungen f{\"u}r die Anwendung der fachdidaktischen Entwicklungsforschung f{\"u}r additive fachliche Lehrveranstaltungen dieser Art herausgestellt werden. Um den Professionsbezug der fachwissenschaftlichen Anteile im Lehramtsstudium zu verbessern, ist der weitere Einbezug des erweiterten Fachwissens f{\"u}r den schulischen Kontext in die fachwissenschaftlichen Studienanteile {\"u}beraus w{\"u}nschenswert.},
language = {de}
}
@article{EnzingmuellerPrechtl2021,
author = {Enzingm{\"u}ller, Carolin and Prechtl, Helmut},
title = {Constructing graphs in biology class},
series = {International journal of science and mathematics education},
volume = {19},
journal = {International journal of science and mathematics education},
number = {1},
publisher = {Springer},
address = {Dordrecht},
issn = {1571-0068},
doi = {10.1007/s10763-019-09975-2},
pages = {1 -- 19},
year = {2021},
abstract = {There has been a growing awareness that graphing is an essential part of the science curriculum. While much research has focused on student conceptions and abilities regarding graphical representations, only few studies have investigated what teachers think about them and how they use graphs in science class. The purpose of this study is to explore educational beliefs, motivation, and teaching practices of German secondary biology teachers regarding graph construction. Via questionnaire surveys, 71 teachers from different regions in Germany rated their beliefs and motivation as well as the frequency of different graph construction activities in biology class. The teachers surveyed in this study were quite motivated in their teaching of graph construction. Furthermore, they tended to believe that graph construction should be practiced explicitly in biology class and that students should learn clear strategies for constructing graphs. We found that teaching subjects and own research experience make a difference in teachers' beliefs and motivation regarding graph construction in biology class. The self-report on classroom practices revealed that participants may provide limited opportunities for students to experience graphing as a social and iterative practice. Implications are drawn for teacher education and professional development as well as for further research in teacher education contexts.},
language = {en}
}
@article{MeridaFettke2021,
author = {Merida, Angel and Fettke, J{\"o}rg},
title = {Starch granule initiation in Arabidopsis thaliana chloroplasts},
series = {The plant journal},
volume = {107},
journal = {The plant journal},
number = {3},
publisher = {Wiley},
address = {Hoboken},
issn = {0960-7412},
doi = {10.1111/tpj.15359},
pages = {688 -- 697},
year = {2021},
abstract = {The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.},
language = {en}
}
@article{RoedelAbdelilahSeyfried2021,
author = {R{\"o}del, Claudia Jasmin and Abdelilah-Seyfried, Salim},
title = {A zebrafish toolbox for biomechanical signaling in cardiovascular development and disease},
series = {Current opinion in hematology},
volume = {28},
journal = {Current opinion in hematology},
number = {3},
publisher = {Lippincott Williams \& Wilkins},
address = {Philadelphia},
issn = {1065-6251},
doi = {10.1097/MOH.0000000000000648},
pages = {198 -- 207},
year = {2021},
abstract = {Purpose of review The zebrafish embryo has emerged as a powerful model organism to investigate the mechanisms by which biophysical forces regulate vascular and cardiac cell biology during development and disease. A versatile arsenal of methods and tools is available to manipulate and analyze biomechanical signaling. This review aims to provide an overview of the experimental strategies and tools that have been utilized to study biomechanical signaling in cardiovascular developmental processes and different vascular disease models in the zebrafish embryo. Within the scope of this review, we focus on work published during the last two years. Recent findings Genetic and pharmacological tools for the manipulation of cardiac function allow alterations of hemodynamic flow patterns in the zebrafish embryo and various types of transgenic lines are available to report endothelial cell responses to biophysical forces. These tools have not only revealed the impact of biophysical forces on cardiovascular development but also helped to establish more accurate models for cardiovascular diseases including cerebral cavernous malformations, hereditary hemorrhagic telangiectasias, arteriovenous malformations, and lymphangiopathies. Summary The zebrafish embryo is a valuable vertebrate model in which in-vivo manipulations of biophysical forces due to cardiac contractility and blood flow can be performed. These analyses give important insights into biomechanical signaling pathways that control endothelial and endocardial cell behaviors. The technical advances using this vertebrate model will advance our understanding of the impact of biophysical forces in cardiovascular pathologies.},
language = {en}
}
@phdthesis{Moeser2021,
author = {M{\"o}ser, Christin},
title = {Modular DNA constructs for oligovalent bio-enhancement and functional screening},
doi = {10.25932/publishup-50728},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-507289},
school = {Universit{\"a}t Potsdam},
pages = {XIV, 148},
year = {2021},
abstract = {Deoxyribonucleic acid (DNA) nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. This dissertation covers three main projects. All of them use variations of functionalized DNA nanostructures that act as platform for oligovalent presentation of ligands. The purpose of this work was to evaluate the ability of DNA nanostructures to precisely display different types of functional molecules and to consequently enhance their efficacy according to the concept of multivalency. Moreover, functionalized DNA structures were examined for their suitability in functional screening assays. The developed DNA-based compound ligands were used to target structures in different biological systems. One part of this dissertation attempted to bind pathogens with small modified DNA nanostructures. Pathogens like viruses and bacteria are known for their multivalent attachment to host cells membranes. By blocking their receptors for recognition and/or fusion with their targeted host in an oligovalent manner, the objective was to impede their ability to adhere to and invade cells. For influenza A, only enhanced binding of oligovalent peptide-DNA constructs compared to the monovalent peptide could be observed, whereas in the case of respiratory syncytial virus (RSV), binding as well as blocking of the target receptors led to an increased inhibition of infection in vitro. In the final part, the ability of chimeric DNA-peptide constructs to bind to and activate signaling receptors on the surface of cells was investigated. Specific binding of DNA trimers, conjugated with up to three peptides, to EphA2 receptor expressing cells was evaluated in flow cytometry experiments. Subsequently, their ability to activate these receptors via phosphorylation was assessed. EphA2 phosphorylation was significantly increased by DNA trimers carrying three peptides compared to monovalent peptide. As a result of activation, cells underwent characteristic morphological changes, where they "round up" and retract their periphery. The results obtained in this work comprehensively prove the capability of DNA nanostructures to serve as stable, biocompatible, controllable platforms for the oligovalent presentation of functional ligands. Functionalized DNA nanostructures were used to enhance biological effects and as tool for functional screening of bio-activity. This work demonstrates that modified DNA structures have the potential to improve drug development and to unravel the activation of signaling pathways.},
language = {en}
}
@article{PaoliniFontanaVanCuongPhametal.2021,
author = {Paolini, Alessio and Fontana, Federica and Van-Cuong Pham, and R{\"o}del, Claudia Jasmin and Seyfried, Salim},
title = {Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish},
series = {Cell reports},
volume = {37},
journal = {Cell reports},
number = {1},
publisher = {Cell Press},
address = {Maryland Heights, MO},
issn = {2211-1247},
doi = {10.1016/j.celrep.2021.109782},
pages = {13},
year = {2021},
abstract = {In the zebrafish embryo, the onset of blood flow generates fluid shear stress on endocardial cells, which are specialized endothelial cells that line the interior of the heart. High levels of fluid shear stress activate both Notch and Klf2 signaling, which play crucial roles in atrioventricular valvulogenesis. However, it remains unclear why only individual endocardial cells ingress into the cardiac jelly and initiate valvulogenesis. Here, we show that lateral inhibition between endocardial cells, mediated by Notch, singles out Delta-like-4-positive endocardial cells. These cells ingress into the cardiac jelly, where they form an abluminal cell population. Delta-like-4-positive cells ingress in response to Wnt9a, which is produced in parallel through an Erk5Klf2-Wnt9a signaling cascade also activated by blood flow. Hence, mechanical stimulation activates parallel mechanosensitive signaling pathways that produce binary effects by driving endocardial cells toward either luminal or abluminal fates. Ultimately, these cell fate decisions sculpt cardiac valve leaflets.},
language = {en}
}
@phdthesis{Michelchen2021,
author = {Michelchen, Sophia},
title = {Etablierung einer Antigen-spezifischen Aktivierung von B-Lymphozyten in vitro},
doi = {10.25932/publishup-53027},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-530272},
school = {Universit{\"a}t Potsdam},
pages = {XII,107},
year = {2021},
abstract = {Monoklonale Antik{\"o}rper sind essenzielle Werkzeuge in der modernen Laboranalytik sowie in der medizinischen Therapie und Diagnostik. Die Herstellung monoklonaler Antik{\"o}rper ist ein zeit- und arbeitsintensiver Prozess. Herk{\"o}mmliche Methoden beruhen auf der Immunisierung von Labortieren, die mitunter mehrere Monate in Anspruch nimmt. Anschließend werden die Antik{\"o}rper-produzierenden B-Lymphozyten bzw. deren Antik{\"o}rpergene isoliert und in Screening-Verfahren untersucht, um geeignete Binder zu identifizieren. Der Transfer der humoralen Immunantwort in eine in vitro Umgebung erlaubt eine Verk{\"u}rzung des Prozesses und umgeht die Notwendigkeit der in vivo Immunisierung. Das komplexe Zusammenspiel aller involvierten Immunzellen in vitro abzubilden, stellt sich allerdings als schwierig dar. Der Schwerpunkt dieser Arbeit war deshalb die Realisierung einer vereinfachten In vitro Immunisierung, die sich auf die Protagonisten der Antik{\"o}rper-Produktion konzentriert: die B-Lymphozyten. Dar{\"u}ber hinaus sollte eine permanente Zelllinie etabliert werden, die zur Antik{\"o}rper-Herstellung eingesetzt werden und die Verwendung von Prim{\"a}rzellen ersetzen w{\"u}rde. Im ersten Teil der Arbeit wurde ein Protokoll zur In vitro Immunisierung muriner BLymphozyten etabliert. In Vorversuchen wurden die optimalen Konditionen f{\"u}r die Antigenspezifische Aktivierung gereinigter Milz-B-Lymphozyten aus nicht-immunisierten M{\"a}usen determiniert. Dazu wurde der Einfluss verschiedener Stimuli auf die Produktion unspezifischer und spezifischer Antik{\"o}rper untersucht. Eine Kombination aus dem Modellantigen VP1 (Hamster Polyomavirus H{\"u}llprotein 1), einem Anti-CD40-Antik{\"o}rper, Interleukin 4 (IL 4) und Lipopolysaccharid (LPS) oder IL 7 induzierte nachweislich eine Antigen-spezifische Antik{\"o}rper-Antwort in vitro. Als Indikatoren einer erfolgreichen Aktivierung der B-Lymphozyten infolge der in vitro Stimulation wurden die rapide Proliferation und die Expression charakteristischer Aktivierungsmarker auf der Zelloberfl{\"a}che nachgewiesen. In einer Zeitreihe {\"u}ber zehn Tage wurde am zehnten Tag der In vitro Immunisierung die verh{\"a}ltnism{\"a}ßig h{\"o}chste Konzentration Antigen-spezifischer IgG-Antik{\"o}rper im Kultur{\"u}berstand der stimulierten Zellen nachgewiesen. Als n{\"a}chster Schritt sollte eine permanente Zelllinie hergestellt werden, die statt prim{\"a}rer BLymphozyten f{\"u}r die zuvor etablierte In vitro Immunisierung eingesetzt werden k{\"o}nnte. Zu diesem Zweck wurden retrovirale Vektoren hergestellt, die durch den Transfer verschiedener Onkogene in murine B-Lymphozyten bzw. deren Vorl{\"a}uferzellen das Proliferationsverhalten der Zellen manipulieren sollen. Es wurden Retroviren mit Doxycyclin-induzierbaren Expressionskassetten mit den Onkogenen cmyc, Bcl2, BclxL und dem Fusionsgen NUP98HOXB4 generiert. Eine Testzelllinie wurde erfolgreich mit den hergestellten Retroviren transduziert und die Funktionalit{\"a}t der hergestellten Viren anhand verschiedener Assays belegt. Die transferierten Gene konnten in der Testzelllinie auf DNAEbene nachgewiesen oder die {\"U}berexpression der entsprechenden Proteine im Western Blot detektiert werden. Es wurden schließlich B-Lymphozyten bzw. unreife Vorl{\"a}uferzellen derselben mit den generierten Retroviren transduziert und mit Knochenmark-{\"a}hnlichen Stromazellen co-kultiviert. Aus keinem der transduzierten Ans{\"a}tze konnte bisher eine Zelllinie oder eine Langzeit-Kultur etabliert werden. Im letzten Teil der Arbeit wurde die Effektivit{\"a}t und {\"U}bertragbarkeit des zuvor etablierten Protokolls zur In vitro Immunisierung muriner B-Lymphozyten anhand verschiedener Antigene gezeigt. Es konnten in vitro spezifische IgG-Antworten gegen VP1, Legionella pneumophila und das Protein Mip, von dem ein Peptid in das zur Immunisierung eingesetzte VP1 integriert wurde, induziert werden. Die stimulierten B-Lymphozyten wurden durch Fusion mit Myelomzellen in permanente Antik{\"o}rper-produzierende Zelllinien transformiert. Dabei konnten mehrere Hybridomzelllinien generiert werden, die spezifische IgGAntik{\"o}rper gegen VP1 oder Mip produzieren. Die generierten Antik{\"o}rper konnten sowohl im Western Blot als auch im ELISA (Enzyme-Linked Immunosorbent Assay) das entsprechende Antigen spezifisch binden. Die hier etablierte In vitro Immunisierung bietet eine effektive Alternative zu bisherigen Verfahren zur Herstellung spezifischer Antik{\"o}rper. Sie ersetzt die Immunisierung von Versuchstieren und reduziert den Zeitaufwand erheblich. In Kombination mit der Hybridomtechnologie k{\"o}nnen die in vitro immunisierten Zellen, wie hier demonstriert, zur Generation von Hybridomzelllinien und zur Herstellung monoklonaler Antik{\"o}rper genutzt werden. Um die Verwendung von Versuchstieren in dieser Methode durch eine ad{\"a}quate permanente Zelllinie zu ersetzen, muss die genetische Ver{\"a}nderung von B-Lymphozyten und unreifen h{\"a}matopoetischen Zellen optimiert werden. Die Ergebnisse bieten eine Basis f{\"u}r eine universelle, Spezies-unabh{\"a}ngige Methodik zur Antik{\"o}rperherstellung und f{\"u}r die Etablierung einer idealen, tierfreien In vitro Immunisierung.},
language = {de}
}
@misc{GoethelListekMesserschmidtetal.2021,
author = {G{\"o}thel, Markus and Listek, Martin and Messerschmidt, Katrin and Schl{\"o}r, Anja and H{\"o}now, Anja and Hanack, Katja},
title = {A New Workflow to Generate Monoclonal Antibodies against Microorganisms},
series = {Mathematisch-Naturwissenschaftliche Reihe},
journal = {Mathematisch-Naturwissenschaftliche Reihe},
number = {20},
issn = {1866-8372},
doi = {10.25932/publishup-52334},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523341},
pages = {17},
year = {2021},
abstract = {Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms.},
language = {en}
}
@article{GoethelListekMesserschmidtetal.2021,
author = {G{\"o}thel, Markus and Listek, Martin and Messerschmidt, Katrin and Schl{\"o}r, Anja and H{\"o}now, Anja and Hanack, Katja},
title = {A New Workflow to Generate Monoclonal Antibodies against Microorganisms},
series = {Applied Sciences},
volume = {11},
journal = {Applied Sciences},
number = {20},
publisher = {MDPI},
address = {Basel},
issn = {1454-5101},
doi = {10.3390/app11209359},
pages = {15},
year = {2021},
abstract = {Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms.},
language = {en}
}
@article{MichelchenMicheelHanack2021,
author = {Michelchen, Sophia and Micheel, Burkhard and Hanack, Katja},
title = {In vitro immunization approach to generate specific murine monoclonal IgG antibodies},
series = {Journal of immunological methods : JIM},
volume = {499},
journal = {Journal of immunological methods : JIM},
publisher = {Elsevier},
address = {Amsterdam},
issn = {0022-1759},
doi = {10.1016/j.jim.2021.113149},
pages = {8},
year = {2021},
abstract = {Generating a monoclonal antibody to date is a time intense process that requires immunization of laboratory animals. The transfer of the humoral immune response into in vitro settings enables a shortening of this process and circumvents the necessity of in vivo immunization. However, to orchestrate the complex interplay of dendritic cells, T and B lymphocytes in vitro is very challenging. We therefore aimed for a simplified approach focusing on the protagonist of antibody production: the B lymphocyte. We activated purified murine B lymphocytes alone in vitro by using combinations of antigen and stimuli. We were able to induce a specific antibody response within ten days of culture against a viral coat protein as model antigen. Antibodies were of both IgM and IgG subclass. The stimulated B lymphocytes were transformed into permanently antibody-producing hybridomas by cell fusion technology. We furthermore used this method to induce a specific antibody response against L. pneumophila in vitro. We thus established a useful and effective in vitro protocol to generate monoclonal antibodies. By overcoming the necessity of in vivo immunization this protocol may be the first step towards a universal strategy to generate antibodies from various species.},
language = {en}
}
@article{FudickarRoderListeketal.2021,
author = {Fudickar, Werner and Roder, Phillip and Listek, Martin and Hanack, Katja and Linker, Torsten},
title = {Pyridinium alkynylanthracenes as sensitizers for photodynamic therapy},
series = {Photochemistry and photobiology},
volume = {98},
journal = {Photochemistry and photobiology},
number = {1},
publisher = {Wiley},
address = {Hoboken},
issn = {0031-8655},
doi = {10.1111/php.13554},
pages = {193 -- 201},
year = {2021},
abstract = {Photodynamic therapy (PDT) is a mild but effective method to treat certain types of cancer upon irradiation with visible light. Here, three isomeric methylpyridinium alkynylanthracenes 1op were evaluated as sensitizers for PDT. Upon irradiation with blue or green light, all three compounds show the ability to initiate strand breaks of plasmid DNA. The mayor species responsible for cleavage is singlet oxygen (O-1(2)) as confirmed by scavenging reagents. Only isomers 1m and 1p can be incorporated into HeLa cells, whereas isomer 1o cannot permeate through the membrane. While isomer 1m targets the cell nucleus, isomer 1p assembles in the cellular cytoplasm and impacts the cellular integrity. This is in accordance with a moderate toxicity of 1p in the dark, whereas 1m exhibits no dark toxicity. Both isomers are suitable as PDT reagents, with a CC50 of 3 mu m and 75 nm, for 1p and 1m, respectively. Thus, derivative 1m, which can be easily synthesized, becomes an interesting candidate for cancer therapy.},
language = {en}
}
@article{HasnatZupokOlasApeltetal.2021,
author = {Hasnat, Muhammad Abrar and Zupok, Arkadiusz and Olas-Apelt, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Leimk{\"u}hler, Silke},
title = {A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical S-adenosylmethionine protein MoaA for the synthesis of active molybdoenzymes},
series = {Journal of bacteriology},
volume = {203},
journal = {Journal of bacteriology},
number = {12},
publisher = {American Society for Microbiology},
address = {Washington},
issn = {1098-5530},
doi = {10.1128/JB.00086-21},
pages = {20},
year = {2021},
abstract = {Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression, and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them have been characterized in detail in Escherichia coli, namely, IscA, SufA, and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster-dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli. Our studies include the identification of the A-type carrier proteins ErpA and IscA, involved in [4Fe-4S] cluster insertion into the radical Sadenosyl-methionine (SAM) enzyme MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not appear to have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth employing nitrate respiration, based on the low level of gene expression.
IMPORTANCE Understanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics, and gene regulation. Remaining critical gaps in our knowledge include how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SufA, and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.},
language = {en}
}
@misc{CahsanKiemelWestburyetal.2021,
author = {Cahsan, Binia De and Kiemel, Katrin and Westbury, Michael V. and Lauritsen, Maike and Autenrieth, Marijke and Gollmann, G{\"u}nter and Schweiger, Silke and Stenberg, Marika and Nystr{\"o}m, Per and Drews, Hauke and Tiedemann, Ralph},
title = {Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad},
series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {14},
issn = {1866-8372},
doi = {10.25932/publishup-52388},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523883},
pages = {17},
year = {2021},
abstract = {Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Sk{\aa}ne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.},
language = {en}
}
@misc{GurkeVidalGorosquietaPajimansetal.2021,
author = {Gurke, Marie and Vidal-Gorosquieta, Amalia and Pajimans, Johanna L. A. and Wȩcek, Karolina and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Hartmann, Stefanie and Grandal-d'Anglade, Aurora and Hofreiter, Michael},
title = {Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence},
series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
number = {4},
issn = {1866-8372},
doi = {10.25932/publishup-52087},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-520875},
pages = {17},
year = {2021},
abstract = {Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.},
language = {en}
}
@article{CahsanKiemelWestburyetal.2021,
author = {Cahsan, Binia De and Kiemel, Katrin and Westbury, Michael V. and Lauritsen, Maike and Autenrieth, Marijke and Gollmann, G{\"u}nter and Schweiger, Silke and Stenberg, Marika and Nystr{\"o}m, Per and Drews, Hauke and Tiedemann, Ralph},
title = {Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad},
series = {Ecology and Evolution},
volume = {11},
journal = {Ecology and Evolution},
number = {14},
publisher = {John Wiley \& Sons, Inc.},
address = {New Jersey},
issn = {2045-7758},
pages = {15},
year = {2021},
abstract = {Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Sk{\aa}ne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.},
language = {en}
}
@article{GurkeVidalGorosquietaPajimansetal.2021,
author = {Gurke, Marie and Vidal-Gorosquieta, Amalia and Pajimans, Johanna L. A. and Wȩcek, Karolina and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Hartmann, Stefanie and Grandal-d'Anglade, Aurora and Hofreiter, Michael},
title = {Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence},
series = {PLoS ONE},
volume = {16},
journal = {PLoS ONE},
number = {4},
publisher = {Public Library of Science},
address = {San Francisco},
issn = {1932-6203},
doi = {10.1371/journal.pone.0249537},
pages = {15},
year = {2021},
abstract = {Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.},
language = {en}
}
@article{GuentherSchmidtQuittetal.2021,
author = {G{\"u}nther, Kerstin and Schmidt, Marcus and Quitt, Heinz and Heinken, Thilo},
title = {Ver{\"a}nderungen der Waldvegetation im Elbe-Havelwinkel von 1960 bis 2015},
series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
number = {41},
publisher = {Floristisch-Soziologische Arbeitsgemeinschaft},
address = {G{\"o}ttingen},
issn = {0722-494X},
doi = {10.14471/2021.41.005},
pages = {53 -- 85},
year = {2021},
abstract = {Forest ecosystems are subject to a variety of influences such as forest management, nitrogen deposition, changes in the groundwater level or the immigration of invasive species. The repetition of historical releves is an important means of documenting the resulting changes in plant communities and determining their main drivers. In 2015, we examined the vegetation change in 140 semi-permanent plots in managed forests in the Elbe valley in the NE German lowlands (Saxony-Anhalt, Brandenburg). The first survey took place from 1956 to 1963. The releves cover an almost uniquely broad spectrum of different site conditions, ranging from wet forests (alluvial, swamp and bog forests of Alnion incanae, Alnion glutinosae and Betulion pubescentis) to acidic mixed oak forests (Quercion roboris) up to acidic, mostly dry pine forests with different nutrient status (Dicrano-Pinion). We analyzed the changes in the vegetation with the help of forest stand data, winner and loser species, alpha- and beta-diversity as well as the Ellenberg indicator values for nitrogen, reaction, moisture and light. In contrast to previous resurvey studies, areas were also taken into account on which a complete change of forest stand had taken place before the second survey. Particularly in the wet forests and acidic forests with a moderately good nutrient supply, changes in the main tree species have been recorded, and many pine stands have been newly established in the meantime. The species richness has decreased overall and in almost all forest types, but the beta-diversity has remained unchanged or has increased. The Ellenberg values indicate a decrease in soil moisture in the wet forests, while the acidic pine forests in particular have become darker, richer in nutrients and more humid. The number of loser species is more than twice as high as that of the winner species, but with different developments in the individual forest types. In particular, the wet forests, the acidic mixed oak forests and the lichen-pine forests have lost most of their characteristic species. The resurvey after more than 50 years shows a different development of the individual forest types. Vegetation changes in the wet forests are mainly due to local groundwater level drawdown and the resulting increased availability of nutrients. The alluvial forests were also strongly influenced by forest interventions. The reasons for the trend towards more humid and more nutrient-rich conditions in formerly dry acidic pine and oak forests are nitrogen depositions and a succession after the abandonment of historical forms of forest use (litter raking, forest pasture). Although the individual forest types have developed differently, eutrophication, falling groundwater levels and silviculture are the most important causes for the changes in vegetation. Silvicultural interventions such as clear cutting and stand conversion with a change of tree species are at the same time the main reason why the vegetation has not been homogenized despite the leveling of the site gradient as measured by the beta-diversity.},
language = {de}
}
@article{DunsingPetrichChiantia2021,
author = {Dunsing, Valentin and Petrich, Annett and Chiantia, Salvatore},
title = {Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection},
series = {eLife},
volume = {10},
journal = {eLife},
publisher = {eLife Sciences Publications},
address = {Cambridge},
issn = {2050-084X},
doi = {10.7554/eLife.69687},
pages = {33},
year = {2021},
abstract = {Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.},
language = {en}
}
@inproceedings{DunsingPetrichChiantia2021,
author = {Dunsing, Valentin and Petrich, Annett and Chiantia, Salvatore},
title = {Spectral detection enables multi-color fluorescence fluctuation spectroscopy studies in living cells},
series = {Biophysical journal : BJ / ed. by the Biophysical Society},
volume = {120},
booktitle = {Biophysical journal : BJ / ed. by the Biophysical Society},
number = {3, Suppl. 1},
publisher = {Cell Press},
address = {Cambridge},
issn = {0006-3495},
doi = {10.1016/j.bpj.2020.11.2206},
pages = {356A -- 356A},
year = {2021},
language = {en}
}
@article{SchneebergerSchulzeScheffleretal.2021,
author = {Schneeberger, Karin and Schulze, Michael and Scheffler, Ingo and Caspers, Barbara A.},
title = {Evidence of female preference for odor of distant over local males in a bat with female dispersal},
series = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
volume = {32},
journal = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
number = {4},
publisher = {Oxford University Press},
address = {Oxford},
issn = {1045-2249},
doi = {10.1093/beheco/arab003},
pages = {657 -- 661},
year = {2021},
abstract = {Geographic variation of sexually selected male traits is common in animals. Female choice also varies geographically and several studies found female preference for local males, which is assumed to lead to local adaptation and, therefore, increases fitness. As females are the nondispersing sex in most mammalian taxa, this preference for local males might be explained by the learning of male characteristics. Studies on the preference of females in female-dispersing species are lacking so far. To find out whether such females would also show preferences for local males, we conducted a study on greater sac-winged bats (Saccopteryx bilineata), a species where females disperse and males stay in their natal colony. Male greater sac-winged bats possess a wing pouch that is filled with odoriferous secretion and fanned toward females during courtship display. In a combination of chemical analysis and behavioral preference tests, we analyzed whether the composition of wing sac secretion varies between two geographically distinct populations (300 km), and whether females show a preference for local or distant male scent. Using gas chromatography, we found significant differences in the composition of the wing sac odors between the two geographically distinct populations. In addition, the behavioral preference experiments revealed that females of both populations preferred the scent of geographically distant males over local males. The wing sac odor might thus be used to guarantee optimal outbreeding when dispersing to a new colony. This is-to our knowledge-the first study on odor preference of females of a species with female-biased dispersal.},
language = {en}
}
@article{SoeriyadiOngleyKehretal.2021,
author = {Soeriyadi, Angela H. and Ongley, Sarah E. and Kehr, Jan-Christoph and Pickford, Russel and Dittmann, Elke and Neilan, Brett A.},
title = {Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase},
series = {ChemBioChem},
volume = {23},
journal = {ChemBioChem},
number = {3},
publisher = {Wiley-VCH},
address = {Weinheim},
issn = {1439-4227},
doi = {10.1002/cbic.202100574},
pages = {6},
year = {2021},
abstract = {Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.},
language = {en}
}
@article{OuedraogoZareKorbeogoetal.2021,
author = {Ou{\´e}draogo, Karim and Zar{\´e}, Alhassane and Korb{\´e}ogo, Gabin and Ou{\´e}draogo, Oumarou and Linst{\"a}dter, Anja},
title = {Resilience strategies of West African pastoralists in response to scarce forage resources},
series = {Pastoralism : research, policy and practice},
volume = {11},
journal = {Pastoralism : research, policy and practice},
number = {1},
publisher = {SpringerOpen},
address = {Heidelberg},
issn = {2041-7136},
doi = {10.1186/s13570-021-00210-8},
pages = {14},
year = {2021},
abstract = {Finding sufficient natural fodder resources to feed livestock has become a challenge for herders in the Sahel zone of Burkina Faso. Despite the existence of pastoral reserves, the issue of fodder shortage remains unsolved. This article highlights the changes in behaviour and the evolution of pastoral practices caused by the scarcity of forage resources. These changes are defined and classified as resilience strategies. Thus, this paper aims to analyse these strategies using new semantics that calls for other forms of perceptions or approach to the questions of pastoralists' resilience strategies. Interviews (semi-structured and casual conversations), ethnographic observations and ethnobotanical surveys were used to collect data. In rangelands, such high value fodder species as Andropogon gayanus, Pennisetum pedicellatum and Dactyloctenium aegyptium that were abundant herbaceous plants during the last decades are disappearing. Concomitantly, species with lower forage value, such as Senna obtusifolia, which are more resilient to ecological disturbance factors, are colonizing rangelands. Faced with these ecological changes, pastoralists are trying to redefine and reconfigure their practices, and this implies a redefinition of their identity. They use resilience strategies such as mowing grasses, building up fodder bundles, conserving crop residues, exploiting Senna obtusifolia (a previously neglected species), using woody fodder and adapting the type of livestock and the size of the herds to the ability of pastoralists to feed them. Strategies that are older than these are the integration of agriculture with livestock and decollectivized transhumance. It is these resilience strategies that this article exposes and analyses as defence mechanisms of Sahelian pastoralists in the face of the depletion of forage resources in their environments.},
language = {en}
}
@article{KindermannDoblerNiedeggenetal.2021,
author = {Kindermann, Liana and Dobler, Magnus and Niedeggen, Daniela and Linst{\"a}dter, Anja},
title = {A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems},
series = {Ecological indicators : integrating monitoring, assessment and management},
volume = {135},
journal = {Ecological indicators : integrating monitoring, assessment and management},
publisher = {Elsevier},
address = {Amsterdam},
issn = {1470-160X},
doi = {10.1016/j.ecolind.2021.108466},
pages = {16},
year = {2021},
abstract = {Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations. Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.},
language = {en}
}
@article{deOliveiraSilvaPiratelliZurelletal.2021,
author = {de Oliveira-Silva, Anna Elizabeth and Piratelli, Augusto Jo{\~a}o and Zurell, Damaris and da Silva, Fernando Rodrigues},
title = {Vegetation cover restricts habitat suitability predictions of endemic Brazilian Atlantic Forest birds},
series = {Perspectives in Ecology and Conservation},
volume = {20},
journal = {Perspectives in Ecology and Conservation},
number = {1},
publisher = {Elsevier},
address = {Oxford},
issn = {2530-0644},
doi = {10.1016/j.pecon.2021.09.002},
pages = {1 -- 8},
year = {2021},
abstract = {Ecological niche models (ENMs) are often used to investigate how climatic variables from known occurrence records can estimate potential species range distribution. Although climate-based ENMs provide critical baseline information, the inclusion of non-climatic predictors related to vegetation cover might generate more realistic scenarios. This assumption is particularly relevant for species with life-history traits related to forest habitats and sensitive to habitat loss and fragmentation. Here, we developed ENMs for 36 Atlantic Forest endemic birds considering two sets of predictor variables: (i) climatic variables only and (ii) climatic variables combined with the percentage of remaining native vegetation. We hypothesized that the inclusion of native vegetation data would decrease the potential range distribution of forest-dependent species by limiting their occurrence in regions harboring small areas of native vegetation habitats, despite otherwise favorable climatic conditions. We also expected that habitat restriction in the climate-vegetation models would be more pronounced for highly forest-dependent birds. The inclusion of vegetation data in the modeling procedures restricted the final distribution ranges of 22 out of 36 modeled species, while the 14 remaining presented an expansion of their ranges. We observed that species with high and medium forest dependency showed higher restriction in range size predictions between predictor sets than species with low forest dependency, which showed no alteration or range expansion. Overall, our results suggest that ENMs based on climatic and landscape variables may be a useful tool for conservationists to better understand the dynamic of bird species distributions in threatened and highly fragmented regions such as the Atlantic Forest hotspot.(c) 2021 Associacao Brasileira de Cie circumflex accent ncia Ecol ogica e Conservacao. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ ).},
language = {en}
}
@article{WangLiMaetal.2021,
author = {Wang, Meng and Li, Panpan and Ma, Yao and Nie, Xiang and Grebe, Markus and Men, Shuzhen},
title = {Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis},
series = {International journal of molecular sciences},
volume = {22},
journal = {International journal of molecular sciences},
number = {1},
publisher = {MDPI},
address = {Basel},
issn = {1422-0067},
doi = {10.3390/ijms22010437},
pages = {20},
year = {2021},
abstract = {Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.},
language = {en}
}
@article{PetrichDunsingBoboneetal.2021,
author = {Petrich, Annett and Dunsing, Valentin and Bobone, Sara and Chiantia, Salvatore},
title = {Influenza A M2 recruits M1 to the plasma membrane},
series = {Biophysical journal : BJ / ed. by the Biophysical Society},
volume = {120},
journal = {Biophysical journal : BJ / ed. by the Biophysical Society},
number = {24},
publisher = {Cell Press},
address = {Cambridge},
issn = {0006-3495},
doi = {10.1016/j.bpj.2021.11.023},
pages = {5478 -- 5490},
year = {2021},
abstract = {Influenza A virus (IAV) is a respiratory pathogen that causes seasonal epidemics with significant mortality. One of the most abundant proteins in IAV particles is the matrix protein 1 (M1), which is essential for the virus structural stability. M1 organizes virion assembly and budding at the plasma membrane (PM), where it interacts with other viral components. The recruitment of M1 to the PM as well as its interaction with the other viral envelope proteins (hemagglutinin [HA], neuraminidase, matrix protein 2 [M2]) is controversially discussed in previous studies. Therefore, we used fluorescence fluctuation microscopy techniques (i.e., scanning fluorescence cross-correlation spectroscopy and number and brightness) to quantify the oligomeric state of M1 and its interactions with other viral proteins in co-transfected as well as infected cells. Our results indicate that M1 is recruited to the PM by M2, as a consequence of the strong interaction between the two proteins. In contrast, only a weak interaction between M1 and HA was observed. M1-HA interaction occurred only in the event that M1 was already bound to the PM. We therefore conclude that M2 initiates the assembly of IAV by recruiting M1 to the PM, possibly allowing its further interaction with other viral proteins.},
language = {en}
}
@article{QiuZhangBicketal.2021,
author = {Qiu, Liang and Zhang, Haoran and Bick, Thomas and Martin, Johannes and Wendler, Petra and B{\"o}ker, Alexander and Glebe, Ulrich and Xing, Chengfen},
title = {Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer},
series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
volume = {60},
journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
number = {20},
publisher = {Wiley-VCH},
address = {Weinheim},
issn = {1433-7851},
doi = {10.1002/anie.202015692},
pages = {11098 -- 11103},
year = {2021},
abstract = {Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies.},
language = {en}
}
@misc{ZurellKoenigMalchowetal.2021,
author = {Zurell, Damaris and K{\"o}nig, Christian and Malchow, Anne-Kathleen and Kapitza, Simon and Bocedi, Greta and Travis, Justin M. J. and Fandos, Guillermo},
title = {Spatially explicit models for decision-making in animal conservation and restoration},
series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
volume = {2022},
journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
edition = {4},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
issn = {1866-8372},
doi = {10.25932/publishup-54991},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549915},
pages = {1 -- 16},
year = {2021},
abstract = {Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79\%), towards the species and population level (80\%) and towards conservation (rather than restoration) applications (71\%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10\% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes.},
language = {en}
}
@article{MalchowBocediPalmeretal.2021,
author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
title = {RangeShiftR},
series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
volume = {44},
journal = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
number = {10},
publisher = {Wiley-Blackwell},
address = {Oxford [u.a.]},
issn = {1600-0587},
doi = {10.1111/ecog.05689},
pages = {1443 -- 1452},
year = {2021},
abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
language = {en}
}
@phdthesis{Egli2021,
author = {Egli, Lukas},
title = {Stabilizing agricultural systems through diversity},
doi = {10.25932/publishup-49684},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-496848},
school = {Universit{\"a}t Potsdam},
pages = {VII, 125},
year = {2021},
abstract = {In the light of climate change, rising demands for agricultural products and the intensification and specialization of agricultural systems, ensuring an adequate and reliable supply of food is fundamental for food security. Maintaining diversity and redundancy has been postulated as one generic principle to increase the resilience of agricultural production and other ecosystem services. For example, if one crop fails due to climate instability and extreme events, others can compensate the losses. Crop diversity might be particularly important if different crops show asynchronous production trends. Furthermore, spatial heterogeneity has been suggested to increase stability at larger scales as production losses in some areas can be buffered by surpluses in undisturbed ones. Besides systematically investigating the mechanisms underlying stability, identifying transformative pathways that foster them is important. In my thesis, I aim at answering the following questions: (i) How does yield stability differ between nations, regions and farms, and what is the effect of crop diversity on yield stability in relation to agricultural inputs, climate heterogeneity, climate instability and time at the national, regional or farm level? (ii) Is asynchrony between crops a better predictor of production stability than crop diversity? (iii) What is the effect of asynchrony between and within crops on stability and how is it related to crop diversity and space, respectively? (iv) What is the state of the art and what are knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with agent-based models and what are potential ways forward? In the first chapter, I provide the theoretical background for the subsequent analyses. I stress the need to better understand the resilience of social-ecological systems and particularly the stability of agricultural production. Moreover, I introduce diversity and spatial heterogeneity as two prominently discussed resilience mechanisms and describe approaches to assess resilience. In the second chapter, I combined agriculture and climate data at three levels of organization and spatial extents to investigate yield stability patterns and their relation to crop diversity, fertilizer, irrigation, climate heterogeneity and instability and time of nations globally, regions in Europe and farms in Germany using statistical analyses. Yield stability decreased from the national to the farm level. Several nations and regions substantially contributed to larger-scale stability. Crop diversity was positively associated with yield stability across all three levels of organization. This effect was typically more profound at smaller scales and in variable climates. In addition to crop diversity, climate heterogeneity was an important stabilizing mechanism especially at larger scales. These results confirm the stabilizing effect of crop diversity and spatial heterogeneity, yet their importance depends on the scale and agricultural management. Building on the findings of the second chapter, I deepened in the third chapter my research on the effect of crop diversity at the national level. In particular, I tested if asynchrony between crops, i.e. between the temporal production patterns of different crops, better predicts agricultural production stability than crop diversity. The stabilizing effect of asynchrony was multiple times higher than the effect of crop diversity, i.e. asynchrony is one important property that can explain why a higher diversity supports the stability of national food production. Therefore, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered. The previous chapters suggest that both asynchrony between crops and spatial heterogeneity are important stabilizing mechanisms. In the fourth chapter, I therefore aimed at better understanding the relative importance of asynchrony between and within crops, i.e. between the temporal production patterns of different crops and between the temporal production patterns of different cultivation areas of the same crop. Better understanding their relative importance is important to inform agricultural management decisions, but so far this has been hardly assessed. To address this, I used crop production data to study the effect of asynchrony between and within crops on the stability of agricultural production in regions in Germany and nations in Europe. Both asynchrony between and within crops consistently stabilized agricultural production. Adding crops increased asynchrony between crops, yet this effect levelled off after eight crops in regions in Germany and after four crops in nations in Europe. Combining already ten farms within a region led to high asynchrony within crops, indicating distinct production patters, while this effect was weaker when combining multiple regions within a nation. The results suggest, that both mechanisms need to be considered in agricultural management strategies that strive for more resilient farming systems. The analyses in the foregoing chapters focused at different levels of organization, scales and factors potentially influencing agricultural stability. However, these statistical analyses are restricted by data availability and investigate correlative relationships, thus they cannot provide a mechanistic understanding of the actual processes underlying resilience. In this regard, agent-based models (ABM) are a promising tool. Besides their ability to measure different properties and to integrate multiple situations through extensive manipulation in a fully controlled system, they can capture the emergence of system resilience from individual interactions and feedbacks across different levels of organization. In the fifth chapter, I therefore reviewed the state of the art and potential knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with ABMs. Next, I derived recommendations for a more effective use of ABMs in resilience research. The review suggests that the potential of ABMs is not utilized in most models as they typically focus on a single dimension of resilience and are mostly limited to one reference state, disturbance type and scale. Moreover, only few studies explicitly test the ability of different mechanisms to support resilience. To solve real-world problems related to the resilience of complex systems, ABMs need to assess multiple stability properties for different situations and under consideration of the mechanisms that are hypothesized to render a system resilient. In the sixth chapter, I discuss the major conclusions that can be drawn from the previous chapters. Moreover, I showcase the use of simulation models to identify management strategies to enhance asynchrony and thus stability, and the potential of ABMs to identify pathways to implement such strategies. The results of my thesis confirm the stabilizing effect of crop diversity, yet its importance depends on the scale, agricultural management and climate. Moreover, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered. As spatial heterogeneity and particularly asynchrony within crops strongly enhances stability, integrated management approaches are needed that simultaneously address multiple resilience mechanisms at different levels of organization, scales and time horizons. For example, the simulation suggests that only increasing the number of crops at both the pixel and landscape level avoids trade-offs between asynchrony between and within crops. If their potential is better exploited, agent-based models have the capacity to systematically assess resilience and to identify comprehensive pathways towards resilient farming systems.},
language = {en}
}
@phdthesis{Stark2021,
author = {Stark, Markus},
title = {Implications of local and regional processes on the stability of metacommunities in diverse ecosystems},
doi = {10.25932/publishup-52639},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-526399},
school = {Universit{\"a}t Potsdam},
pages = {x, 167},
year = {2021},
abstract = {Anthropogenic activities such as continuous landscape changes threaten biodiversity at both local and regional scales. Metacommunity models attempt to combine these two scales and continuously contribute to a better mechanistic understanding of how spatial processes and constraints, such as fragmentation, affect biodiversity. There is a strong consensus that such structural changes of the landscape tend to negatively effect the stability of metacommunities. However, in particular the interplay of complex trophic communities and landscape structure is not yet fully understood. In this present dissertation, a metacommunity approach is used based on a dynamic and spatially explicit model that integrates population dynamics at the local scale and dispersal dynamics at the regional scale. This approach allows the assessment of complex spatial landscape components such as habitat clustering on complex species communities, as well as the analysis of population dynamics of a single species. In addition to the impact of a fixed landscape structure, periodic environmental disturbances are also considered, where a periodical change of habitat availability, temporally alters landscape structure, such as the seasonal drying of a water body. On the local scale, the model results suggest that large-bodied animal species, such as predator species at high trophic positions, are more prone to extinction in a state of large patch isolation than smaller species at lower trophic levels. Increased metabolic losses for species with a lower body mass lead to increased energy limitation for species on higher trophic levels and serves as an explanation for a predominant loss of these species. This effect is particularly pronounced for food webs, where species are more sensitive to increased metabolic losses through dispersal and a change in landscape structure. In addition to the impact of species composition in a food web for diversity, the strength of local foraging interactions likewise affect the synchronization of population dynamics. A reduced predation pressure leads to more asynchronous population dynamics, beneficial for the stability of population dynamics as it reduces the risk of correlated extinction events among habitats. On the regional scale, two landscape aspects, which are the mean patch isolation and the formation of local clusters of two patches, promote an increase in \$\beta\$-diversity. Yet, the individual composition and robustness of the local species community equally explain a large proportion of the observed diversity patterns. A combination of periodic environmental disturbance and patch isolation has a particular impact on population dynamics of a species. While the periodic disturbance has a synchronizing effect, it can even superimpose emerging asynchronous dynamics in a state of large patch isolation and unifies trends in synchronization between different species communities. In summary, the findings underline a large local impact of species composition and interactions on local diversity patterns of a metacommunity. In comparison, landscape structures such as fragmentation have a negligible effect on local diversity patterns, but increase their impact for regional diversity patterns. In contrast, at the level of population dynamics, regional characteristics such as periodic environmental disturbance and patch isolation have a particularly strong impact and contribute substantially to the understanding of the stability of population dynamics in a metacommunity. These studies demonstrate once again the complexity of our ecosystems and the need for further analysis for a better understanding of our surrounding environment and more targeted conservation of biodiversity.},
language = {en}
}
@inproceedings{StephanBarbirzRobinsonetal.2021,
author = {Stephan, Mareike Sophia and Barbirz, Stefanie and Robinson, Tom and Yandrapalli, Naresh and Dimova, Rumiana},
title = {Bacterial mimetic systems for studying bacterial inactivation and infection},
series = {Biophysical journal : BJ / ed. by the Biophysical Society},
volume = {120},
booktitle = {Biophysical journal : BJ / ed. by the Biophysical Society},
number = {3},
publisher = {Cell Press},
address = {Cambridge},
issn = {0006-3495},
doi = {10.1016/j.bpj.2020.11.1087},
pages = {148A -- 148A},
year = {2021},
language = {en}
}
@inproceedings{DennisInaebnit2021,
author = {Dennis, Alice B. and In{\"a}bnit, Thomas},
title = {Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus)},
series = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
volume = {61},
booktitle = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
publisher = {Oxford University Press},
address = {Oxford},
issn = {1540-7063},
doi = {10.1093/icb/icab001},
pages = {E195 -- E196},
year = {2021},
language = {en}
}
@article{PetazziKoikkarahAjiTischleretal.2021,
author = {Petazzi, Roberto Arturo and Koikkarah Aji, Amit and Tischler, Nicole D. and Chiantia, Salvatore},
title = {Detection of envelope glycoprotein assembly from old world hantaviruses in the Golgi apparatus of living cells},
series = {Journal of virology},
volume = {95},
journal = {Journal of virology},
number = {4},
publisher = {American Society for Microbiology},
address = {Baltimore, Md.},
issn = {1098-5514},
doi = {10.1128/JVI.01238-20},
pages = {18},
year = {2021},
abstract = {Hantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, protein-protein interactions leading to the formation of new virions in infected cells are not fully understood. We used quantitative fluorescence microscopy (i.e., number and brightness analysis and fluorescence fluctuation spectroscopy) to monitor the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we quantified protein-protein interactions for the glycoproteins Gn and Gc from Puumala and Hantaan orthohantaviruses in several cellular models. The oligomerization of each protein was analyzed in relation to subcellular localization, concentration, and the concentration of its interaction partner. Our results indicate that, when expressed separately, Gn and Gc form, respectively, homo-tetrameric and homo-dimeric complexes, in a concentration-dependent manner. Site-directed mutations or deletion mutants showed the specificity of their homotypic interactions. When both glycoproteins were coexpressed, we observed in the Golgi apparatus clear indication of GnGc interactions and the formation of Gn-Gc multimeric protein complexes of different sizes, while using various labeling schemes to minimize the influence of the fluorescent tags. Such large glycoprotein multimers may be identified as multiple Gn viral spikes interconnected via Gc-Gc contacts. This observation provides the possible first evidence for the initial assembly steps of the viral envelope within this organelle, and does so directly in living cells.
IMPORTANCE In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. Therefore, it is important to improve our quantitative understanding of the viral assembly process in infected cells, from a molecular point of view. By applying advanced fluorescence microscopy methods, we monitored the formation of viral spike complexes in different cell types. Our data support a model for hantavirus assembly according to which viral spikes are formed via the clustering of hetero-dimers of the two viral glycoproteins Gn and Gc. Furthermore, the observation of large Gn-Gc hetero-multimers provide the possible first evidence for the initial assembly steps of the viral envelope, directly in the Golgi apparatus of living cells.},
language = {en}
}
@article{SandhageHofmannLinstaedterKindermannetal.2021,
author = {Sandhage-Hofmann, Alexandra and Linst{\"a}dter, Anja and Kindermann, Liana and Angombe, Simon and Amelung, Wulf},
title = {Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass},
series = {Global change biology},
volume = {27},
journal = {Global change biology},
number = {19},
publisher = {Blackwell Science},
address = {Oxford [u.a.]},
issn = {1354-1013},
doi = {10.1111/gcb.15779},
pages = {4601 -- 4614},
year = {2021},
abstract = {Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.},
language = {en}
}
@article{SchefflerHermanussenRogol2021,
author = {Scheffler, Christiane and Hermanussen, Michael and Rogol, Alan D.},
title = {Stunting},
series = {Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence},
volume = {106},
journal = {Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence},
number = {8},
publisher = {BMJ Publishing Group},
address = {London},
issn = {0003-9888},
doi = {10.1136/archdischild-2020-319240},
pages = {819 -- 820},
year = {2021},
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{MarzetzWacker2021,
author = {Marzetz, Vanessa and Wacker, Alexander},
title = {Evaluating the relevance of species sorting and physiological plasticity of phytoplankton communities grown in a multifactor environment},
series = {Freshwater biology / Freshwater Biological Association},
volume = {66},
journal = {Freshwater biology / Freshwater Biological Association},
number = {10},
publisher = {Wiley-Blackwell},
address = {Oxford},
issn = {0046-5070},
doi = {10.1111/fwb.13810},
pages = {1992 -- 2003},
year = {2021},
abstract = {The two important mechanisms influencing the response of phytoplankton communities to alterations of abiotic factors in their environment are difficult to distinguish: species sorting resulting from a change in interspecific competitive pressure, and phenotypic plasticity (here explicitly physiological plasticity i.e. species-specific physiological adjustment). A shift in species composition as well as physiological adjustments in species can lead to changes in fatty acid composition that determine the food quality for zooplankton consumers. We used phytoplankton communities consisting of five species and exposed them to two different light intensities, two light conditions (constant and variable), and two levels of phosphorus supply. Changes in fatty acid and species composition were analyzed. We compared community pairs differing in one factor by calculating the Bray-Curtis similarity index for the composition of both variables. Comparing the Bray-Curtis similarity index of the species composition with the index of the fatty acid composition was used to estimate the effects of species sorting and physiological plasticity. Changes in nutrient supply influenced fatty acid responses based on species sorting and physiological plasticity the most. On one hand, the relevance of physiological plasticity was highest at cultivation in different nutrient supplies but the same light environment. Conversely with low nutrients species sorting appeared to dominate the response to changes in light, while at high nutrients physiological plasticity appeared to influence the response. Overall, under low phosphorus supply the communities showed a lower total fatty acid content per carbon and had increased proportions of saturated and monounsaturated fatty acids. Instead, communities in low light produced more of eicosapentaenoic acid. Our results suggest that the relevance of species sorting and physiological plasticity in shaping the community response highly depends on the environmental factors that influence the system. Nutrient supply had the largest effect, while light had more limited conditional effects. However, all of these factors are important in shaping the food quality of the phytoplankton community for higher trophic levels.},
language = {en}
}
@article{JohnOlasMuellerRoeber2021,
author = {John, Sheeba and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd},
title = {Regulation of alternative splicing in response to temperature variation in plants},
series = {Journal of experimental botany},
volume = {72},
journal = {Journal of experimental botany},
number = {18},
publisher = {Oxford Univ. Press},
address = {Oxford},
issn = {0022-0957},
doi = {10.1093/jxb/erab232},
pages = {6150 -- 6163},
year = {2021},
abstract = {Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.},
language = {en}
}
@article{DeSousaMotaDinizCoelhoetal.2021,
author = {De Sousa Mota, Cristiano and Diniz, Ana and Coelho, Catarina and Santos-Silva, Teresa and Esmaeeli Moghaddam Tabalvandani, Mariam and Leimk{\"u}hler, Silke and Cabrita, Eurico J. and Marcelo, Filipa and Rom{\~a}o, Maria Jo{\~a}o},
title = {Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy},
series = {Journal of medicinal chemistry / American Chemical Society},
volume = {64},
journal = {Journal of medicinal chemistry / American Chemical Society},
number = {17},
publisher = {American Chemical Society},
address = {Washington},
issn = {0022-2623},
doi = {10.1021/acs.jmedchem.1c01125},
pages = {13025 -- 13037},
year = {2021},
abstract = {Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.},
language = {en}
}
@article{BrandesSicksBerger2021,
author = {Brandes, Stefanie and Sicks, Florian and Berger, Anne},
title = {Behaviour classification on giraffes (Giraffa camelopardalis) using machine learning algorithms on triaxial acceleration data of two commonly used GPS devices and its possible application for their management and conservation},
series = {Sensors},
volume = {21},
journal = {Sensors},
number = {6},
publisher = {MDPI},
address = {Basel},
issn = {1424-8220},
doi = {10.3390/s21062229},
pages = {22},
year = {2021},
abstract = {Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6\%/99.7\%; drinking: 96.7\%/97.0\%) than those with a higher variety of body postures (such as standing: 90.7-91.0\%/75.2-76.7\%; rumination: 89.6-91.6\%/53.5-86.5\%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.},
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}
}