TY  - JOUR
A1  - Fedders, Ronja
A1  - Muenzner, Matthias
A1  - Weber, Pamela
A1  - Sommerfeld, Manuela
A1  - Knauer, Miriam
A1  - Kedziora, Sarah
A1  - Kast, Naomi
A1  - Heidenreich, Steffi
A1  - Raila, Jens
A1  - Weger, Stefan
A1  - Henze, Andrea
A1  - Schupp, Michael
T1  - Liver-secreted RBP4 does not impair glucose homeostasis in mice
JF  - The journal of biological chemistry
N2  - 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.
KW  - liver
KW  - retinoid-binding protein
KW  - glucose metabolism
KW  - insulin resistance
KW  - mouse
KW  - TTR
Y1  - 2018
U6  - https://doi.org/10.1074/jbc.RA118.004294
SN  - 1083-351X
VL  - 293
IS  - 39
SP  - 15269
EP  - 15276
PB  - American Society for Biochemistry and Molecular Biology
CY  - Bethesda
ER  - 
TY  - JOUR
A1  - Wojcik, Laurie Anne
A1  - Ceulemans, Ruben
A1  - Gaedke, Ursula
T1  - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs
JF  - Ecology and Evolution
N2  - 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.
KW  - functional diversity
KW  - nutrient spike
KW  - pulse perturbation
KW  - regime shift
KW  - robustness
KW  - tritrophic food web
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8214
SN  - 2045-7758
N1  - Wojcik and Ceulemans shared first authorship.
VL  - 11
IS  - 22
SP  - 15639
EP  - 15663
PB  - John Wiley & Sons, Inc.
CY  - Hoboken (New Jersey)
ER  - 
TY  - THES
A1  - Ting, Michael Kien Yin
T1  - Circadian-regulated dynamics of translation in Arabidopsis thaliana
Y1  - 2021
ER  - 
TY  - THES
A1  - Brunacci, Nadia
T1  - Oligodepsipeptides as matrix for drug delivery systems and submicron particulate carriers
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Garrido, Claudia
A1  - Leimkühler, Silke
T1  - The inactivation of human aldehyde oxidase 1 by hydrogen peroxide and superoxide
JF  - Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1124/dmd.121.000549
SN  - 1521-009X
SN  - 0090-9556
VL  - 49
IS  - 9
SP  - 729
EP  - 735
PB  - American Society for Pharmacology and Experimental Therapeutics
CY  - Bethesda
ER  - 
TY  - JOUR
A1  - Ceulemans, Ruben
A1  - Guill, Christian
A1  - Gaedke, Ursula
T1  - Top predators govern multitrophic diversity effects in tritrophic food webs
JF  - Ecology : a publication of the Ecological Society of America
N2  - 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.
KW  - food-web efficiency
KW  - functional diversity
KW  - machine learning
KW  - nutrient
KW  - exploitation
KW  - production
KW  - random forest
KW  - temporal variability
KW  - top
KW  - predator
KW  - trait diversity
Y1  - 2021
U6  - https://doi.org/10.1002/ecy.3379
SN  - 0012-9658
SN  - 1939-9170
VL  - 102
IS  - 7
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Sauer, Michael
A1  - Grebe, Markus
T1  - Plant cell biology
BT  - PIN polarity maintained
JF  - Current biology : CB
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1016/j.cub.2021.03.070
SN  - 0960-9822
SN  - 1879-0445
VL  - 31
IS  - 9
SP  - R449
EP  - R451
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - THES
A1  - Tung, Wing Tai
T1  - Polymeric fibrous scaffold on macro/microscale towards tissue regeneration
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Stark, Markus
A1  - Bach, Moritz
A1  - Guill, Christian
T1  - Patch isolation and periodic environmental disturbances have idiosyncratic effects on local and regional population variabilities in meta-food chains
JF  - Theoretical ecology
N2  - 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.
KW  - Metacommunity dynamics
KW  - Dispersal
KW  - Patch isolation
KW  - Stability
KW  - Synchronization
KW  - Disturbance
Y1  - 2021
U6  - https://doi.org/10.1007/s12080-021-00510-0
SN  - 1874-1738
SN  - 1874-1746
VL  - 14
IS  - 3
SP  - 489
EP  - 500
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Guill, Christian
A1  - Hülsemann, Janne
A1  - Klauschies, Toni
T1  - Self-organised pattern formation increases local diversity in metacommunities
JF  - Ecology letters
N2  - 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.
KW  - biomass-trait feedback
KW  - fitness gradient
KW  - food chain
KW  - functional
KW  - diversity
KW  - metacommunity
KW  - self-organisation
KW  - source-sink dynamics
KW  - spatio-temporal pattern
KW  - trait-based aggregate model
KW  - Turing instability
Y1  - 2021
U6  - https://doi.org/10.1111/ele.13880
SN  - 1461-023X
SN  - 1461-0248
VL  - 24
IS  - 12
SP  - 2624
EP  - 2634
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Romero-Mujalli, Daniel
A1  - Rochow, Markus
A1  - Kahl, Sandra M.
A1  - Paraskevopoulou, Sofia
A1  - Folkertsma, Remco
A1  - Jeltsch, Florian
A1  - Tiedemann, Ralph
T1  - Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies
JF  - Ecology and Evolution
N2  - 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.
KW  - developmental canalization
KW  - environmental change
KW  - genetic accommodation
KW  - Individual-based models
KW  - limits
KW  - many-to-one genotype–phenotype map
KW  - noise color
KW  - phenotypic plasticity
KW  - reaction norms
KW  - stochastic fluctuations
Y1  - 2020
SN  - 2045-7758
VL  - 11
IS  - 11
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Cahsan, Binia De
A1  - Westbury, Michael V.
A1  - Paraskevopoulou, Sofia
A1  - Drews, Hauke
A1  - Ott, Moritz
A1  - Gollmann, Günter
A1  - Tiedemann, Ralph
T1  - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian
JF  - Evolutionary Applications
N2  - 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.
KW  - adaptive introgression
KW  - admixture
KW  - Bombina bombina
KW  - genetic rescue
KW  - mitogenomes
KW  - transcriptomics
Y1  - 2020
SN  - 1752-4563
VL  - 14
IS  - 6
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Spikes, Montrai
A1  - Rodríguez-Silva, Rodet
A1  - Bennett, Kerri-Ann
A1  - Bräger, Stefan
A1  - Josaphat, James
A1  - Torres-Pineda, Patricia
A1  - Ernst, Anja
A1  - Havenstein, Katja
A1  - Schlupp, Ingo
A1  - Tiedemann, Ralph
T1  - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario
JF  - BMC Research Notes
N2  - 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 Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, 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 Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, 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 Miragoâne clade.
KW  - Cytochrome b
KW  - Island biogeography
KW  - Fresh water fish
KW  - Phylogeny
Y1  - 2021
U6  - https://doi.org/10.1186/s13104-021-05843-x
SN  - 1756-0500
VL  - 14
SP  - 1
EP  - 8
PB  - BMC Research Notes / Biomed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Krüger, Johanna
A1  - Foerster, Verena Elisabeth
A1  - Trauth, Martin H.
A1  - Hofreiter, Michael
A1  - Tiedemann, Ralph
T1  - Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core
JF  - Frontiers in Earth Science
N2  - 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.
KW  - Chew Bahir
KW  - hybridization capture
KW  - ICDP
KW  - paleoclimate
KW  - past biosphere
KW  - sedaDNA
KW  - sediment core
Y1  - 2021
U6  - https://doi.org/10.3389/feart.2021.683010
SN  - 2296-6463
SP  - 1
EP  - 20
PB  - Frontiers in Earth Science
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Trindade, Inês
T1  - License to flower
BT  - LEAFY has pioneer activity
JF  - Molecular plant
Y1  - 2021
U6  - https://doi.org/10.1016/j.molp.2021.04.007
SN  - 1674-2052
SN  - 1752-9867
VL  - 14
IS  - 5
SP  - 719
EP  - 720
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Gräf, Ralph
A1  - Grafe, Marianne
A1  - Meyer, Irene
A1  - Mitic, Kristina
A1  - Pitzen, Valentin
T1  - The dictyostelium centrosome
JF  - Cells : open access journal
N2  - 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.
KW  - microtubule-organizing center
KW  - microtubule-organization
KW  - centrosome
KW  - Dictyostelium
KW  - mitosis
Y1  - 2021
U6  - https://doi.org/10.3390/cells10102657
SN  - 2073-4409
VL  - 10
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - THES
A1  - Cadek, Chris
T1  - Charakterisierung der Funktion von TusA-homologen Proteinen im Schwefelmetabolismus von Escherichia coli
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Raatz, Larissa
A1  - Pirhofer-Walzl, Karin
A1  - Müller, Marina E.H.
A1  - Scherber, Christoph
A1  - Joshi, Jasmin Radha
T1  - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?
JF  - Ecology and Evolution
N2  - 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.
KW  - arable weeds
KW  - cereal leaf beetle
KW  - fungal pathogens
KW  - herbivory
KW  - structural equation model
KW  - wheat
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8046
SN  - 1467-6435
VL  - 11
SP  - 13232
EP  - 13246
PB  - Wiley-Blackwell
CY  - Oxford
ET  - 19
ER  - 
TY  - JOUR
A1  - Trindade, Inês
T1  - A drop of immunity
JF  - Molecular plant
Y1  - 2021
U6  - https://doi.org/10.1016/j.molp.2021.07.022
SN  - 1674-2052
SN  - 1752-9867
VL  - 14
IS  - 9
SP  - 1437
EP  - 1438
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Petrović, Saša
A1  - Wendler, Petra
T1  - A RADD approach to probing AAA plus protein function
JF  - Nature structural & molecular biology
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1038/s41594-021-00579-5
SN  - 1545-9993
SN  - 1545-9985
VL  - 28
IS  - 4
SP  - 329
EP  - 330
PB  - Nature Publishing Group
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Leimkühler, Silke
T1  - Transition metals in catalysis
BT  - the functional relationship of Fe-S clusters and molybdenum or tungsten cofactor-containing enzyme systems
JF  - Inorganics : open access journal
Y1  - 2021
U6  - https://doi.org/10.3390/inorganics9010006
SN  - 2304-6740
VL  - 9
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - THES
A1  - Gibert, Arthur
T1  - Influence of Amyloid Aggregates on the Trafficking and Signaling of GPCRs
T1  - Einfluss von Amyloidaggregaten auf den Transport und die Signalübertragung von G-Protein-gekoppelten Rezeptoren
N2  - 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.
N2  - Die Prävalenz von Krankheiten, die mit fehlgefalteten Proteinen assoziiert sind, nimmt mit dem Alter zu. Wenn die zellulären Abwehrmechanismen weniger effizient werden, können fehlgefaltete Proteine nicht nur einfache Aggregate bilden, sondern auch stabilere Cross-β-Strukturen, die am Ende zu sogenannten Amyloidaggregaten führen können. Amyloidaggregate sind mit neurodegenerativen Erkrankungen wie z. B. der Alzheimer Erkrankung und dem Huntington-Syndrom assoziiert. Die Bildung von Amyloidablagerungen, ihre Toxizität und die zellulären Abwehrmechanismen wurden in den letzten Jahren intensiv untersucht. Über die Auswirkungen von Proteinaggregaten auf die zelluläre Signaltransduktion ist jedoch überraschend wenig bekannt. Es ist auch nicht bekannt, ob bereits das Vorhandensein von löslichen Vorstadien dieser zur Aggregation neigenden Protein, die Signaltransduktion von Zellen beeinflusst.
In dieser Studie wurden Amyloidaggregate des auf dem Huntingtin-Protein basierenden Konstrukts HttExon1Q74 und seine noch löslichen Formen verwendet, um deren Wirkung auf die Internalisierung und Rezeptoraktivierung von G-Protein-gekoppelten Rezeptoren (GPCRs) zu analysieren. GPCR bilden die größte Proteinfamilie von Oberflächenrezeptoren in Säugerzellen und spielen eine entscheidende Rolle in der zellulären Signaltransduktion. Es konnte gezeigt werden, dass aggregiertes HttExon1Q74, aber nicht seine noch lösliche Form, die ligandeninduzierte Clathrin-vermittelte Endozytose (CME) verschiedener GPCRs hemmt. Höchstwahrscheinlich beruht dieser inhibitorische Effekt auf einer Sequestrierung des HSC70-Chaperons zu den HttExon1Q74-Aggregaten. In früheren Studien konnte bereits gezeigt werden, dass HSC70 die für CME notwendig ist. Unter Verwendung des VasopressinV1a-Rezeptors (V1aR) und des Corticotropin-Releasing-Faktor-Rezeptors 1 (CRF1R) als Modellproteine, konnte in dieser Arbeit ferner gezeigt werden, dass das Vorhandensein von HttExon1Q74-Aggregaten und die Hemmung der ligandeninduzierten CME zu einer Akkumulation desensibilisierter Rezeptoren in der Plasmamembran führt. Dies stört wiederum die Gq-vermittelte Ca2+-Signalisierung und die Gs-vermittelte cAMP-Signalisierung des V1aR bzw. des CRF1R. Im Gegensatz zu HttExon1Q74-Amyloidaggregaten hemmten lösliches HttExon1Q74 sowie amorphe Proteinaggregate die GPCR-Internalisierung und –Signalisierung nicht. Dies zeigt, dass Amyloidaggregate zelluläre Signaltransduktionsmechanismen spezifisch beeinträchtigen können.
Darüber hinaus konnten vorläufige Experimente zeigen, dass HttExon1Q74-Aggregate eine Erhöhung der Membranexpression des Serotonintranporters SERT verursachen, eines Membranproteins das strukturell und funktionell nicht mit GPCR verwandt ist. Da SERT das wichtigste pharmakologische Zielmolekül bei der Behandlung von depressiven Syndromen ist, könnten diese Daten dazu beitragen, besser zu verstehen, warum Depressionen in sehr frühen Stadien von neurodegenerativen Erkrankungen gehäuft auftreten.
KW  - GPCR
KW  - neurodegenerative
KW  - disease
KW  - protein trafficking
KW  - cell signaling
KW  - Huntington
KW  - GPCR
KW  - Huntington
KW  - Zellsignalisierung
KW  - neurodegenerative Erkrankung
KW  - Proteinhandel
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-506659
ER  - 
TY  - THES
A1  - Schaarschmidt, Stephanie
T1  - Evaluation and application of omics approaches  to characterize molecular responses to abiotic stresses in plants
T1  - Evaluierung und Anwendung von Omics-Methoden zur Charakterisierung von abiotischem Stress in Pflanzen auf molekularer Ebene
N2  - Aufgrund des globalen Klimawandels ist die Gewährleistung der Ernährungssicherheit für eine wachsende Weltbevölkerung eine große Herausforderung. Insbesondere abiotische Stressoren wirken sich negativ auf Ernteerträge aus. Um klimaangepasste Nutzpflanzen zu entwickeln, ist ein umfassendes Verständnis molekularer Veränderungen in der Reaktion auf unterschiedlich starke Umweltbelastungen erforderlich. Hochdurchsatz- oder "Omics"-Technologien können dazu beitragen, Schlüsselregulatoren und Wege abiotischer Stressreaktionen zu identifizieren. Zusätzlich zur Gewinnung von Omics-Daten müssen auch Programme und statistische Analysen entwickelt und evaluiert werden, um zuverlässige biologische Ergebnisse zu erhalten. 
Ich habe diese Problemstellung in drei verschiedenen Studien behandelt und dafür 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 Fähigkeit 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 für alle Programme. Bei der Durchführung einer differentiellen Genexpressionsanalyse zwischen Pflanzen, die bei 20 °C oder 4 °C (Kälteakklimatisierung) exponiert wurden, ergab sich eine große paarweise Überlappung zwischen den Programmen. In der zweiten Studie habe ich die Transkriptome von zehn verschiedenen Oryza sativa (Reis) Kultivaren sequenziert. Dafür 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 Vollständigkeitsgrades (BUSCO), der Transkriptlänge und der Anzahl einzigartiger Transkripte pro Genloci. Für 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 Veränderungen in Metabolitprofilen von acht Reissorten gemessen und analysiert, die dem Stress hoher Nachttemperaturen (HNT) ausgesetzt waren und während der Trocken- und Regenzeit im Feld auf den Philippinen angebaut wurden. Es wurden jahreszeitlich bedingte Veränderungen im Metabolitspiegel sowie für agronomische Parameter identifiziert und mögliche Stoffwechselwege, die einen Ertragsrückgang unter HNT-Bedingungen verursachen, vorgeschlagen.
Zusammenfassend konnte ich zeigen, dass der Vergleich der RNA-seq Programme den Pflanzenwissenschaftler*innen helfen kann, sich für das richtige Werkzeug für 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 unabhängig vom Organismus. Mit dem Metabolomik-Ansatz für HNT-Stress in Reis habe ich stress- und jahreszeitenspezifische Metabolite identifiziert, die in Zukunft als molekulare Marker für die Verbesserung von Nutzpflanzen verwendet werden könnten.
N2  - Due to global climate change providing food security for an increasing world population is a big challenge. Especially abiotic stressors have a strong negative effect on crop yield. To develop climate-adapted crops a comprehensive understanding of molecular alterations in the response of varying levels of environmental stresses is required. High throughput or ‘omics’ technologies can help to identify key-regulators and pathways of abiotic stress responses. In addition to obtain omics data also tools and statistical analyses need to be designed and evaluated to get reliable biological results.
To address these issues, I have conducted three different studies covering two omics technologies. In the first study, I used transcriptomic data from the two polymorphic Arabidopsis thaliana accessions, namely Col-0 and N14, to evaluate seven computational tools for their ability to map and quantify Illumina single-end reads. Between 92% and 99% of the reads were mapped against the reference sequence. The raw count distributions obtained from the different tools were highly correlated. Performing a differential gene expression analysis between plants exposed to 20 °C or 4°C (cold acclimation), a large pairwise overlap between the mappers was obtained. In the second study, I obtained transcript data from ten different Oryza sativa (rice) cultivars by PacBio Isoform sequencing that can capture full-length transcripts. De novo reference transcriptomes were reconstructed resulting in 38,900 to 54,500 high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g. for protein completeness level (BUSCO), transcript length, and number of unique transcripts per gene loci. For the heat and drought tolerant aus cultivar N22,  I identified around 650 unique and novel transcripts of which 56 were significantly differentially expressed in developing seeds during combined drought and heat stress. In the last study, I measured and analyzed the changes in metabolite profiles of eight rice cultivars exposed to high night temperature (HNT) stress and grown during the dry and wet season on the field in the Philippines. Season-specific changes in metabolite levels, as well as for agronomic parameters, were identified and metabolic pathways causing a yield decline at HNT conditions suggested.
In conclusion, the comparison of mapper performances can help plant scientists to decide on the right tool for their data. The de novo reconstruction of rice cultivars without a genome sequence provides a targeted, cost-efficient approach to identify novel genes responding to stress conditions for any organism. With the metabolomics approach for HNT stress in rice, I identified stress and season-specific metabolites which might be used as molecular markers for crop improvement in the future.
KW  - Arabidopsis thaliana
KW  - Oryza sativa
KW  - RNA-seq
KW  - PacBio IsoSeq
KW  - metabolomics
KW  - high night temperature
KW  - combined heat and drought stress
KW  - natural genetic variation
KW  - differential gene expression
KW  - Arabidopsis thaliana
KW  - Oryza sativa
KW  - PacBio IsoSeq
KW  - RNA-seq
KW  - kombinierter Hitze- und Trockenstress
KW  - erhöhte Nachttemperaturen
KW  - Differenzielle Genexpression
KW  - Metabolomik
KW  - natürliche genetische Variation
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-509630
ER  - 
TY  - THES
A1  - Moga, Akanksha
T1  - Reconstitution of molybdenum cofactor biosynthesis in giant vesicles
N2  - 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.
N2  - Die synthetische Biologie wird in der von unten-nach-oben-Methode eingesetzt, um zu verstehen, wie eine Zelle funktioniert. Dafür werden Techniken zur Herstellung lipidbasierter vesikul rer Strukturen als zellul re Nachahmungen entwickelt. Die gebräuchlichste Technik zur Herstellung von Zellnachahmungen oder synthetischen Zellen ist die Elektroformations- und Schwellmethode. Diese Techniken können jedoch Makromoleküle wie Proteine, Enzyme, DNA und sogar Liposomen nicht effizient als synthetische Organellen einkapseln. Daher ist es dringend erforderlich, neue Techniken zu entwickeln, die dieses Problem umgehen und die künstliche Zelle zu einer Realität machen, in der es möglich ist, eine eukaryotische Zelle durch Einkapselung von Makromolekülen zu imitieren. Das Ziel dieser Arbeit war es, ein komplexes Zellensystemmodel zu konstruieren, bei dem riesige unilamellare Vesikel (GUVs) zur Rekonstruktion des mitochondrialen Molybd n-Kofaktor-Biosynthesewegs verwendet werden. Dieser Stoffwechselweg ist bei allen Lebensformen hoch konserviert und daher aufgrund von St rungen, die durch Fehlfunktionen hervorgerufen werden, für seine biologische Bedeutung relevant. Darüber hinaus ist die Biosynthese selbst eine mehrstufige enzymatische Reaktion, die in verschiedenen Kompartimenten abläuft. Zunächst wird GTP in der mitochondrialen Matrix in Gegenwart von cPMP-Synthase zu cPMP umgewandelt. Anschlie end wird das produzierte cPMP über die Membran zum Zytosol transportiert, wo es von der MPT-Synthase in MPT umgewandelt wird. Dieser Biosyntheseweg bietet eine M glichkeit, den allgemeinen Herausforderungen bei der Entwicklung einer synthetischen Zelle zu begegnen, um große Biomoleküle mit guter Effizienz und Kontrolle zu verkapseln und die am Prozess beteiligten enzymatischen Reaktionen zu bewerten.

Zu diesem Zweck wurde die emulsionsbasierte Technik entwickelt und optimiert, die eine schnelle Produktion von GUVs (~18 min) mit hoher Verkapselungseffizienz (80%) ermöglicht. M glich wurde dies durch die Optimierung verschiedener Parameter wie Dichte,  ltyp, Einfluss von Zentrifugationsgeschwindigkeit/-zeit, Lipidkonzentration, pH-Wert, Temperatur und Emulsionstropfenvolumen. Darüber hinaus wurde die Methode in Mikrotiterplatten für das direkte Experimentieren und die Visualisierung nach der GUV-Bildung optimiert. Mit dieser Technik wurden die beiden Schritte, die Bildung von cPMP aus GTP und die Bildung von MPT aus cPMP, in verschiedenen GUVs eingekapselt, um die beiden Kompartimente nachzuahmen. Zwei unabhängige fluoreszenzbasierte Detektionssysteme wurden eingerichtet, um die erfolgreiche Einkapselung und Umwandlung der Reaktanten zu best tigen. Alternativ wurden die Enzyme mittels bakterieller Expression produziert und gemessen. Nach der erfolgreichen Einkapselung und Auswertung der enzymatischen Reaktionen wurde der cPMP-Transport durch die mitochondriale Membran mit Hilfe von GUVs unter Verwendung einer komplexen mitochondrialen Lipidzusammensetzung nachgeahmt. Es wurde festgestellt, dass die cPMP-Wechselwirkung mit der Lipiddoppelschicht zu einer transienten Porenbildung und zum Auslaufen des inneren Inhalts führt.

Insgesamt kann der Schluss gezogen werden, dass in dieser Arbeit eine neuartige Technik für die schnelle Herstellung funktioneller synthetischer Zellen optimiert wurde. Einzelne enzymatische Schritte des Moco-Biosynthesewegs wurden in diesen zellul ren Mimiken erfolgreich implementiert und quantifiziert.
KW  - GUVs
KW  - Molybdenum cofactor biosynthetic
KW  - Microscopy
KW  - Inverted emulsion-based method
KW  - Mikroskop
KW  - Biochemie
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-510167
ER  - 
TY  - THES
A1  - Ceulemans, Ruben
T1  - Diversity effects on ecosystem functions of tritrophic food webs
T1  - Diversität beeinflusst Ökosystemfunktionen tritrophischer Nahrungsnetze
N2  - 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.
N2  - Wissenschaftliche Erkenntnisse über die in natürlichen Ökoystemen beobachtete Artenvielfalt hat gezeigt, dass die Artenvielfalt fast überall auf der Erde rapide abnimmt. Dieser Rückgang ist hauptsächlich auf den zunehmenden menschlichen Einfluss auf die Umwelt zurückzuführen. Insbesondere die zunehmende Landnutzung z. B. für die Landwirtschaft, die Verschmutzung und die überfischung wirken sich negativ auf die Biodiversität aus. Den Einfluss von Biodiversität auf die Funktion von natürlichen Ökosystemen ist ein sehr aktives Forschungsgebiet der Ökologie. Insbesondere hat sich herausgestellt, dass die Biodiversität einen entscheidenden Einfluss auf wichtige Eigenschaften von Ökosystemen hat, wie z.B. die Menge an Biomasse, die sich etablieren kann, wie groß die Schwankungen der Biomasse im Laufe der Zeit sind, wie effizient Energie durch das gesamte Ökosystem übertragen wird und wie es auf Umweltstörungen reagiert.
In dieser Dissertation wird  der Zusammenhang zwischen Biodiversität und Ökosystemfunktionen mit Hilfe mathematischer Modelle von Nahrungsnetzen untersucht um mit Hilfe dieses Ansatz wichtige Eigenschaften und deren Relevanz zu ermitteln. Ein Nahrungsnetz beschreibt einen zentralen Teil dessen, wie Arten in einem Ökosystem miteinander interagieren, nämlich wer wen frisst. Unsere Modelle enthalten drei trophische Ebenen: eine basale Ebene (z.B. Pflanzen), die einer mittleren Ebene (Pflanzenfresser) als Nahrungsquelle dient, die wiederum von einer oberen Ebene (Fleischfresser) gefressen werden. Die Koexistenz mehrerer Arten auf einer trophischen Ebene ist über Trade-offs zwischen wichtigen Merkmalen der Arten sichergestellt. Ein Trade-off zwischen Fraßschutz und Wachstum bedeutet zum Beispiel, dass jeder Mechanismus, mit dem sich eine Art vor Fressfeinden schützen kann (z. B. die Bildung von Stacheln), mit einer geringeren Wachstumsrate erkauft wird (die Pflanze muss Energie für die Bildung der Stacheln aufgewendet werden). Auf diese Weise ist die Koexistenz mehrerer Arten möglich: kein Fraßschutz und eine hohe Wachstumsrate, gegenüber hohem Fraßschutz und einer niedrigen Wachstumsrate. 
Wir zeigen, dass die Eigenschaften der obersten trophischen Ebene, wie z. B. ihr Biomasseanteil und ihre Diversität, einen sehr großen Einfluss auf die Eigenschaften aller anderen trophischen Ebenen im Nahrungsnetz ausüben. Insbesondere beobachten wir, dass eine hohe Biomasse und Diversität auf der obersten trophischen Ebene zu einem Nahrungsnetz führt, das zeitlich stabiler ist, die verfügbaren anorganischen Nährstoffe besser ausnutzt und die erhöhte Produktivität der basalen trophischen Ebene effizienter an die Spitze des Nahrungsnetzes weitergibt. Darüber hinaus stellen wir fest, dass die oberste trophische Ebene eine Schlüsselrolle bei der Abschwächung von Auswirkungen auf ein  Nahrungsnetz durch externe Störungen spielt. Zudem verstärkt sich dieser Effekt  der obersten trophischen Ebene, wenn die anderen trophischen Ebenen ebenfalls eine hohe Diversität aufzeigen. 
Unsere Ergebnisse unterstreichen somit die Bedeutung von Diversität in allen Nahrungsnetzen, um einen Fortbestand von Ökosystemdienstleistungen zu gewährleisten, auf die wir angewiesen sind.
KW  - food webs
KW  - trait variation
KW  - trait diversity
KW  - Nahrungsnetze
KW  - Merkmalsvielfalt
KW  - Merkmalsvariation
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-503259
ER  - 
TY  - THES
A1  - Liu, Yue
T1  - Polymeric objects switchable between two shapes
N2  - 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.
KW  - shape-memory polymer
KW  - compliant mechanism
KW  - atomic force microscopy
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Steppert, Isabel
A1  - Schönfelder, Jessy
A1  - Schultz, Carolyn
A1  - Kuhlmeier, Dirk
T1  - Rapid in vitro differentiation of bacteria by ion mobility spectrometry
JF  - Applied Microbiology and Biotechnology
N2  - 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.
KW  - Bacteria identification
KW  - Volatile organic compounds (VOC)
KW  - Ion mobility
KW  - spectrometry (IMS)
KW  - Antibiotic resistance
KW  - Infection
KW  - Diagnostic
Y1  - 2021
U6  - https://doi.org/10.1007/s00253-021-11315-w
SN  - 0175-7598
SN  - 1432-0614
VL  - 105
IS  - 10
SP  - 4297
EP  - 4307
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Strong, Catherine R. C.
A1  - Scherz, Mark D.
A1  - Caldwell, Michael Wayne
T1  - Deconstructing the Gestalt
BT  - new concepts and tests of homology, as exemplified by a re-conceptualization of "microstomy" in squamates
JF  - The anatomical record : AR ; advances in integrative anatomy and evolutionary biology ; an official publication of the American Association of Anatomists, AAA
N2  - 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.
KW  - ancestral state reconstruction
KW  - functional morphology
KW  - homology
KW  - skull
KW  - anatomy
KW  - snake evolution
Y1  - 2021
U6  - https://doi.org/10.1002/ar.24630
SN  - 1932-8486
SN  - 1932-8494
VL  - 304
IS  - 10
SP  - 2303
EP  - 2351
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Guljamow, Arthur
A1  - Barchewitz, Tino
A1  - Große, Rebecca
A1  - Timm, Stefan
A1  - Hagemann, Martin
A1  - Dittmann, Elke
T1  - Diel Variations of Extracellular Microcystin Influence the
Subcellular Dynamics of RubisCO in Microcystis aeruginosa
PCC 7806
JF  - Microorganisms : open access journal
N2  - 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.
KW  - cyanobacterial bloom
KW  - Microcystis
KW  - microcystin
KW  - RubisCO
KW  - extracellular signaling
Y1  - 2021
U6  - https://doi.org/10.3390/microorganisms9061265
SN  - 2076-2607
VL  - 9
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - GEN
A1  - Wojcik, Laurie Anne
A1  - Ceulemans, Ruben
A1  - Gaedke, Ursula
T1  - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1251 
KW  - functional diversity
KW  - nutrient spike
KW  - pulse perturbation
KW  - regime shift
KW  - robustness
KW  - tritrophic food web
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-553730
SN  - 1866-8372
N1  - Wojcik and Ceulemans shared first authorship.
IS  - 1251
ER  - 
TY  - GEN
A1  - Bornhorst, Dorothee
A1  - Abdelilah-Seyfried, Salim
T1  - Strong as a Hippo’s Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1236 
KW  - Hippo signaling
KW  - Yap1/Wwtr1 (Taz)
KW  - cardiac development
KW  - mechanobiology
KW  - endocardium
KW  - myocardium
KW  - zebrafish
KW  - intra-organ-communication
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-548731
SN  - 1866-8372
SP  - 1
EP  - 10
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Spikes, Montrai
A1  - Rodríguez-Silva, Rodet
A1  - Bennett, Kerri-Ann
A1  - Bräger, Stefan
A1  - Josaphat, James
A1  - Torres-Pineda, Patricia
A1  - Ernst, Anja
A1  - Havenstein, Katja
A1  - Schlupp, Ingo
A1  - Tiedemann, Ralph
T1  - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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 Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, 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 Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, 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 Miragoâne clade.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1238 
KW  - Cytochrome b
KW  - Island biogeography
KW  - Fresh water fish
KW  - Phylogeny
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-548882
SN  - 1866-8372
SP  - 1
EP  - 8
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Krüger, Johanna
A1  - Foerster, Verena Elisabeth
A1  - Trauth, Martin H.
A1  - Hofreiter, Michael
A1  - Tiedemann, Ralph
T1  - Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1244 
KW  - Chew Bahir
KW  - hybridization capture
KW  - ICDP
KW  - paleoclimate
KW  - past biosphere
KW  - sedaDNA
KW  - sediment core
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550071
SN  - 1866-8372
SP  - 1
EP  - 20
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Raatz, Larissa
A1  - Pirhofer-Walzl, Karin
A1  - Müller, Marina E.H.
A1  - Scherber, Christoph
A1  - Joshi, Jasmin Radha
T1  - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?
JF  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1240 
KW  - arable weeds
KW  - cereal leaf beetle
KW  - fungal pathogens
KW  - herbivory
KW  - structural equation model
KW  - wheat
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549622
SN  - 1866-8372
SP  - 13232
EP  - 13246
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Guljamow, Arthur
A1  - Barchewitz, Tino
A1  - Große, Rebecca
A1  - Timm, Stefan
A1  - Hagemann, Martin
A1  - Dittmann, Elke
T1  - Diel Variations of Extracellular Microcystin Influence the
Subcellular Dynamics of RubisCO in Microcystis aeruginosa
PCC 7806
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1154 
KW  - cyanobacterial bloom
KW  - Microcystis
KW  - microcystin
KW  - RubisCO
KW  - extracellular signaling
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-521287
SN  - 1866-8372
IS  - 1154
ER  - 
TY  - GEN
A1  - Romero-Mujalli, Daniel
A1  - Rochow, Markus
A1  - Kahl, Sandra M.
A1  - Paraskevopoulou, Sofia
A1  - Folkertsma, Remco
A1  - Jeltsch, Florian
A1  - Tiedemann, Ralph
T1  - Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1170 
KW  - developmental canalization
KW  - environmental change
KW  - genetic accommodation
KW  - Individual-based models
KW  - limits
KW  - many-to-one genotype–phenotype map
KW  - noise color
KW  - phenotypic plasticity
KW  - reaction norms
KW  - stochastic fluctuations
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523201
SN  - 1866-8372
IS  - 1170
ER  - 
TY  - GEN
A1  - Cahsan, Binia De
A1  - Westbury, Michael V.
A1  - Paraskevopoulou, Sofia
A1  - Drews, Hauke
A1  - Ott, Moritz
A1  - Gollmann, Günter
A1  - Tiedemann, Ralph
T1  - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1168 
KW  - adaptive introgression
KW  - admixture
KW  - Bombina bombina
KW  - genetic rescue
KW  - mitogenomes
KW  - transcriptomics
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523140
SN  - 1866-8372
IS  - 6
ER  - 
TY  - THES
A1  - Borghi, Gian Luca
T1  - Evolution and diversity of photosynthetic metabolism in C3, C3-C4 intermediate and C4 plants
T1  - Evolution und Diversität des photosynthetischen Stoffwechsels in C3-, C3-C4-Intermediär- und C4-Pflanzen
N2  - 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.
N2  - Bei C3-Pflanzen diffundiert CO2 in das Blatt und wird durch den Calvin-Benson-Zyklus in den Mesophyllzellen assimiliert. Dies lässt Rubisco für seine Nebenreaktion mit O2 offen, was zu einem verschwenderischen Kreislauf führt, der als Photorespiration bekannt ist. Ein starker Rückgang der atmosphärischen CO2-Konzentration vor etwa 30 Millionen Jahren hat die Nebenreaktion mit O2 weiter verstärkt. Der Druck, die Photorespiration zu reduzieren, hat in über 60 Pflanzengattungen zur Entwicklung eines CO2-Konzentrationsmechanismus namens C4-Photosynthese geführt. In diesem Mechanismus wird CO2 zunächst in organische C4-Kohlenstoffsäuren eingebaut, die zur Bündelscheide diffundieren und dort decarboxyliert werden, um CO2 für Rubisco bereitzustellen. Einige Gattungen, wie z.B. Flaveria, enthalten mehrere Arten, die verschiedene Schritte dieses komplexen Evolutionsprozesses darstellen. Die Mehrheit der terrestrischen Pflanzenarten hat jedoch keinen CO2-Konzentrationsmechanismus entwickelt und betreibt C3-Photosynthese.
Diese Arbeit vergleicht den Photosynthese-Metabolismus in mehreren Spezies mit C3-, C4- und intermediären Arten der Photosynthese. Metaboliten-Profiling und stabile Isotopenmarkierung wurden durchgeführt, um interspezifische Unterschiede im Metabolitenprofil und damit die Funktionsweise der Stoffwechselwege zu erkennen. Die Ergebnisse wurden integrativen Datenanalysen wie hierarchischem Clustering und Hauptkomponentenanalyse unterzogen und durch Korrelationsanalysen vertieft, um spezifische metabolische Merkmale und Reaktionsschritte aufzudecken, die konserviert oder zwischen Spezies verschieden sind.
Die wichtigsten Ergebnisse sind, dass sich die Metabolitenprofile des Calvin-Benson-Zyklus zwischen C3- und C4-Spezies und zwischen verschiedenen C3-Spezies unterscheiden, einschließlich einer sehr unterschiedlichen Reaktion auf steigende Strahlungsintensität bei Arabidopsis und Reis. Diese Ergebnisse bestätigen, dass der Calvin-Benson-Zyklus zwischen C3- und C4-Spezies und, höchst unerwartet, sogar zwischen verschiedenen C3-Spezies divergiert. Darüber hinaus unterstützen die primären Stoffwechselprofile das aktuelle C4-Evolutionsmodell in der Gattung Flaveria, liefern auch neue Erkenntnisse und eröffnen neue Fragen. Die Metabolitenprofile weisen auch auf eine fortschreitende Anpassung des Calvin-Benson-Zyklus während der Evolution der C4-Photosynthese hin. Insgesamt unterstreicht diese Dissertation die Bedeutung eines metabolitenzentrierten Ansatzes, um Unterschiede in Arten aufzudecken, die anscheinend dieselben Photosynthesewege teilen, und als valide Methode zur Untersuchung des evolutionären Übergangs zwischen C3- und C4-Photosynthese.
KW  - Photosynthesis
KW  - C4
KW  - Evolution
KW  - Photosynthese
KW  - C4
KW  - Evolution
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-522200
ER  - 
TY  - THES
A1  - Krumbholz, Julia
T1  - Identification of chemical mediators that regulate the specialized metabolism in Nostoc punctiforme
T1  - Identifizierung chemischer Mediatoren, die den spezialisierten Metabolismus in Nostoc punctiforme regulieren
N2  - 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.
N2  - Sekundärmetabolite, auch Naturstoffe genannt, werden von einer Vielzahl an Organismen, darunter Bakterien und Pilzen, hergestellt. Aufgrund ihrer Vielzahl an verschiedenen Bioaktivitäten, einschließlich pharmakologisch relevanter Wirkungen, sind mikrobielle Naturstoffe eine wichtige Grundlage für die Arzneimittelentwicklung. Naturstoffe werden durch eine Ansammlung lokal gruppierter Gene, sogenannten Biosynthese-Genclustern (BGC), im Genom kodiert. Moderne bioinformatische Methoden durchsuchen Genom-Daten nach Genen, die typische biosynthetische Enzyme kodieren. Auf Grundlage dessen können verschiedenste BGCs vorhergesagt werden. Bislang konnte allerdings nur für einen kleinen Teil der vorhergesagten BGCs das dazugehörige Produkt identifiziert und charakterisiert werden.

Cyanobakterien sind nachweislich eine reichhaltige, aber weitestgehend unerschlossene Quelle für Naturstoffe. Insbesondere mehrzellige Gattungen, wie Nostoc, tragen eine Vielzahl an BGCs in ihren Genomen.
Ein Hauptziel dieser Studie war es, neue Konzepte für die Entdeckungen von Naturstoffen in Cyanobakterien zu entwickeln. Nostoc punctiforme PCC 73102 (N. punctiforme) erwies sich als besonders geeigneter Stamm für diese Aufgabe, da er eine Vielzahl weitestgehend ununtersuchter Gencluster besitzt und zugänglich für genetische Modifikationen ist. Eine Kombination aus Genome Mining, Bioaktivitäts-Screening, verschiedenen Kultivierungsbedingungen und Metabolic Engineering führte zur Entdeckung zweier neuer Polyketide und gewährte im Verlauf der Studie erstmals Einblicke in den spezialisierten Metabolismus von N. punctiforme.

Die Kultivierung von N. punctiforme in sehr hohen Zelldichten, ermöglicht durch sehr hohe Lichtintensitäten und erhöhte CO2-Verfügbarkeit, führte zu einer verstärkten Metabolitproduktion und komplexen Metabolitextrakten. Unter Verwendung einer Bibliothek von CFP-Reportermutanten, bei der jede Mutante eines der vorhergesagten BGCs repräsentiert, konnte gezeigt werden, dass 8 von 15 BGCs unter Hochzelldichte-Kultivierungsbedingungen hochreguliert wurden. Zudem zeigte sich, dass der Überstand einer dichten Kultur, auch unter konventionellen Kultivierungsbedingungen, vier der regulierten BGCs beeinflussen kann. Dies lässt vermuten, dass sich unter Hochzelldichte-Kultivierungsbedingungen ein chemischer Mediator, welcher von einem der beeinflussten BGCs produziert wird, im Überstand anhäuft und die Expression anderer BGCs als Teil eines zelldichte-abhängigen Regelkreises kontrollieren kann. Um herauszufinden, welches der BGCs ein Hauptauslöser des vermuteten Regelkreises sein könnte, wurde versucht die Expression von vier BGCs (pks1, pks2, ripp3, ripp4) mittels Überexpression von potentiell biosynthese-spezifischen regulatorischen Genen zu aktivieren. Eine transkriptionelle Analyse der Mutanten ergab, dass nur der Stamm, welcher das pks1 BGC aktivieren sollte (AraC_PKS1), einen positiven Effekt auf die Expression des zu erwartenden BGCs hatte. Eine RNA-Sequenzierungsstudie ergab, dass in der AraC_PKS1 Mutante neben dem pks1 BGC auch die kryptischen BGCs ripp3 und ripp4 eine erhöhte Transkription aufwiesen. Zudem wurde beobachtet, dass sich die Sekundärmetabolitproduktion in der Mutante durch Kultivierung unter erhöhten Licht-Intensitäten und CO2-Leveln erweitern lässt. Unabhängig von den Kultivierungsbedingungen, hat die erhöhte Produktion des pks1 Regulators NvlA in der Mutante einen Einfluss auf andere regulatorische Faktoren, wie Sigma-Faktoren und das RNA-Chaperon Hfq. Die Analyse des Zell- und Überstandsextrakts der AraC_PKS1 Mutante führte zur Entdeckung zweier neuer Polyketide, Nostoclid und Nostovalerolacton, welche beide vom pks1 BGC codiert werden. Die Zugabe dieser Polyketide zum N. punctiforme Wildtyp zeigte, dass diese in der Lage sind einen Teil der Sekundärmetabolit-Effekte der AraC_PKS1 Mutante zu reproduzieren. Dies lässt darauf schließen, dass beide Polyketide als Signalstoffe innerhalb eines regulatorischen Netzwerks agieren. Da nicht alle transkriptionellen Effekte der AraC_PKS1 Mutante durch die Zugabe der pks1 Produkte reproduziert werden konnten, ist anzunehmen, dass der Regulator NvlA einen globalen Effekt hat und nicht ausschließlich die pks1 Biosynthese reguliert.

Diese Studie war die erste, welche einen potentiell biosynthese-spezifischen Regulator für die gezielte Aktivierung von BGC-Expression in Cyanobakterien verwendet hat. Diese Strategie führte neben der Entdeckung zweier neuer Polyketide, zu ersten Einblicken in den regulatorischen Mechanismus, der den spezialisierten Metabolismus in N. punctiforme kontrolliert. Diese Studie veranschaulicht, dass das Verstehen regulatorischer Mechanismen für die Entdeckung neuer Naturstoffe hilfreich sein kann. Die Studien-Ergebnisse können die Entwicklung neuer Screening-Strategien für bioaktive Metabolite in Cyanobakterien anregen und können dabei helfen Hochtiter-Produktionsplattformen für cyanobakterielle Naturstoffe zu entwickeln.
KW  - cyanobacteria
KW  - natural products
KW  - specialized metabolites
KW  - gene cluster activation
KW  - Nostoc punctiforme
KW  - Cyanobakterien
KW  - Sekundärmetabolite
KW  - Naturstoffe
KW  - Gencluster-Aktivierung
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-540240
ER  - 
TY  - THES
A1  - Hasnat, Muhammad Abrar
T1  - A-Type Carrier Proteins are involved in [4Fe-4S] Cluster insertion into the Radical S-adenosylmethionine (SAM) Protein MoaA and other molybdoenzymes
N2  - 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.
KW  - enzyme
KW  - gene
KW  - iron sulfur clusters
KW  - Enzyme
KW  - Gen
KW  - Eisen-Schwefel-Cluster
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-530791
ER  - 
TY  - THES
A1  - Dahmani, Ismail
T1  - Influenza A virus matrix protein M1
T1  - Influenza-A-Virus-Matrixprotein M1
BT  - structural determinants of membrane binding and protein- induced deformation
BT  - strukturelle Determinanten der Membranbindung und protein-induzierte Deformation
N2  - 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.
N2  - Das Influenza-A-Virus (IAV) ist ein Erreger, der für schwere saisonale Epidemien verantwortlich ist, die jedes Jahr Menschen und Tiere bedrohen. Während des viralen Assemblierungsprozesses in den infizierten Zellen muss sich die Plasmamembran (PM) an bestimmten Stellen zu einem Vesikel zur extrazellulären Seite biegen. Studien an zellulären Modellen haben ergeben, dass verschiedene virale Proteine (einschließlich M1) für die Induktion der Membrankrümmung in diesem Zusammenhang verantwortlich sein könnten, ein eindeutiger Konsens wurde jedoch nicht erreicht.

M1 ist das am häufigsten vorkommende Protein in IAV-Partikeln. Es spielt eine wichtige Rolle bei der Virusassemblierung und Knospung. M1 wird zur Wirtszellmembran rekrutiert, wo es sich mit Lipiden und anderen viralen Proteinen assoziiert. Die Einzelheiten der Interaktionen von M1 mit der zellulären PM sowie die M1-vermittelte Membranverbiegung am Ort der Virusfreisetzung sind jedoch noch nicht geklärt.

In dieser Arbeit wurden mehrere experimentelle Ansätze zur Analyse von M1-Lipiden und M1-M1 Wechselwirkungen untersucht. Mittels SPR-Analyse wurde die Membranassoziation für M1 in voller Länge und verschiedene gentechnisch veränderte M1-Konstrukte (d. h. N- und C-terminal verkürzte Konstrukte und eine Mutante der polybasischen Region) quantifiziert; so konnten neue Erkenntnisse über die Proteinregionen, die die Bindung von M1 an Membranen steuern, gewonnen werden. Mit Hilfe der Fluoreszenzmikroskopie, kryogener Transmissionselektronenmikroskopie (cryo-TEM) und dreidimensionaler (3D) Tomographie (cryo-ET) konnten wir zeigen, dass M1 tatsächlich in der Lage ist, die Membran von Vesikeln, die negativ geladene Lipide enthalten, zu deformieren (und zwar ohne andere virale Komponenten). Außerdem bewies die sFCS-Analyse, dass eine einfache Proteinbindung nicht ausreicht, um eine Umstrukturierung der Membran zu bewirken. Vielmehr scheint es, dass stabile M1-M1-Wechselwirkungen und die Bildung von Multimeren erforderlich sind, um die dreidimensionale Struktur der Doppelschicht Struktur durch die Bildung eines Proteingerüsts zu verändern.

Um schließlich den Knospungsmechanismus zu imitieren, der durch die laterale Organisation der Virusmembrankomponenten auf Lipid-Raft-Domänen entsteht, haben wir Vesikel mit Lipiddomänen erzeugt. Unsere Ergebnisse zeigten, dass die lokale Bindung von M1 an räumlich begrenzte saure Lipide innerhalb der Membrandomänen der Vesikel zu einer lokalen Krümmung von M1 nach innen führt.
KW  - Influenza A virus
KW  - Influenza
KW  - Pathogen
KW  - Lipids
KW  - Epidemic
KW  - Epidemics
KW  - Plasma membrane
KW  - Viral assembly
KW  - Virus
KW  - Vesicle
KW  - Giant Vesicles
KW  - Budozone
KW  - M1-M1 interaction
KW  - Virion
KW  - Membrane deformation
KW  - IAV particles
KW  - membrane binding
KW  - M1-lipids
KW  - protein binding
KW  - GUV
KW  - Giant unilamellar vesicles
KW  - Budozone
KW  - Epidemie
KW  - Epidemien
KW  - GUV
KW  - Riesenvesikel
KW  - riesige unilamellare Vesikel
KW  - IAV-Partikel
KW  - Influenza
KW  - Influenza-A-Virus
KW  - Lipide
KW  - M1-M1-Interaktion
KW  - M1-Lipide
KW  - Membrandeformation
KW  - Pathogen
KW  - Plasmamembran
KW  - Vesikel
KW  - Virusassemblierung, Virion
KW  - Virus
KW  - Membranbindung
KW  - Proteinbindung
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-527409
ER  - 
TY  - GEN
A1  - Münch, Juliane
A1  - Abdelilah-Seyfried, Salim
T1  - Sensing and Responding of Cardiomyocytes to Changes of Tissue Stiffness in the Diseased Heart
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1234 
KW  - mechanobiology
KW  - tissue stiffness
KW  - cardiomyocyte
KW  - heart regeneration
KW  - titin
KW  - collagen
KW  - agrin
KW  - extracellular matrix
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-545805
SN  - 1866-8372
ER  - 
TY  - JOUR
A1  - Flöder, Sabine
A1  - Yong, Joanne
A1  - Klauschies, Toni
A1  - Gaedke, Ursula
A1  - Poprick, Tobias
A1  - Brinkhoff, Thorsten
A1  - Moorthi, Stefanie
T1  - Intraspecific trait variation alters the outcome of competition in freshwater ciliates
JF  - Ecology and evolution
N2  - 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.
KW  - ciliate predators
KW  - intraspecific trait variation
KW  - microalgal resource
KW  - predator trait variation
KW  - predator-prey systems
KW  - resource competition
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.7828
SN  - 2045-7758
VL  - 11
IS  - 15
SP  - 10225
EP  - 10243
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Baunach, Martin
A1  - Chowdhury, Somak
A1  - Stallforth, Pierre
A1  - Dittmann-Thünemann, Elke
T1  - The landscape of recombination events that create nonribosomal peptide diversity
JF  - Molecular biology and evolution : MBE
N2  - 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.
KW  - evolution
KW  - recombination
KW  - structural diversity
KW  - natural products
KW  - nonribosomal peptide synthetases
KW  - microbial ecology
Y1  - 2021
U6  - https://doi.org/10.1093/molbev/msab015
SN  - 0737-4038
SN  - 1537-1719
VL  - 38
IS  - 5
SP  - 2116
EP  - 2130
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Ruthsatz, Katharina
A1  - Scherz, Mark D.
A1  - Vences, Miguel
T1  - Dissecting the tree of life
BT  - the prospect of open-access digital resources in morphology, anatomy and taxonomy in training the next generation of zoologists
JF  - Zootaxa : an international journal of zootaxonomy ;
Y1  - 2021
U6  - https://doi.org/10.11646/zootaxa.5016.3.10
SN  - 1175-5326
SN  - 1175-5334
VL  - 5016
IS  - 3
SP  - 448
EP  - 450
PB  - Magnolia Press
CY  - Auckland
ER  - 
TY  - JOUR
A1  - Schneeberger, Karin
A1  - Eccard, Jana
T1  - Experience of social density during early life is associated with attraction to conspecific odour in the common vole (Microtus arvalis)
JF  - Ethology : international journal of behavioural biology
N2  - 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.
KW  - early experience
KW  - olfactory
KW  - population cycles
KW  - priming
KW  - rodents
Y1  - 2021
U6  - https://doi.org/10.1111/eth.13211
SN  - 0179-1613
SN  - 1439-0310
VL  - 127
IS  - 10
SP  - 908
EP  - 913
PB  - Wiley-Blackwell
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes
JF  - Ecography
N2  - 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.
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
SN  - 1600-0587
VL  - 44
IS  - 10
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - GEN
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1178 
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523979
SN  - 1866-8372
IS  - 10
ER  - 
TY  - JOUR
A1  - Köker, Latife
A1  - Akçaalan, Reyhan
A1  - Dittmann, Elke
A1  - Albay, Meriç
T1  - Depth profiles of protein-bound microcystin in Küçükçekmece Lagoon
JF  - 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
N2  - 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.
KW  - Microcystis
KW  - Microcystin
KW  - Protein-bound microcystin
KW  - Mcy gene
KW  - Kucukcekmece Lagoon
Y1  - 2021
U6  - https://doi.org/10.1016/j.toxicon.2021.05.005
SN  - 0041-0101
SN  - 1879-3150
VL  - 198
SP  - 156
EP  - 163
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Münch, Juliane
A1  - Abdelilah-Seyfried, Salim
T1  - Sensing and responding of cardiomyocytes to changes of tissue stiffness in the diseased heart
JF  - Frontiers in cell developmental biology
N2  - 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.
KW  - mechanobiology
KW  - tissue stiffness
KW  - cardiomyocyte
KW  - heart regeneration
KW  - titin
KW  - collagen
KW  - agrin
KW  - extracellular matrix
Y1  - 2020
U6  - https://doi.org/10.3389/fcell.2021.642840
SN  - 2296-634X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Bornhorst, Dorothee
A1  - Abdelilah-Seyfried, Salim
T1  - Strong as a Hippo’s Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development
JF  - Frontiers in Cell and Developmental Biology
N2  - 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.
KW  - Hippo signaling
KW  - Yap1/Wwtr1 (Taz)
KW  - cardiac development
KW  - mechanobiology
KW  - endocardium
KW  - myocardium
KW  - zebrafish
KW  - intra-organ-communication
Y1  - 2021
U6  - https://doi.org/10.3389/fcell.2021.731101
SN  - 2296-634X
VL  - 9
SP  - 1
EP  - 10
PB  - Frontiers Media
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Eilers, Elisabeth Johanna
A1  - Kleine, Sandra
A1  - Eckert, Silvia
A1  - Waldherr, Simon
A1  - Müller, Caroline
T1  - Flower production, headspace volatiles, pollen nutrients, and florivory in tanacetum vulgare chemotypes
JF  - Frontiers in plant science : FPLS
N2  - 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.
KW  - terpenoids
KW  - gas chromatography-mass spectrometry (GC-MS)
KW  - Asteraceae
KW  - protein
KW  - lipid-ratio
KW  - insect behavior
KW  - Phalacridae
KW  - chemodiversity
Y1  - 2021
U6  - https://doi.org/10.3389/fpls.2020.611877
SN  - 1664-462X
VL  - 11
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Steppert, Claus
A1  - Steppert, Isabel
A1  - Sterlacci, William
A1  - Bollinger, Thomas
T1  - Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath
BT  - a proof of concept study
JF  - 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)
N2  - 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,
KW  - breath analysis
KW  - ion mobility spectrometry
KW  - COVID-19
KW  - influenza-A
Y1  - 2021
U6  - https://doi.org/10.1088/1752-7163/abe5ca
SN  - 1752-7163
VL  - 15
IS  - 2
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Apriyanto, Ardha
A1  - Tambunan, Van Basten
T1  - Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil
JF  - Data in Brief
N2  - 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.
KW  - Whole-genome sequencing
KW  - NGS
KW  - Simple Sequence Repeat
KW  - Weevil
KW  - Curculionidae
KW  - Oil Palm
KW  - Pollinator
KW  - Genomics
Y1  - 2021
U6  - https://doi.org/10.1016/j.dib.2021.106745
SN  - 2352-3409
VL  - 34
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Li, Xiaoxiao
A1  - Yang, Wei
A1  - Sun, Tao
A1  - Gaedke, Ursula
T1  - Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed
JF  - Marine biology : international journal on life in oceans and coastal waters
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1007/s00227-021-03878-z
SN  - 0025-3162
SN  - 1432-1793
VL  - 168
IS  - 5
PB  - Springer
CY  - Berlin ; Heidelberg
ER  - 
TY  - JOUR
A1  - Warmt, Christian
A1  - Fenzel, Carolin Kornelia
A1  - Henkel, Jörg
A1  - Bier, Frank Fabian
T1  - Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes
JF  - Scientific reports
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1038/s41598-021-99774-z
SN  - 2045-2322
VL  - 11
IS  - 1
PB  - Macmillan Publishers Limited, part of Springer Nature
CY  - [London]
ER  - 
TY  - JOUR
A1  - Mazza, Valeria
A1  - Günther, Anja
T1  - City mice and country mice
BT  - innovative problem solving in rural and urban noncommensal rodents
JF  - Animal behaviour
N2  - 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.
KW  - animal personality
KW  - anthropogenic environment
KW  - Apodemus agrarius
KW  - HIREC
KW  - individual differences
KW  - innovation
KW  - problem solving
KW  - rodent
KW  - urbanization
Y1  - 2021
U6  - https://doi.org/10.1016/j.anbehav.2020.12.007
SN  - 0003-3472
SN  - 1095-8282
VL  - 172
SP  - 197
EP  - 210
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - THES
A1  - Woehlecke, Sandra
T1  - Das erweiterte Fachwissen für den schulischen Kontext als Leitlinie für eine additive fachliche Lehrveranstaltung im Lehramtsstudium Biologie
T1  - School-related content knowledge as a guideline for an additive subject-based course for preservice biology teachers
N2  - Das Fachwissen von Lehrkräften weist für die Ausprägung fachdidaktischer Expertise eine hohe Bedeutung auf. Welche Merkmale universitäre Lehrveranstaltungen aufweisen sollten, um Lehramtsstudierenden ein berufsspezifisches Fachwissen zu vermitteln, ist jedoch überwiegend noch unklar. 
Innerhalb des Projekts PSI-Potsdam wurde auf theoretischer Grundlage das fachübergreifende Modell des erweiterten Fachwissens für den schulischen Kontext entwickelt. Als Ansatz zur Verbesserung des Biologie-Lehramtsstudiums diente dieses Modell als Konzeptionsgrundlage für eine additive Lehrveranstaltung. Hierbei werden Lerngelegenheiten geboten, um das universitär erworbene Fachwissen über 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 für Lehramtsstudierende der Biologie gestaltet sein, um ein erweitertes Fachwissen für den schulischen Kontext für den zellbiologischen Themenbereich „Struktur und Funktion der Biomembran“ zu fördern?
Anhand fallübergreifender 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 universitär vermittelter Inhalte bei den untersuchten Studierenden auffallend unterscheidet, wobei dem Schulwissen ein deutlich höheres Interesse entgegengebracht wird. Die Berufsrelevanz fachlicher Inhalte wird seitens der Studierenden häufig am Schulwissen festgemacht.
Innerhalb konkreter Einzelfallanalysen (n = 6) wird anhand von Lernpfaden dargestellt, wie sich über mehrere Design-Experimente hinweg fachliche Konzepte entwickelt haben. Bei der Beschreibung wird vor allem auf Schlüsselstellen und Hürden im Lernprozess fokussiert. Aus diesen Ergebnissen folgend werden vorgenommene Iterationen für die einzelnen Zyklen beschrieben, die ebenfalls anhand der iterativen Entwicklung der Design-Prinzipien dargelegt werden. 
Es konnte gezeigt werden, dass die Schlüsselstellen sehr individuell aufgrund der subjektiv fokussierten Inhalte zu Tage treten. Meist treten sie jedoch im Zusammenhang mit der Verknüpfung verschiedener fachlicher Konzepte oder durch kooperative Aufschlüsselungen von Konzepten auf. Fachliche Hürden konnten hingegen in Form von fachlich unangemessenen Vorstellungen fallübergreifend 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 für 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 fördern. 
Insgesamt scheint das Modell des erweiterten Fachwissens für den schulischen Kontext äußerst geeignet zu sein, um anhand der Facetten und deren Beschreibungen Lerngelegenheiten oder Gestaltungsprinzipien für diese zu konzipieren. Für das untersuchte Lehr-Lernarrangement haben sich kleinere Adaptationen des Modells als sinnvoll erwiesen. Hinsichtlich der Methodologie konnten Ableitungen für die Anwendung der fachdidaktischen Entwicklungsforschung für additive fachliche Lehrveranstaltungen dieser Art herausgestellt werden.
Um den Professionsbezug der fachwissenschaftlichen Anteile im Lehramtsstudium zu verbessern, ist der weitere Einbezug des erweiterten Fachwissens für den schulischen Kontext in die fachwissenschaftlichen Studienanteile überaus wünschenswert.
N2  - The content knowledge of teachers is of great importance for the development of pedagogical content knowledge and its application in teaching. However, the characteristics of university courses in order to provide pre-service biology teachers with job-specific content knowledge are still unclear. Within the project PSI-Potsdam a theory-based interdisciplinary model of school-related content knowledge (SRCK) was developed. This model served as a conceptual basis for an additive course within the biology teacher training curriculum. Learning opportunities are offered to apply the university-acquired subject matter knowledge to school contexts (e.g. through the deconstruction and subsequent reconstruction of texts for school purposes). The effects of the seminar, especially the learning processes, were observed in several cycles in the format of design research. One of the central research questions is: How can a learning opportunity for perspective Biology teachers be designed, to promote SRCK with regard to the topic “structure and function of the biomembrane"? 
Cross-case analyses (n = 29) show existing attitudes towards teacher training. As an important result, it can be emphasized, that the subject interest in school- and university-taught content differs strikingly among the students. School knowledge is shown a significantly higher interest. The professional relevance of subject-related content is often determined by a perceived proximity to school knowledge. 
Within concrete individual case analyses (n = 6), learning paths are used to show how subject-specific concepts have developed over several design experiments. The description focuses primarily on key points and obstacles in the learning process. Within this framework, iterations made for the individual cycles are described. It could be shown that the key points come to light very individually due to the focused content. In most cases, however, they occur in connection with the linking of different concepts or through cooperative explanations of concepts. Obstacles in the learning processes, on the other hand, could be identified across cases in the form of inappropriate ideas. This concerns, among other things, the idea of the biomembrane as a wall, which goes hand in hand with the ideas of a protective function and a shaping function of the biomembrane. Furthermore, a number of possibilities could be shown, how the SRCK was applied in the learning tasks. It was established that certain learning opportunities are appropriate to promote certain facets of SRCK. Overall, the model of SRCK seems to be extremely suitable in order to design learning opportunities. For the investigated teaching-learning arrangement, smaller adaptations of the model have proven as useful. 
In order to improve the professional relevance of the teacher training programme, the further inclusion of the SRCK in the subject-specific study components is highly desirable.
KW  - Professionswissen
KW  - Fachwissen
KW  - Studierendenvorstellungen
KW  - Biomembran
KW  - Erweitertes Fachwissen für den schulischen Kontext
KW  - professional competence
KW  - Design Research
KW  - Design Research
KW  - content knowledge
KW  - biomembrane
KW  - school-related content knowledge
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-521209
ER  - 
TY  - JOUR
A1  - Enzingmüller, Carolin
A1  - Prechtl, Helmut
T1  - Constructing graphs in biology class
BT  - Secondary biology teachers’ beliefs, motivation, and self-reported practices
JF  - International journal of science and mathematics education
N2  - 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.
KW  - Biology teachers
KW  - Beliefs and motivation
KW  - Classroom practices
KW  - Graph
KW  - construction
KW  - Secondary school
Y1  - 2019
U6  - https://doi.org/10.1007/s10763-019-09975-2
SN  - 1571-0068
SN  - 1573-1774
VL  - 19
IS  - 1
SP  - 1
EP  - 19
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Merida, Angel
A1  - Fettke, Jörg
T1  - Starch granule initiation in Arabidopsis thaliana chloroplasts
JF  - The plant journal
N2  - 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.
KW  - starch granules
KW  - starch metabolism
KW  - starch granule initiation
KW  - starch
KW  - granule number per chloroplast
KW  - starch morphology
KW  - Arabidopsis thaliana
Y1  - 2021
U6  - https://doi.org/10.1111/tpj.15359
SN  - 0960-7412
SN  - 1365-313X
VL  - 107
IS  - 3
SP  - 688
EP  - 697
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Rödel, Claudia Jasmin
A1  - Abdelilah-Seyfried, Salim
T1  - A zebrafish toolbox for biomechanical signaling in cardiovascular development and disease
JF  - Current opinion in hematology
N2  - 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.
KW  - angiogenesis
KW  - cardiovascular system
KW  - Danio rerio (zebrafish)
KW  - genetic
KW  - tools
KW  - mechanobiology
Y1  - 2021
U6  - https://doi.org/10.1097/MOH.0000000000000648
SN  - 1065-6251
SN  - 1531-7048
VL  - 28
IS  - 3
SP  - 198
EP  - 207
PB  - Lippincott Williams & Wilkins
CY  - Philadelphia
ER  - 
TY  - THES
A1  - Möser, Christin
T1  - Modular DNA constructs for oligovalent bio-enhancement and functional screening
T1  - Modulare DNA-Konstrukte für oligovalente Bio-Verstärkung und funktionelles Screening
N2  - 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.
N2  - Desoxyribonukleinsäure (DNS, engl. DNA) - Nanostrukturen ermöglichen die Anbringung funktioneller Moleküle an nahezu jede einzigartige Stelle der zugrunde liegenden Struktur. Aufgrund der Basenpaar-Strukturauflösung von DNA können mehrere Moleküle (z.B. Liganden) entsprechend der Geometrie ihres gewünschten Ziels räumlich angeordnet und genau kontrolliert werden, was zu optimierten Bindungs- und/oder Signalwechselwirkungen führt.
Diese Dissertation umfasst drei Hauptprojekte. Alle Projekte verwenden Varianten von funktionalisierten DNA-Nanostrukturen, die als Plattform für die oligovalente Präsentation von Liganden dienen. Ziel der vorliegenden Arbeit war es, die Fähigkeit von DNA-Nanostrukturen zur präzisen Positionierung verschiedener Arten von funktionellen Molekülen zu evaluieren und folglich die Wirksamkeit der Moleküle gemäß dem Konzept der Multivalenz zu erhöhen. Außerdem wurde untersucht, wie funktionalisierte DNA-Strukturen in verschiedenen Verfahren zur Erforschung von biologischen Interaktionen eingesetzt werden können. Die entwickelten DNA-basierten Liganden wurden verwendet, um Strukturen auf verschiedenen biologischen Systemen gezielt zu binden.
In einem Teil dieser Dissertation wurde versucht, Krankheitserreger mit kleinen modifizierten DNA-Nanostrukturen zu binden. Pathogene, wie Viren und Bakterien, sind für ihre multivalente Anheftung an Wirtszellmembranen bekannt. Durch die oligovalente Blockierung ihrer Rezeptoren für die Erkennung und/oder Fusion mit ihrem Wirt sollte ihre Fähigkeit, sich an Zielzellen anzuheften und in diese einzudringen, beeinträchtigt werden. Bei Influenza A Viren konnte nur eine verstärkte Bindung von oligovalenten Peptid-DNA-Konstrukten im Vergleich zu monovalenten Peptiden beobachtet werden, wohingegen bei Respiratorischen Synzytial-Viren (RSV) sowohl die Bindung als auch die Blockierung der Zielrezeptoren zu einer verstärkten Hemmung der Infektion in vitro führte.
Im letzten Teil wurden chimäre DNA-Peptidkonstrukte auf ihre Fähigkeit, an Signalrezeptoren auf der Oberfläche von Zellen zu binden und diese zu aktivieren, getestet. Die spezifische Bindung von mit bis zu drei Peptiden konjugierten DNA-Trimeren an EphA2-Rezeptor-exprimierende Zellen wurde in Durchflusszytometrie-Experimenten untersucht. Anschließend wurde ihre Fähigkeit, diese Rezeptoren durch Phosphorylierung zu aktivieren, beurteilt. Die Phosphorylierung von EphA2 war durch DNA-Trimere, die drei Peptide trugen, im Vergleich zu monovalenten Peptiden signifikant erhöht. Infolge der Aktivierung kommt es zu charakteristischen morphologischen Veränderungen der Zellen, bei denen diese ihre Peripherie "abrunden" und zurückziehen.
Die in dieser Arbeit erzielten Ergebnisse beweisen umfassend die Fähigkeit von DNA-Nanostrukturen, als stabile, biokompatible, kontrollierbare Plattformen für die oligovalente Präsentation funktioneller Liganden zu fungieren. Funktionalisierte DNA-Nanostrukturen wurden zur Verstärkung biologischer Effekte und als Werkzeug für das funktionelle Screening von biologischen Interaktionen verwendet. Diese Arbeit zeigt, dass modifizierte DNA-Strukturen das Potenzial haben, die Medikamentenentwicklung zu verbessern und die Aktivierung von Signalwegen zu entschlüsseln.
KW  - DNA
KW  - multivalency
KW  - influenza
KW  - respiratory syncytial virus
KW  - nanostructure
KW  - ephrin
KW  - DNA
KW  - Ephrin
KW  - Influenza
KW  - Multivalenz
KW  - Nanostruktur
KW  - Respiratorisches Synzytial-Virus
KW  - DNS
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-507289
ER  - 
TY  - JOUR
A1  - Paolini, Alessio
A1  - Fontana, Federica
A1  - Van-Cuong Pham, 
A1  - Rödel, Claudia Jasmin
A1  - Seyfried, Salim
T1  - Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish
JF  - Cell reports
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1016/j.celrep.2021.109782
SN  - 2211-1247
VL  - 37
IS  - 1
PB  - Cell Press
CY  - Maryland Heights, MO
ER  - 
TY  - THES
A1  - Michelchen, Sophia
T1  - Etablierung einer Antigen-spezifischen Aktivierung von B-Lymphozyten in vitro
N2  - Monoklonale Antikörper sind essenzielle Werkzeuge in der modernen Laboranalytik sowie in der medizinischen Therapie und Diagnostik. Die Herstellung monoklonaler Antikörper ist ein zeit- und arbeitsintensiver Prozess. Herkömmliche Methoden beruhen auf der Immunisierung von Labortieren, die mitunter mehrere Monate in Anspruch nimmt. Anschließend werden die Antikörper-produzierenden B-Lymphozyten bzw. deren Antikörpergene isoliert und in Screening-Verfahren untersucht, um geeignete Binder zu identifizieren.

Der Transfer der humoralen Immunantwort in eine in vitro Umgebung erlaubt eine Verkürzung 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 Antikörper-Produktion konzentriert: die B-Lymphozyten. Darüber hinaus sollte eine permanente Zelllinie etabliert werden, die zur Antikörper-Herstellung eingesetzt werden und die Verwendung von Primärzellen ersetzen würde.

Im ersten Teil der Arbeit wurde ein Protokoll zur In vitro Immunisierung muriner BLymphozyten etabliert. In Vorversuchen wurden die optimalen Konditionen für die Antigenspezifische Aktivierung gereinigter Milz-B-Lymphozyten aus nicht-immunisierten Mäusen
determiniert. Dazu wurde der Einfluss verschiedener Stimuli auf die Produktion unspezifischer und spezifischer Antikörper untersucht. Eine Kombination aus dem Modellantigen VP1 (Hamster Polyomavirus Hüllprotein 1), einem Anti-CD40-Antikörper, Interleukin 4 (IL 4) und Lipopolysaccharid (LPS) oder IL 7 induzierte nachweislich eine Antigen-spezifische Antikörper-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 Zelloberfläche nachgewiesen. In einer Zeitreihe über zehn Tage wurde am zehnten Tag der In vitro Immunisierung die verhältnismäßig höchste Konzentration Antigen-spezifischer IgG-Antikörper im Kulturüberstand der stimulierten Zellen nachgewiesen.

Als nächster Schritt sollte eine permanente Zelllinie hergestellt werden, die statt primärer BLymphozyten für die zuvor etablierte In vitro Immunisierung eingesetzt werden könnte. Zu diesem Zweck wurden retrovirale Vektoren hergestellt, die durch den Transfer verschiedener Onkogene in murine B-Lymphozyten bzw. deren Vorläuferzellen 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 Funktionalität der hergestellten Viren anhand verschiedener Assays belegt. Die transferierten Gene konnten in der Testzelllinie auf DNAEbene nachgewiesen oder die Überexpression der entsprechenden Proteine im Western Blot detektiert werden. Es wurden schließlich B-Lymphozyten bzw. unreife Vorläuferzellen derselben mit den generierten Retroviren transduziert und mit Knochenmark-ähnlichen Stromazellen co-kultiviert. Aus keinem der transduzierten Ansätze konnte bisher eine Zelllinie oder eine Langzeit-Kultur etabliert werden.

Im letzten Teil der Arbeit wurde die Effektivität und Übertragbarkeit 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 Antikörper-produzierende Zelllinien transformiert.
Dabei konnten mehrere Hybridomzelllinien generiert werden, die spezifische IgGAntikörper gegen VP1 oder Mip produzieren. Die generierten Antikörper 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 Antikörper. Sie ersetzt die Immunisierung von Versuchstieren und reduziert den Zeitaufwand erheblich. In Kombination mit der Hybridomtechnologie können die in vitro immunisierten Zellen, wie hier demonstriert, zur Generation von Hybridomzelllinien und zur Herstellung monoklonaler Antikörper genutzt werden. Um die Verwendung von Versuchstieren in dieser Methode durch eine adäquate permanente Zelllinie zu ersetzen, muss die genetische Veränderung von B-Lymphozyten und unreifen hämatopoetischen Zellen optimiert werden. Die Ergebnisse bieten eine Basis  für eine universelle, Spezies-unabhängige Methodik zur Antikörperherstellung und für die
Etablierung einer idealen, tierfreien In vitro Immunisierung.
N2  - Monoclonal antibodies are essential tools in modern analytics as well as medical therapy and diagnostics. The production of such is a time consuming and labor intensive process. Common methods rely on the immunization of laboratory animals which comprises up to several months. Subsequently antibody producing B lymphocytes or their antibody coding genes are isolated and screened for suitable binders.
The transfer of the humoral immune reaction into an in vitro setting allows to shorten this process and circumvents the necessity of in vivo immunization. The imitation of the complex interaction between all involved immune cells however is difficult to mimic in vitro. Consequently, the main focus of this thesis was the establishment of a simplified in vitro immunization focusing only on the protagonists of antibody production: B lymphocytes. Furthermore a permanent cell line should be generated for the implementation in antibody production and to replace the use of primary cells.
In the first part of this work a protocol for the in vitro immunization of murine B lymphocytes was established. In preliminary experiments the optimal conditions for the antigen specific activation of spleen B lymphocytes isolated from non-immunized mice were determined. Therefore the influence of various stimuli on the production of unspecific and specific antibodies was investigated. A combination of the model antigen VP1 (Hamster Polyomavirus capsid protein 1), an anti-CD40 antibody, interleukin 4 (IL 4) and lipopolysaccharide (LPS) or IL 7 evidently induced an antigen specific antibody response in vitro. To proof successful B lymphocyte activation following the in vitro stimulation rapid cell proliferation and the expression of characteristic activation markers on cell surfaces were shown. Over the course of ten days of in vitro immunization the production of antigen specific IgG antibodies in the supernatant of stimulated B lymphocytes was monitored peaking on day ten.
Next a permanent cell line was to be established for replacing primary B lymphocytes in the previously established in vitro immunization. For this purpose several retroviral vectors were generated to manipulate the proliferative behavior of B lymphocytes or their progenitor cells by transferring different oncogenes into those cells. Retroviruses with doxycycline inducible expression cassettes carrying the oncogenes cmyc, Bcl2, BclxL and the fusion gene NUP98HOXB4 were generated. A model cell line was successfully transduced with the generated retroviruses. The functionality of these viruses was shown in several assays. In the
model cell line the transferred genes were shown to be part of their genome or the overexpression of the corresponding proteins was shown in Western Blots or fluorescent microscopy. Finally, B lymphocytes or respectively immature progenitor cells of such were transduced with the generated retroviruses and co-cultured with bone marrow-like stroma cells. Cells could be cultured for several weeks past their natural lifespan. However, none of the approaches led to the generation of a permanent cell line or the establishment of a long term culture system.
In the final part of this thesis the effectivity and transferability of the previously established protocol for the in vitro immunization of murine B lymphocytes was shown by applying various antigens. Specific IgG responses were induced in vitro against VP1, Legionella pneumophila and the protein Mip, a peptide of which had been included in a VP1 carrier protein used for immunization. The stimulated B lymphocytes were fused with myeloma cells to produce permanent antibody secreting cell lines. Thereby several hybridoma cell lines were generated producing specific IgG antibodies against VP1 or Mip. The generated antibodies were purified and shown to specifically bind their antigen in ELISA and Western Blot.
This protocol for in vitro immunization presented here poses an effective alternative to conventional methods for the production of specific antibodies. It replaces the immunization of laboratory animals and greatly reduces the time needed. As shown here, in combination with the hybridoma technology these in vitro immunized cells can be used for the generation of hybridoma cell lines and subsequently for the production of monoclonal antibodies. To replace the use of laboratory animals used in this method by a permanent cell line the genetic manipulation of B lymphocytes and immature hematopoietic cells needs to be optimized. The results provide a foundation for a universal, species-independent method for antibody production and for the establishment of an ideal, animal-free in vitro immunization.
KW  - B-Lymphozyten
KW  - Antikörper
KW  - Antibodies
KW  - B lymphocytes
KW  - in vitro immunization
KW  - In vitro-Immunisierung
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-530272
ER  - 
TY  - GEN
A1  - Göthel, Markus
A1  - Listek, Martin
A1  - Messerschmidt, Katrin
A1  - Schlör, Anja
A1  - Hönow, Anja
A1  - Hanack, Katja
T1  - A New Workflow to Generate Monoclonal Antibodies against Microorganisms
T2  - Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1174 
KW  - monoclonal antibody
KW  - antibody producing cell selection
KW  - hybridoma
KW  - epitope prediction
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523341
SN  - 1866-8372
IS  - 20
ER  - 
TY  - JOUR
A1  - Göthel, Markus
A1  - Listek, Martin
A1  - Messerschmidt, Katrin
A1  - Schlör, Anja
A1  - Hönow, Anja
A1  - Hanack, Katja
T1  - A New Workflow to Generate Monoclonal Antibodies against Microorganisms
JF  - Applied Sciences
N2  - 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.
KW  - monoclonal antibody
KW  - antibody producing cell selection
KW  - hybridoma
KW  - epitope prediction
Y1  - 2021
U6  - https://doi.org/10.3390/app11209359
SN  - 1454-5101
VL  - 11
IS  - 20
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Michelchen, Sophia
A1  - Micheel, Burkhard
A1  - Hanack, Katja
T1  - In vitro immunization approach to generate specific murine monoclonal IgG antibodies
JF  - Journal of immunological methods : JIM
N2  - 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.
KW  - Monoclonal antibody
KW  - Hybridoma technology
KW  - In vitro immunization
KW  - B cell activation
Y1  - 2021
U6  - https://doi.org/10.1016/j.jim.2021.113149
SN  - 0022-1759
SN  - 1872-7905
VL  - 499
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Fudickar, Werner
A1  - Roder, Phillip
A1  - Listek, Martin
A1  - Hanack, Katja
A1  - Linker, Torsten
T1  - Pyridinium alkynylanthracenes as sensitizers for photodynamic therapy
JF  - Photochemistry and photobiology
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1111/php.13554
SN  - 0031-8655
SN  - 1751-1097
VL  - 98
IS  - 1
SP  - 193
EP  - 201
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Hasnat, Muhammad Abrar
A1  - Zupok, Arkadiusz
A1  - Olas-Apelt, Justyna Jadwiga
A1  - Müller-Röber, Bernd
A1  - Leimkühler, Silke
T1  - A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical S-adenosylmethionine protein MoaA for the synthesis of active molybdoenzymes
JF  - Journal of bacteriology
N2  - 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. <br /> 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.
KW  - iron-sulfur clusters
KW  - Moco biosynthesis
KW  - MoaA
KW  - A-type carrier protein
KW  - FNR
KW  - nitrate reductase
KW  - molybdenum cofactor
Y1  - 2021
U6  - https://doi.org/10.1128/JB.00086-21
SN  - 1098-5530
VL  - 203
IS  - 12
PB  - American Society for Microbiology
CY  - Washington
ER  - 
TY  - GEN
A1  - Cahsan, Binia De
A1  - Kiemel, Katrin
A1  - Westbury, Michael V.
A1  - Lauritsen, Maike
A1  - Autenrieth, Marijke
A1  - Gollmann, Günter
A1  - Schweiger, Silke
A1  - Stenberg, Marika
A1  - Nyström, Per
A1  - Drews, Hauke
A1  - Tiedemann, Ralph
T1  - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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 (Skåne), 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1177 
KW  - Bombina bombina
KW  - heat shock protein
KW  - introgression
KW  - major histocompatibility complex
KW  - scaled mass index
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523883
SN  - 1866-8372
IS  - 14
ER  - 
TY  - GEN
A1  - Gurke, Marie
A1  - Vidal-Gorosquieta, Amalia
A1  - Pajimans, Johanna L. A.
A1  - Wȩcek, Karolina
A1  - Barlow, Axel
A1  - González-Fortes, Gloria M.
A1  - Hartmann, Stefanie
A1  - Grandal-d’Anglade, Aurora
A1  - Hofreiter, Michael
T1  - Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
KW  - Haplogroups
KW  - Mitochondria
KW  - Cattle
KW  - Genomics
KW  - Domestic animals
KW  - Livestock
KW  - Single nucleotide polymorphisms
KW  - Neolithic period
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-520875
SN  - 1866-8372
IS  - 4
ER  - 
TY  - JOUR
A1  - Cahsan, Binia De
A1  - Kiemel, Katrin
A1  - Westbury, Michael V.
A1  - Lauritsen, Maike
A1  - Autenrieth, Marijke
A1  - Gollmann, Günter
A1  - Schweiger, Silke
A1  - Stenberg, Marika
A1  - Nyström, Per
A1  - Drews, Hauke
A1  - Tiedemann, Ralph
T1  - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad
JF  - Ecology and Evolution
N2  - 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 (Skåne), 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.
KW  - Bombina bombina
KW  - heat shock protein
KW  - introgression
KW  - major histocompatibility complex
KW  - scaled mass index
Y1  - 2021
SN  - 2045-7758
VL  - 11
IS  - 14
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Gurke, Marie
A1  - Vidal-Gorosquieta, Amalia
A1  - Pajimans, Johanna L. A.
A1  - Wȩcek, Karolina
A1  - Barlow, Axel
A1  - González-Fortes, Gloria M.
A1  - Hartmann, Stefanie
A1  - Grandal-d’Anglade, Aurora
A1  - Hofreiter, Michael
T1  - Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence
JF  - PLoS ONE
N2  - 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.
KW  - Haplogroups
KW  - Mitochondria
KW  - Cattle
KW  - Genomics
KW  - Domestic animals
KW  - Livestock
KW  - Single nucleotide polymorphisms
KW  - Neolithic period
Y1  - 2020
U6  - https://doi.org/10.1371/journal.pone.0249537
SN  - 1932-6203
VL  - 16
IS  - 4
PB  - Public Library of Science
CY  - San Francisco
ER  - 
TY  - JOUR
A1  - Dunsing, Valentin
A1  - Petrich, Annett
A1  - Chiantia, Salvatore
T1  - Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection
JF  - eLife
N2  - 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.
KW  - fluorescence
KW  - optical microscopy
KW  - virus assembly
KW  - protein-protein
KW  - interactions
KW  - diffusion
KW  - Viruses
Y1  - 2021
U6  - https://doi.org/10.7554/eLife.69687
SN  - 2050-084X
VL  - 10
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - CHAP
A1  - Dunsing, Valentin
A1  - Petrich, Annett
A1  - Chiantia, Salvatore
T1  - Spectral detection enables multi-color fluorescence fluctuation spectroscopy studies in living cells
BT  - Meeting abstract: 65th Annual Meeting of the Biophysical Society (BPS), Feb. 22-26, 2021
T2  - Biophysical journal : BJ / ed. by the Biophysical Society
Y1  - 2021
U6  - https://doi.org/10.1016/j.bpj.2020.11.2206
SN  - 0006-3495
SN  - 1542-0086
VL  - 120
IS  - 3, Suppl. 1
SP  - 356A
EP  - 356A
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Schneeberger, Karin
A1  - Schulze, Michael
A1  - Scheffler, Ingo
A1  - Caspers, Barbara A.
T1  - Evidence of female preference for odor of distant over local males in a bat with female dispersal
JF  - Behavioral ecology : the official journal of the International Society for Behavioral Ecology
N2  - 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.
KW  - bats
KW  - dispersal
KW  - female preference
KW  - male philopatry
KW  - odor
KW  - olfaction
Y1  - 2021
U6  - https://doi.org/10.1093/beheco/arab003
SN  - 1045-2249
SN  - 1465-7279
VL  - 32
IS  - 4
SP  - 657
EP  - 661
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Soeriyadi, Angela H.
A1  - Ongley, Sarah E.
A1  - Kehr, Jan-Christoph
A1  - Pickford, Russel
A1  - Dittmann, Elke
A1  - Neilan, Brett A.
T1  - Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase
JF  - ChemBioChem
N2  - 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.
KW  - a domain
KW  - indolactams
KW  - MbtH
KW  - natural products
KW  - teleocidin
Y1  - 2021
U6  - https://doi.org/10.1002/cbic.202100574
SN  - 1439-4227
SN  - 1439-7633
VL  - 23
IS  - 3
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Ouédraogo, Karim
A1  - Zaré, Alhassane
A1  - Korbéogo, Gabin
A1  - Ouédraogo, Oumarou
A1  - Linstädter, Anja
T1  - Resilience strategies of West African pastoralists in response to scarce forage resources
JF  - Pastoralism : research, policy and practice
N2  - 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.
KW  - Pastoralism
KW  - Forage values
KW  - Burkina Faso
KW  - Ecological changes
Y1  - 2021
U6  - https://doi.org/10.1186/s13570-021-00210-8
SN  - 2041-7136
VL  - 11
IS  - 1
PB  - SpringerOpen
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Kindermann, Liana
A1  - Dobler, Magnus
A1  - Niedeggen, Daniela
A1  - Linstädter, Anja
T1  - A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems
JF  - Ecological indicators : integrating monitoring, assessment and management
N2  - 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.
KW  - Damage assessment
KW  - Disturbance impacts
KW  - Tree growth classes
KW  - Method
KW  - comparison
KW  - Flexible sampling strategy
KW  - Tree allometry
KW  - Woody
KW  - aboveground biomass
Y1  - 2021
U6  - https://doi.org/10.1016/j.ecolind.2021.108466
SN  - 1470-160X
SN  - 1872-7034
VL  - 135
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - de Oliveira-Silva, Anna Elizabeth
A1  - Piratelli, Augusto João
A1  - Zurell, Damaris
A1  - da Silva, Fernando Rodrigues
T1  - Vegetation cover restricts habitat suitability predictions of endemic Brazilian Atlantic Forest birds
JF  - Perspectives in Ecology and Conservation
N2  - 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/ ).
KW  - Conservation
KW  - Ecological niche modeling
KW  - Forest dependency
KW  - Fragmentation
KW  - Habitat loss
KW  - Landscape
KW  - Life-history traits
Y1  - 2021
U6  - https://doi.org/10.1016/j.pecon.2021.09.002
SN  - 2530-0644
VL  - 20
IS  - 1
SP  - 1
EP  - 8
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Wang, Meng
A1  - Li, Panpan
A1  - Ma, Yao
A1  - Nie, Xiang
A1  - Grebe, Markus
A1  - Men, Shuzhen
T1  - Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis
JF  - International journal of molecular sciences
N2  - 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.
KW  - Arabidopsis thaliana
KW  - auxin
KW  - auxin biosynthesis
KW  - cycloeucalenol
KW  - CPI1
KW  - sitosterol
KW  - sterol
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22010437
SN  - 1422-0067
VL  - 22
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Petrich, Annett
A1  - Dunsing, Valentin
A1  - Bobone, Sara
A1  - Chiantia, Salvatore
T1  - Influenza A M2 recruits M1 to the plasma membrane
BT  - a fluorescence fluctuation microscopy study
JF  - Biophysical journal : BJ / ed. by the Biophysical Society
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1016/j.bpj.2021.11.023
SN  - 0006-3495
SN  - 1542-0086
VL  - 120
IS  - 24
SP  - 5478
EP  - 5490
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Qiu, Liang
A1  - Zhang, Haoran
A1  - Bick, Thomas
A1  - Martin, Johannes
A1  - Wendler, Petra
A1  - Böker, Alexander
A1  - Glebe, Ulrich
A1  - Xing, Chengfen
T1  - Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition
N2  - 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.
KW  - galactose-decorated monomer
KW  - glyco-inside nano-assemblies
KW  - morphology
KW  - evolution
KW  - PISA
KW  - RAFT dispersion polymerization
Y1  - 2021
U6  - https://doi.org/10.1002/anie.202015692
SN  - 1433-7851
SN  - 1521-3773
VL  - 60
IS  - 20
SP  - 11098
EP  - 11103
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - GEN
A1  - Zurell, Damaris
A1  - König, Christian
A1  - Malchow, Anne-Kathleen
A1  - Kapitza, Simon
A1  - Bocedi, Greta
A1  - Travis, Justin M. J.
A1  - Fandos, Guillermo
T1  - Spatially explicit models for decision-making in animal conservation and restoration
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1243 
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549915
SN  - 1866-8372
VL  - 2022
SP  - 1
EP  - 16
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ET  - 4
ER  - 
TY  - JOUR
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR
BT  - an R package for individual-based simulation of spatial changes
JF  - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos
N2  - 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.
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
U6  - https://doi.org/10.1111/ecog.05689
SN  - 1600-0587
VL  - 44
IS  - 10
SP  - 1443
EP  - 1452
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - THES
A1  - Egli, Lukas
T1  - Stabilizing agricultural systems through diversity
N2  - 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.
N2  - In Anbetracht des Klimawandels, steigender Nachfrage nach landwirtschaftlichen Produkten und der weitgehenden Intensivierung und Spezialisierung landwirtschaftlicher Systeme ist eine ausreichende und zuverlässige Nahrungsmittelproduktion zentral für die Ernährungssicherheit. Eine hohe Nutzpflanzenvielfalt und räumliche Heterogenität können helfen, die Resilienz bzw. Widerstandsfähigkeit der landwirtschaftlichen Produktion zu stärken. Fällt zum Beispiel die Ernte einer Nutzpflanze aufgrund einer Dürre aus, können andere die Verluste ausgleichen. Außerdem können Produktionsverluste in einigen Gebieten durch Überschüsse in anderen Gebieten kompensiert werden.
In meiner Arbeit habe ich mittels umfassender Landwirtschafts- und Klimadaten und statistischer Analysen untersucht, wie sich insbesondere Nutzpflanzenvielfalt und Klimaheterogenität auf zeitliche Ertragsstabilität auswirken. Zudem habe ich evaluiert, ob asynchrone Produktionstrends unterschiedlicher Nutzpflanzen den stabilisierenden Effekt einer hohen Nutpflanzenvielfalt erklären können. Außerdem habe ich den Effekt asynchroner Produktionstrends unterschiedlicher Nutzpflanzen und von unterschiedlichen Anbaugebieten derselben Nutzpflanze in Bezug auf Produktionsstabilität verglichen und mit einer Computersimulation eruiert, wie diese Mechanismen durch Diversifizierung verändert werden. Zum Schluss habe ich untersucht, wie umfassend die Resilienz ökologischer und sozioökologischer Systeme mittels agentenbasierter Modelle bislang erforscht wurde.
Die Untersuchungen dieser Arbeit zeigen, dass Nutzpflanzenvielfalt die landwirtschaftliche Produktion auf sämtlichen untersuchten Organisationsebenen stabilisiert. Asynchrone Produktionstrends unterschiedlicher Nutzpflanzen können erklären, warum eine höhere Diversität die Produktion stabilisiert. Daneben sind asynchrone Produktionstrends unterschiedlicher Anbaugebiete besonders wichtig. Meine Simulation zeigt, dass nur eine Diversifizierung auf Feld- und Landschaftsebene asynchrone Produktionsmuster zwischen Nutpflanzen und Anbaugebieten gleichzeitig erhöht oder zumindest keine der beiden Mechanismen verringert. Agentenbasierte Modelle bieten die Möglichkeit, Resilienz systematisch zu untersuchen und Wege aufzuzeigen, die zu resilienteren Anbausystemen führen. Meine Ergebnisse unterstreichen die Notwendigkeit umfassenderer Ansätze um eine resiliente, produktive und nachhaltige landwirtschaftliche Produktion in Zeiten globaler Veränderungsprozesse zu erreichen. Dies beinhaltet insbesondere eine Diversifizierung der Nutzpflanzen auf unterschiedlichen Ebenen unter Berücksichtigung der zeitlichen Produktionstrends sowie eine nachhaltige Nutzung landwirtschaftlicher Betriebsmittel.
T2  - Stabilisierung landwirtschaftlicher Systeme durch Diversität
KW  - Agent-based models
KW  - Agroecology
KW  - Resilience
KW  - Social-ecological systems
KW  - Sustainability
KW  - Agentenbasierte Modelle
KW  - Agrarökologie
KW  - Resilienz
KW  - Sozialökologische Systeme
KW  - Nachhaltigkeit
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-496848
ER  - 
TY  - THES
A1  - Stark, Markus
T1  - Implications of local and regional processes on the stability of metacommunities in diverse ecosystems
T1  - Auswirkungen lokaler und regionaler Prozesse auf die Stabilität von Metagemeinschaften in diversen Ökosystemen
N2  - 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.
N2  - Seit geraumer Zeit prägt der Mensch seine Umwelt und greift in die Struktur von Landschaften ein. In den letzten Jahrzehnten wurde die Landschaftsnutzung intensiviert und Ökosyteme weltweit anthropogen überprägt. Solche Veränderungen der Landschaft sind mit Verantwortlich für den derzeit rapiden Verlust an Biodiversität auf lokaler wie regionaler Ebene. 

Metagemeinschafts-Modelle versuchen diese beiden Ebenen zu kombinieren und kontinuierlich zu einem besseren mechanistischen Verständnis beizutragen, wie räumliche Prozesse, so z. B. Fragmentierung von Biotopen, die Biodiversität  beeinflussen. Es besteht dabei ein großer Konsens, dass sich solche Änderungen der Landschaft tendenziell negativ auf die Stabilität von Metagemeinschaften auswirken. Jedoch ist insbesondere das Zusammenspiel von komplexen trophischen Gemeinschaften und räumlichen Prozessen längst nicht vollständig verstanden. 

In der vorliegenden Arbeit wird ein Metagemeinschafts-Modellansatz verwendet, der auf einem dynamischen und räumlich expliziten Modell basiert, das Populationsdynamiken auf der lokalen Ebene und Migrationsdynamiken auf der regionalen Ebene integriert. Dieser Ansatz erlaubt die Bewertung komplexer räumlicher Landschaftskomponenten wie z. B. die Auswirkung von Habitatsclustern auf Populationsdynamiken einzelner Arten bis hin zur Diversität komplexer Artengemeinschaften. Zusätzlich zum Einfluss von einzelner konstanter räumlicher Strukturen werden auch periodische Umweltstörungen berücksichtigt, bei der ein Wechsel der Habitatverfügbarkeit, die räumliche Struktur der Landschaft temporär verändert, wie z. B. die Austrocknung eines Gewässers.

Auf der lokalen Ebene deuten die Modellergebnisse darauf hin, dass Tierarten mit einer großen Körpermasse, wie z. B. Raubtierarten in höheren trophischen Positionen, in einem Zustand großer Habitat-Isolation stärker vom Aussterben bedroht sind, als Arten mit geringer Körpermasse auf unteren trophischen Ebenen. Arten mit einer geringerer Körpermasse haben einen erhöhten metabolischen Verlust, der zu einer Energielimitierung auf den höheren trophischen Ebenen führt. Dies kann eine Erklärung dafür sein, dass  Arten mit großer Körpermasse ein höheres Aussterberisiko in den Modellergebnissen aufweisen. Dieser Effekt ist vor allem in Nahrungsnetzen ausgeprägt, bei denen Arten empfindlicher auf metabolische Verluste durch Migration und eine Veränderung der Habitat Struktur reagieren. Neben der Bedeutung der Zusammensetzung der Arten eines Nahrungsnetzes für die Diversität, haben lokale Fraßinteraktionen ebenfalls Auswirkungen auf die Synchronisierung von Populationsdynamiken. Ein geringerer Fraßdruck führt zu mehr asynchronen Populationsdynamiken, die diese Dynamiken einer Metapopulation stabilisiert, sodass das Risiko von Aussterbeereignissen einzelner Arten sinkt. 

Auf der regionalen Ebene führen als landschaftliche Aspekte, neben der mittleren Habitat-Isolation, ebenso die Bildung von lokalen Clustern aus zwei Habitaten zu einer Zunahme der Beta-Diversität. Jedoch erklären die individuelle Zusammensetzung und Robustheit der lokalen Arten- gemeinschaft gleichermaßen einen großen Anteil der zu beobachteten Diversitätsmuster. Eine Kombination aus periodischen Umweltstörungen und Habitat-Isolation hat insbesondere einen Einfluss auf die Populationsdynamiken einzelner Arten. Populationsdynamiken können durch periodische Umweltstörungen synchronisiert werden, und dabei die sonst auftauchende asynchronen Populationsdynamiken bei einer größeren Habitat-Isolation überlagern. Die dadurch vereinheitlichen Trends in der Synchronisierung erhöhen das Risiko korrelierter Aussterbeereignisse einer Art. 

Zusammenfassend lassen sich zwei große Einflussfaktoren auf die lokalen Diversitätsmuster der Metagemeinschaften feststellen. Zum Einen die lokale Artenzusammensetzung und zum Anderen die Interaktionen der Arten. Im Vergleich dazu, haben räumliche Komponenten wie die Fragmentierung der Landschaft einen vernachlässigbaren Einfluss auf die lokalen Diversitätsmuster und gewinnen erst für regionale Diversitätsmuster an Gewicht. Im Gegensatz dazu spielen auf der Ebene der Populationsdynamik besonders regionale Eigenschaften, wie die periodische Umweltstörung und Habitat-Isolation, eine Rolle und tragen wesentlich zum Verständnis der Stabilität von Populationsdynamiken der Metagemeinschaft bei.
Diese Untersuchungen zeigen einmal mehr die Komplexität unserer Ökosysteme und die Notwendigkeit weiterer Analysen für ein besseres Verständnis unserer umgebenen Umwelt und gezielteren Schutz der Biodiversität.
KW  - Fragmentation
KW  - Ecology
KW  - Food Web
KW  - Metacommunity
KW  - Disturbance
KW  - Störungen
KW  - Ökologie
KW  - Nahrungsnetze
KW  - Fragmentierung
KW  - Metagemeinschaften
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-526399
ER  - 
TY  - CHAP
A1  - Stephan, Mareike Sophia
A1  - Barbirz, Stefanie
A1  - Robinson, Tom
A1  - Yandrapalli, Naresh
A1  - Dimova, Rumiana
T1  - Bacterial mimetic systems for studying bacterial inactivation and infection
BT  - Meeting abstract: 65th Annual Meeting of the Biophysical Society (BPS), Feb. 22-26, 2021
T2  - Biophysical journal : BJ / ed. by the Biophysical Society
Y1  - 2021
U6  - https://doi.org/10.1016/j.bpj.2020.11.1087
SN  - 0006-3495
SN  - 1542-0086
VL  - 120
IS  - 3
SP  - 148A
EP  - 148A
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - CHAP
A1  - Dennis, Alice B.
A1  - Inäbnit, Thomas
T1  - Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus)
T2  - Integrative and comparative biology / Society of Integrative and Comparative Biology
Y1  - 2021
U6  - https://doi.org/10.1093/icb/icab001
SN  - 1540-7063
SN  - 1557-7023
VL  - 61
SP  - E195
EP  - E196
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Petazzi, Roberto Arturo
A1  - Koikkarah Aji, Amit
A1  - Tischler, Nicole D.
A1  - Chiantia, Salvatore
T1  - Detection of envelope glycoprotein assembly from old world hantaviruses in the Golgi apparatus of living cells
JF  - Journal of virology
N2  - 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. <br /> 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.
KW  - fluorescence fluctuation microscopy
KW  - number and brightness
KW  - virus
KW  - assembly
KW  - fluorescence correlation spectroscopy
KW  - protein-protein
KW  - interaction
KW  - fluorescence microscopy
KW  - fluorescent image analysis
Y1  - 2021
U6  - https://doi.org/10.1128/JVI.01238-20
SN  - 1098-5514
VL  - 95
IS  - 4
PB  - American Society for Microbiology
CY  - Baltimore, Md.
ER  - 
TY  - JOUR
A1  - Sandhage-Hofmann, Alexandra
A1  - Linstädter, Anja
A1  - Kindermann, Liana
A1  - Angombe, Simon
A1  - Amelung, Wulf
T1  - Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass
JF  - Global change biology
N2  - 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.
KW  - carbon sequestration
KW  - conservation
KW  - elephants
KW  - soil organic carbon
KW  - woody biomass
Y1  - 2021
U6  - https://doi.org/10.1111/gcb.15779
SN  - 1354-1013
SN  - 1365-2486
VL  - 27
IS  - 19
SP  - 4601
EP  - 4614
PB  - Blackwell Science
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Yildiz, Tugba
A1  - Leimkühler, Silke
T1  - TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli
JF  - Journal of bacteriology
N2  - 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. <br /> 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.
KW  - iron-sulfur clusters
KW  - tRNA thio modifications
KW  - FtsZ ring formation
KW  - cell
KW  - division
KW  - TusA
KW  - RpoS
KW  - Fis
KW  - FtsZ
Y1  - 2021
U6  - https://doi.org/10.1128/JB.00659-20
SN  - 1098-5530
VL  - 203
IS  - 7
PB  - American Society for Microbiology
CY  - Washington
ER  - 
TY  - JOUR
A1  - Marzetz, Vanessa
A1  - Wacker, Alexander
T1  - Evaluating the relevance of species sorting and physiological plasticity of phytoplankton communities grown in a multifactor environment
JF  - Freshwater biology / Freshwater Biological Association
N2  - 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.
KW  - fatty acid composition
KW  - light intensity
KW  - light variability
KW  - nutrient
KW  - supply
KW  - resource competition
Y1  - 2021
U6  - https://doi.org/10.1111/fwb.13810
SN  - 0046-5070
SN  - 1365-2427
VL  - 66
IS  - 10
SP  - 1992
EP  - 2003
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - John, Sheeba
A1  - Olas, Justyna Jadwiga
A1  - Müller-Röber, Bernd
T1  - Regulation of alternative splicing in response to temperature variation in plants
JF  - Journal of experimental botany
N2  - 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.
KW  - alternative splicing
KW  - ambient temperature
KW  - cold
KW  - heat
KW  - plants
KW  - stress
KW  - adaptation
Y1  - 2021
U6  - https://doi.org/10.1093/jxb/erab232
SN  - 0022-0957
SN  - 1460-2431
VL  - 72
IS  - 18
SP  - 6150
EP  - 6163
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - De Sousa Mota, Cristiano
A1  - Diniz, Ana
A1  - Coelho, Catarina
A1  - Santos-Silva, Teresa
A1  - Esmaeeli Moghaddam Tabalvandani, Mariam
A1  - Leimkühler, Silke
A1  - Cabrita, Eurico J.
A1  - Marcelo, Filipa
A1  - Romão, Maria João
T1  - Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy
BT  - the raloxifene case
JF  - Journal of medicinal chemistry / American Chemical Society
N2  - 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.
Y1  - 2021
U6  - https://doi.org/10.1021/acs.jmedchem.1c01125
SN  - 0022-2623
SN  - 1520-4804
VL  - 64
IS  - 17
SP  - 13025
EP  - 13037
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Brandes, Stefanie
A1  - Sicks, Florian
A1  - Berger, Anne
T1  - 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
JF  - Sensors
N2  - 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.
KW  - giraffe
KW  - triaxial acceleration
KW  - machine learning
KW  - random forests
KW  - behavior classification
KW  - giraffe conservation
Y1  - 2021
U6  - https://doi.org/10.3390/s21062229
SN  - 1424-8220
VL  - 21
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - GEN
A1  - Bergholz, Kolja
A1  - Kober, Klarissa
A1  - Jeltsch, Florian
A1  - Schmidt, Kristina
A1  - Weiß, Lina
T1  - Trait means or variance
BT  - What determines plant species' local and regional occurrence in fragmented dry grasslands?
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1151 
KW  - LMA
KW  - niche width
KW  - plant functional trait
KW  - scale-dependency
KW  - species abundance
KW  - trait-environment relationship
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-519905
SN  - 1866-8372
SP  - 3357
EP  - 3365
ER  - 
TY  - JOUR
A1  - Bergholz, Kolja
A1  - Kober, Klarissa
A1  - Jeltsch, Florian
A1  - Schmidt, Kristina
A1  - Weiß, Lina
T1  - Trait means or variance
BT  - What determines plant species' local and regional occurrence in fragmented dry grasslands?
JF  - Ecology and evolution
N2  - 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.
KW  - LMA
KW  - niche width
KW  - plant functional trait
KW  - scale-dependency
KW  - species abundance
KW  - trait-environment relationship
Y1  - 2020
U6  - https://doi.org/10.1002/ece3.7287
SN  - 2045-7758
VL  - 11
IS  - 7
SP  - 3357
EP  - 3365
PB  - John Wiley & Sons, Inc.
ER  - 
TY  - JOUR
A1  - Kim, Shin Woong
A1  - Leifheit, Eva F.
A1  - Maaß, Stefanie
A1  - Rillig, Matthias C.
T1  - Time-dependent toxicity of tire particles on soil nematodes
JF  - Frontiers in Environmental Science
N2  - Tire-wear particles (TWPs) are being released into the environment by wearing down during car driving, and are considered an important microplastic pollution source. The chemical additive leaching from these polymer-based materials and its potential effects are likely temporally dynamic, since amounts of potentially toxic compounds can gradually increase with contact time of plastic particles with surrounding media. In the present study, we conducted soil toxicity tests using the soil nematode Caenorhabditis elegans with different soil pre-incubation (30 and 75 days) and exposure (short-term exposure, 2 days; lifetime exposure, 10 days) times. Soil pre-incubation increased toxicity of TWPs, and the effective concentrations after the pre-incubation were much lower than environmentally relevant concentrations. The lifetime of C. elegans was reduced faster in the TWP treatment groups, and the effective concentration for lifetime exposure tests were 100- to 1,000-fold lower than those of short-term exposure tests. Water-extractable metal concentrations (Cr, Cu, Ni, Pb, and Zn) in the TWP-soils showed no correlation with nominal TWP concentrations or pre-incubation times, and the incorporated metals in the TWPs may be not the main reason of toxicity in this study. Our results show that toxic effects of TWPs can be time-dependent, both in terms of the microplastic particles themselves and their interactions in the soil matrix, but also because of susceptibility of target organisms depending on developmental stage. It is vital that future works consider these aspects, since otherwise effects of microplastics and TWPs could be underestimated.
KW  - Caenorhabditis elegans
KW  - exposure time
KW  - lifetime
KW  - microplastics
KW  - soil
KW  - incubation
Y1  - 2021
U6  - https://doi.org/10.3389/fenvs.2021.744668
SN  - 2296-665X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Mazza, Valeria
A1  - Czyperreck, Inken
A1  - Eccard, Jana
A1  - Dammhahn, Melanie
T1  - Cross-Context Responses to Novelty in Rural and Urban Small Mammals
JF  - Frontiers in Ecology and Evolution
N2  - The Anthropocene is the era of urbanization. The accelerating expansion of cities occurs at the expense of natural reservoirs of biodiversity and presents animals with challenges for which their evolutionary past might not have prepared them. Cognitive and behavioral adjustments to novelty could promote animals’ persistence under these altered conditions. We investigated the structure of, and covariance between, different aspects of responses to novelty in rural and urban small mammals of two non-commensal rodent species. We ran replicated experiments testing responses to three novelty types (object, food, or space) of 47 individual common voles (Microtus arvalis) and 41 individual striped field mice (Apodemus agrarius). We found partial support for the hypothesis that responses to novelty are structured, clustering (i) speed of responses, (ii) intensity of responses, and (iii) responses to food into separate dimensions. Rural and urban small mammals did not differ in most responses to novelty, suggesting that urban habitats do not reduce neophobia in these species. Further studies investigating whether comparable response patters are found throughout different stages of colonization, and along synurbanization processes of different duration, will help illuminate the dynamics of animals’ cognitive adjustments to urban life.
KW  - animal cognition
KW  - anthropogenic environment
KW  - HIREC
KW  - novelty
KW  - neophobia
KW  - neophilia
KW  - rodents
KW  - urbanization
Y1  - 2021
U6  - https://doi.org/10.3389/fevo.2021.661971
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  -