Refine
Has Fulltext
- yes (55) (remove)
Year of publication
- 2022 (55) (remove)
Document Type
- Doctoral Thesis (27)
- Postprint (23)
- Article (3)
- Habilitation Thesis (1)
- Master's Thesis (1)
Is part of the Bibliography
- yes (55)
Keywords
- functional traits (3)
- AFLP (2)
- Bewegungsökologie (2)
- GPS (2)
- Koexistenz (2)
- MSAP (2)
- Transkriptionsfaktoren (2)
- animal personality (2)
- antibody (2)
- coexistence (2)
- cytosine methylation (2)
- ecology (2)
- fence ecology (2)
- genome scan (2)
- light pollution (2)
- miRNA (2)
- microplastics (2)
- movement ecology (2)
- rotifer (2)
- spatial autocorrelation (2)
- transcription factors (2)
- ungulate (2)
- veterinary cordon fence (2)
- Ökologie (2)
- 7-Methylheptadecan (1)
- 7-methylheptadecane (1)
- ALAN (1)
- ARMS (1)
- Africa (1)
- Agentenbasierte Modelle (1)
- Aldehydoxidase (1)
- Amaranthus retroflexus (1)
- Angiogenese (1)
- Animal personality (1)
- Antikörper (1)
- Antikörpercharakterisierung (1)
- Antikörpervalidierung (1)
- Arabidopsis thaliana (1)
- Asplanchna brightwellii (1)
- Aufnahme (1)
- Autophagie (1)
- Baumgrenze (1)
- Bead (1)
- Biodiversität (1)
- Biofilm (1)
- Biologieunterricht (1)
- Bioreaktor (1)
- Bisulfit Sequenzierung (1)
- Blaulicht (1)
- Boten-RNA (mRNA) (1)
- Brachionus calyciflorus (1)
- Breitengrad (1)
- CBD (1)
- CDK5RAP2 (1)
- CRISPR/Cas9 (1)
- CaM4 (1)
- Carabidae beetles (1)
- Central Europe (1)
- Centrosom (1)
- Cep192 (1)
- Chenopodium album (1)
- Chloroplast (1)
- Chloroplasten (1)
- Chukotka vegetation (1)
- Clathrin-bedeckte Vesikel (1)
- Co-Transfektion (1)
- Cyanobakterien-Biomarker (1)
- Cytosin-Methylierung (1)
- Damage assessment (1)
- Datura stramonium (1)
- De novo Assemblierung (1)
- Detektionssystem (1)
- Deutschland (1)
- Dictyostelium (1)
- Dielektrophorese (1)
- Disturbance impacts (1)
- Disturbance indicator (1)
- E. coli (1)
- ENTH domain proteins (1)
- ENTH-Domänenproteine (1)
- Effekt (1)
- Elephant disturbance (1)
- Energy expenditure (1)
- Epigenetik (1)
- Epigenom Editierung (1)
- Erigeron annuus (1)
- Erigeron canadensis (1)
- European hare (1)
- Fluoreszenzmikroskopie (1)
- GWAS (1)
- Gemeinschaftsgarten-Experiment (1)
- Genom-Scan (1)
- Gentechnik (1)
- Germany (1)
- Gerüste aus Fasergeflecht (1)
- Gießharz (1)
- Gießharzpräparate (1)
- Glasfaser (1)
- H3K4me (1)
- HSF (1)
- HUVEC (1)
- Hefe (1)
- HepG2 hepatocytes (1)
- HepG2-Zellen (1)
- Herstellung (1)
- Histon Methylierung (1)
- Hitzeschock-Transkriptionsfaktor (1)
- Hitzestress-Gedächtnis (1)
- Hydrogele (1)
- Illuminance (1)
- In vitro transcription technology (1)
- In-vitro-Transkriptionstechnologie (1)
- Insekten (1)
- Inter-individual differences (1)
- Intraspezifische Variation (1)
- Ionenmobilitätsspektrometrie (IMS) (1)
- JUB1 (1)
- Kanalisierung (1)
- Klassifikation der Landbedeckung (1)
- Klimawandel (1)
- Krankheitsökologie (1)
- LAVESI (1)
- LCSM (1)
- Lactuca serriola (1)
- Larix (1)
- Larix cajanderi (1)
- Legionella (1)
- Legionellen (1)
- Lipophagie (1)
- Locally structured correlation (1)
- Locally structured standard deviation (1)
- Lysosom (1)
- Lärche (1)
- Makrophagen-Aktivierung (1)
- Mechanobiologie (1)
- Messenger RNA (mRNA) (1)
- Metabolismus (1)
- Metagemeinschaften (1)
- Microtus arvalis (1)
- Mikrofluidik (1)
- Mikroplastik (1)
- Mikrosatelliten (1)
- Mitochondrien (1)
- Mitteleuropa (1)
- Modellierung (1)
- Movement ecology (1)
- Multiplex (1)
- Myodes glareolus (1)
- Nahrungsnetze (1)
- Network clustering (1)
- ODBA (1)
- Omicron (1)
- Osteogenese (1)
- PEEU (1)
- Pace-of-Life Syndrom (1)
- Palmitat (1)
- Paläoökologie (1)
- Paramutation (1)
- Peptid (1)
- Pflanzenanpassung (1)
- Pflanzenforschung (1)
- Pflanzenökologie (1)
- Phylogeographie (1)
- Planktonnahrungsnetz (1)
- Plantago major (1)
- Polyneuropathie (1)
- Populationspersistenz (1)
- Populationsstruktur (1)
- Protein complexes (1)
- Proteinkinase A (1)
- Protein–protein interaction (1)
- Präparate (1)
- Punicalagin (1)
- RNA-Seq (1)
- Rotatorien (1)
- Rotifera (1)
- SARS-CoV-2 (1)
- Saccharomyces cerevisiae (1)
- Senecio vulgaris (1)
- Seneszenz (1)
- Sensor (1)
- Sequenzierungstechnologien der nächsten Generation (1)
- Shotgun Sequenzierung (1)
- Siberia (1)
- Sibirien (1)
- Silene vulgaris (1)
- Solanum nigrum (1)
- Solidago canadensis (1)
- Solidago gigantea (1)
- Sommerekzem (1)
- Sonchus oleraceus (1)
- Species comparison (1)
- Specific wood density (1)
- Standard deviation (1)
- Steifheit (1)
- Stimuli (1)
- Synthetische Biologie (1)
- THC (1)
- TMAO reductase (1)
- TRPV1 (1)
- Thioester (1)
- Transkriptionsfaktor (1)
- Tree allometry (1)
- Tripleurospermum inodorum (1)
- Trockenstress (1)
- Tundra-Taiga (1)
- Variance (1)
- Vegetation von Tschukotka (1)
- Vegetationsveränderungen (1)
- Vegetationsveränderungen in der Subarktis (1)
- Vernetzer (1)
- Veronica persica (1)
- Waldausdehnung (1)
- Wood specific gravity (1)
- Woody aboveground biomass (1)
- Zebularin (1)
- Zellsortierung (1)
- abiotic stress (1)
- abiotischer Stress (1)
- above-ground biomass (1)
- accelerometer (1)
- acid mine drainage (1)
- adaptive Differenzierung (1)
- adaptive differentiation (1)
- agent-based model (1)
- agricultural landscape (1)
- alte DNA (1)
- alte sedimentäre DNA (1)
- ancient DNA (1)
- ancient sedimentary DNA (1)
- angeborene Immunantwort (1)
- angiogenesis (1)
- animal behaviour (1)
- anthropogene Einwirkung (1)
- anthropogener globaler Wandel (1)
- anthropogenic global change (1)
- anthropogenic impact (1)
- antibiotic inactivation (1)
- antibody characterization (1)
- antibody validation (1)
- aquaculture (1)
- artificial light at night (ALAN) (1)
- automated radio telemetry (1)
- autophagy (1)
- bacterial infections (1)
- bakterielle Infektionen (1)
- behavioral type (1)
- biodiversity (1)
- biofilm (1)
- biology classes (1)
- bioreactor (1)
- bis-MGD (1)
- bisulfite sequencing (1)
- blue light (1)
- budding yeast (1)
- buffer zones (1)
- calmodulin (1)
- camelid antibody (1)
- camelid heavy-chain-only antibodies (1)
- canalization (1)
- casting resin (1)
- cell sorting (1)
- centrosome (1)
- chaperone (1)
- chloroplast (1)
- chloroplasts (1)
- chronic pain (1)
- chronischer Schmerz (1)
- clathrin-coated vesicles (1)
- climate change (1)
- co-delivery of multiple genes (1)
- co-transfection (1)
- common-garden experiment (1)
- community model (1)
- cross-species capture (1)
- crosslinker (1)
- cyanobacteria biomarker (1)
- de novo assembly (1)
- detection system (1)
- dielectrophoresis (1)
- disease ecology (1)
- drought stress (1)
- ecosystem functioning (1)
- effect (1)
- energy expenditure (1)
- environmental change (1)
- environmental pollution (1)
- enzymatic inactivation (1)
- enzyme optimization (1)
- epigenetics (1)
- epigenome editing (1)
- expansion microscopy (1)
- extremophiles (1)
- fence interaction (1)
- fiber mesh scaffolds (1)
- fitness (1)
- florfenicol (1)
- fluorescence microscopy (1)
- food web (1)
- food webs (1)
- freshwater (1)
- functional diversity (1)
- funktionelle Diversität (1)
- genetic engineering (1)
- giving-up density (1)
- glacial refugia (1)
- glass fiber (1)
- glaziale Refugien (1)
- hADSC (1)
- heat stress memory (1)
- heavy-chain-only antibody (1)
- heliozoa (1)
- high throughput sequencing (1)
- histone methylation (1)
- hoher Durchsatz Sequenzierung (1)
- home range (1)
- hoverflies (1)
- human aldehyde oxidase (1)
- hybridization capture (1)
- hydrogels (1)
- immobilization (1)
- industrial farming (1)
- ingestion (1)
- innate immune response (1)
- insects (1)
- inter-individual differences (1)
- intraguild predation (1)
- intraspecific variation (1)
- invasiv (1)
- invasive (1)
- ion mobility spectrometry (IMS) (1)
- land-cover classification (1)
- landscape homogenization (1)
- landscape of fear (1)
- larch (1)
- latitudinal clines (1)
- lebende Materialien (1)
- lipophagy (1)
- living materials (1)
- local adaptation (1)
- lokale Anpassung (1)
- lysosome (1)
- mRNA chemistry (1)
- mRNA-Chemie (1)
- macrophage activation (1)
- mechanobiology (1)
- metabolic-profiling (1)
- metabolism (1)
- metacommunities (1)
- microbial diversity (1)
- microbial ecology (1)
- microfluidics (1)
- microsatellites (1)
- mikrobielle Vielfalt (1)
- mikrobielle Ökologie (1)
- mining lakes (1)
- mitochondria (1)
- modelling (1)
- molecular species identification (1)
- molybdenum cofactor (1)
- movement speed (1)
- museum specimens (1)
- nacheiszeitliche Wiederbesiedlung (1)
- nanobodies (1)
- natural particle (1)
- neutralization (1)
- next generation sequencing (1)
- nicht-Mendelsche Vererbung (1)
- nicht-einheimisch (1)
- nichtinvasive Diagnostik (1)
- non-Mendelian inheritance (1)
- non-invasive Diagnostics (1)
- non-native (1)
- novel biomarkers (1)
- nuclear pore complex (1)
- nucleic acids (1)
- nucleoporins (1)
- oberirdische Biomasse (1)
- osteogenesis (1)
- pace-of-life syndrome (1)
- paleoecology (1)
- palmitate (1)
- paper-based (1)
- papier-basiert (1)
- paramutation (1)
- parentage (1)
- peptide (1)
- perceived predation risk (1)
- phenotypic variation (1)
- phylogeography (1)
- phänotypische Variation (1)
- plankton food web (1)
- plant adaptation (1)
- plant ecology (1)
- plant functional trait (1)
- plant research (1)
- polyneuropathy (1)
- population persistence (1)
- population structure (1)
- postglacial recolonization (1)
- preparation (1)
- primary human macrophages (1)
- primäre humane Makrophagen (1)
- production (1)
- punicalagin (1)
- reactive oxygen species (ROS) (1)
- reaktive Sauerstoffspezies (ROS) (1)
- reciprocal transplant experiment (1)
- reproductive success (1)
- resource-tracking (1)
- reziprokes Transplantationsexperiment (1)
- ruderal (1)
- räumliche Autokorrelation (1)
- semi-closed mitosis (1)
- senescence (1)
- sensor (1)
- shotgun sequencing (1)
- shrubification (1)
- simultane Einbringung multipler Gene (1)
- single domain antibodies (1)
- solar powered light-emitting diode (1)
- solitary bees (1)
- spatially explicit (1)
- species coexistence (1)
- starch degradation (1)
- starch granule number regulation (1)
- starch initiation (1)
- stiffness (1)
- stimuli (1)
- subarctic vegetation change (1)
- summer eczema (1)
- synthetic biology (1)
- syrphids (1)
- target capture (1)
- target enrichment (1)
- thioester (1)
- toxicity (1)
- trans-Golgi Netzwerk (1)
- trans-Golgi network (1)
- transcription factor (1)
- transgenerational response (1)
- tree infilling (1)
- treeline (1)
- tundra-taiga (1)
- type specimens (1)
- vegetation change (1)
- vesicle transport (1)
- video analysis (1)
- viral infections (1)
- virale Infektionen (1)
- volatile organic compounds (VOCs) (1)
- volatile organische Substanzen (VOCs) (1)
- wild bees (1)
- wildlife and habitat management (1)
- wildlife conservation (1)
- zebularine (1)
- Ökokline (1)
- Ökosystemfunktionen (1)
Institute
- Institut für Biochemie und Biologie (55) (remove)
Welcome to the Dark Side
(2022)
Differences in natural light conditions caused by changes in moonlight are known to affect perceived predation risk in many nocturnal prey species. As artificial light at night (ALAN) is steadily increasing in space and intensity, it has the potential to change movement and foraging behavior of many species as it might increase perceived predation risk and mask natural light cycles. We investigated if partial nighttime illumination leads to changes in foraging behavior during the night and the subsequent day in a small mammal and whether these changes are related to animal personalities. We subjected bank voles to partial nighttime illumination in a foraging landscape under laboratory conditions and in large grassland enclosures under near natural conditions. We measured giving-up density of food in illuminated and dark artificial seed patches and video recorded the movement of animals. While animals reduced number of visits to illuminated seed patches at night, they increased visits to these patches at the following day compared to dark seed patches. Overall, bold individuals had lower giving-up densities than shy individuals but this difference increased at day in formerly illuminated seed patches. Small mammals thus showed carry-over effects on daytime foraging behavior due to ALAN, i.e., nocturnal illumination has the potential to affect intra- and interspecific interactions during both night and day with possible changes in personality structure within populations and altered predator-prey dynamics.
Das Centrosom von Dictyostelium ist acentriolär aufgebaut, misst ca. 500 nm und besteht aus einer dreischichten Core-Struktur mit umgebender Corona, an der Mikrotubuli nukleieren. In dieser Arbeit wurden das centrosomale Protein Cep192 und mögliche Interaktionspartner am Centrosom eingehend untersucht. Die einleitende Lokalisationsuntersuchung von Cep192 ergab, dass es während der gesamten Mitose an den Spindelpolen lokalisiert und im Vergleich zu den anderen Strukturproteinen der Core-Struktur am stärksten exprimiert ist. Die dauerhafte Lokalisation an den Spindelpolen während der Mitose wird für Proteine angenommen, die in den beiden identisch aufgebauten äußeren Core-Schichten lokalisieren, die das mitotische Centrosom formen. Ein Knockdown von Cep192 führte zur Ausbildung von überzähligen Mikrotubuli-organisierenden Zentren (MTOC) sowie zu einer leicht erhöhten Ploidie. Deshalb wird eine Destabilisierung des Centrosoms durch die verminderte Cep192-Expression angenommen. An Cep192 wurden zwei kleine Tags, der SpotH6- und BioH6-Tag, etabliert, die mit kleinen fluoreszierenden Nachweiskonjugaten markiert werden konnten. Mit den so getagten Proteinen konnte die hochauflösende Expansion Microscopy für das Centrosom optimiert werden und die Core-Struktur erstmals proteinspezifisch in der Fluoreszenzmikroskopie dargestellt werden. Cep192 lokalisiert dabei in den äußeren Core-Schichten. Die kombinierte Markierung von Cep192 und den centrosomalen Proteinen CP39 und CP91 in der Expansion Microscopy erlaubte die Darstellung des dreischichtigen Aufbaus der centrosomalen Core-Struktur, wobei CP39 und CP91 zwischen Cep192 in der inneren Core-Schicht lokalisieren. Auch die Corona wurde in der Expansion Microscopy untersucht: Das Corona-Protein CDK5RAP2 lokalisiert in räumlicher Nähe zu Cep192 in der inneren Corona. Ein Vergleich der Corona-Proteine CDK5RAP2, CP148 und CP224 in der Expansion Microscopy ergab unterscheidbare Sublokalisationen der Proteine innerhalb der Corona und relativ zur Core-Struktur. In Biotinylierungsassays mit den centrosomalen Core-Proteinen CP39 und CP91 sowie des Corona-Proteins CDK5RAP2 konnte Cep192 als möglicher Interaktionspartner identifiziert werden.
Die Ergebnisse dieser Arbeit zeigen die wichtige Funktion des Proteins Cep192 im Dictyostelium-Centrosom und ermöglichen durch die Kombination aus Biotinylierungsassays und Expansion Microscopy der untersuchten Proteine ein verbessertes Verständnis der Topologie des Centrosoms.
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
The increasing introduction of non-native plant species may pose a threat to local biodiversity. However, the basis of successful plant invasion is not conclusively understood, especially since these plant species can adapt to the new range within a short period of time despite impoverished genetic diversity of the starting populations. In this context, DNA methylation is considered promising to explain successful adaptation mechanisms in the new habitat. DNA methylation is a heritable variation in gene expression without changing the underlying genetic information. Thus, DNA methylation is considered a so-called epigenetic mechanism, but has been studied in mainly clonally reproducing plant species or genetic model plants. An understanding of this epigenetic mechanism in the context of non-native, predominantly sexually reproducing plant species might help to expand knowledge in biodiversity research on the interaction between plants and their habitats and, based on this, may enable more precise measures in conservation biology.
For my studies, I combined chemical DNA demethylation of field-collected seed material from predominantly sexually reproducing species and rearing offsping under common climatic conditions to examine DNA methylation in an ecological-evolutionary context. The contrast of chemically treated (demethylated) plants, whose variation in DNA methylation was artificially reduced, and untreated control plants of the same species allowed me to study the impact of this mechanism on adaptive trait differentiation and local adaptation. With this experimental background, I conducted three studies examining the effect of DNA methylation in non-native species along a climatic gradient and also between climatically divergent regions.
The first study focused on adaptive trait differentiation in two invasive perennial goldenrod species, Solidago canadensis sensu latu and S. gigantea AITON, along a climate gradient of more than 1000 km in length in Central Europe. I found population differences in flowering timing, plant height, and biomass in the temporally longer-established S. canadensis, but only in the number of regrowing shoots for S. gigantea. While S. canadensis did not show any population structure, I was able to identify three genetic groups along this climatic gradient in S. gigantea. Surprisingly, demethylated plants of both species showed no change in the majority of traits studied. In the subsequent second study, I focused on the longer-established goldenrod species S. canadensis and used molecular analyses to infer spatial epigenetic and genetic population differences in the same specimens from the previous study. I found weak genetic but no epigenetic spatial variation between populations. Additionally, I was able to identify one genetic marker and one epigenetic marker putatively susceptible to selection. However, the results of this study reconfirmed that the epigenetic mechanism of DNA methylation appears to be hardly involved in adaptive processes within the new range in S. canadensis.
Finally, I conducted a third study in which I reciprocally transplanted short-lived plant species between two climatically divergent regions in Germany to investigate local adaptation at the plant family level. For this purpose, I used four plant families (Amaranthaceae, Asteraceae, Plantaginaceae, Solanaceae) and here I additionally compared between non-native and native plant species. Seeds were transplanted to regions with a distance of more than 600 kilometers and had either a temperate-oceanic or a temperate-continental climate. In this study, some species were found to be maladapted to their own local conditions, both in non-native and native plant species alike. In demethylated individuals of the plant species studied, DNA methylation had inconsistent but species-specific effects on survival and biomass production. The results of this study highlight that DNA methylation did not make a substantial contribution to local adaptation in the non-native as well as native species studied.
In summary, my work showed that DNA methylation plays a negligible role in both adaptive trait variation along climatic gradients and local adaptation in non-native plant species that either exhibit a high degree of genetic variation or rely mainly on sexual reproduction with low clonal propagation. I was able to show that the adaptive success of these non-native plant species can hardly be explained by DNA methylation, but could be a possible consequence of multiple introductions, dispersal corridors and meta-population dynamics. Similarly, my results illustrate that the use of plant species that do not predominantly reproduce clonally and are not model plants is essential to characterize the effect size of epigenetic mechanisms in an ecological-evolutionary context.
Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
The role of the GMP nucleotides of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor of the DMSO reductase family has long been a subject of discussion. The recent characterization of the bis-molybdopterin (bis-Mo-MPT) cofactor present in the E. coli YdhV protein, which differs from bis-MGD solely by the absence of the nucleotides, now enables studying the role of the nucleotides of bis-MGD and bis-MPT cofactors in Moco insertion and the activity of molybdoenzymes in direct comparison. Using the well-known E. coli TMAO reductase TorA as a model enzyme for cofactor insertion, we were able to show that the GMP nucleotides of bis-MGD are crucial for the insertion of the bis-MGD cofactor into apo-TorA.
Phenotypic plasticity can increase individual fitness when environmental conditions change over time. Inducible defences are a striking example, allowing species to react to fluctuating predation pressure by only expressing their costly defended phenotype under high predation risk. Previous theoretical investigations have focused on how this affects predator–prey dynamics, but the impact on competitive outcomes and broader community dynamics has received less attention. Here we use a small food web model, consisting of two competing plastic autotrophic species exploited by a shared consumer, to study how the speed of inducible defences across three trade-off constellations affects autotroph coexistence, biomasses across trophic levels, and temporal variability. Contrary to the intuitive idea that faster adaptation increases autotroph fitness, we found that higher switching rates reduced individual fitness as it consistently provoked more maladaptive switching towards undefended phenotypes under high predation pressure. This had an unexpected positive impact on the consumer, increasing consumer biomass and lowering total autotroph biomass. Additionally, maladaptive switching strongly reduced autotroph coexistence through an emerging source-sink dynamic between defended and undefended phenotypes. The striking impact of maladaptive switching on species and food web dynamics indicates that this mechanism may be of more critical importance than previously recognized.
In this thesis, a collection of studies is presented that advance research on complex food webs in several directions. Food webs, as the networks of predator-prey interactions in ecosystems, are responsible for distributing the resources every organism needs to stay alive. They are thus central to our understanding of the mechanisms that support biodiversity, which in the face of increasing severity of anthropogenic global change and accelerated species loss is of highest importance, not least for our own well-being.
The studies in the first part of the thesis are concerned with general mechanisms that determine the structure and stability of food webs. It is shown how the allometric scaling of metabolic rates with the species' body masses supports their persistence in size-structured food webs (where predators are larger than their prey), and how this interacts with the adaptive adjustment of foraging efforts by consumer species to create stable food webs with a large number of coexisting species. The importance of the master trait body mass for structuring communities is further exemplified by demonstrating that the specific way the body masses of species engaging in empirically documented predator-prey interactions affect the predator's feeding rate dampens population oscillations, thereby helping both species to survive. In the first part of the thesis it is also shown that in order to understand certain phenomena of population dynamics, it may be necessary to not only take the interactions of a focal species with other species into account, but to also consider the internal structure of the population. This can refer for example to different abundances of age cohorts or developmental stages, or the way individuals of different age or stage interact with other species.
Building on these general insights, the second part of the thesis is devoted to exploring the consequences of anthropogenic global change on the persistence of species. It is first shown that warming decreases diversity in size-structured food webs. This is due to starvation of large predators on higher trophic levels, which suffer from a mismatch between their respiration and ingestion rates when temperature increases. In host-parasitoid networks, which are not size-structured, warming does not have these negative effects, but eutrophication destabilises the systems by inducing detrimental population oscillations. In further studies, the effect of habitat change is addressed. On the level of individual patches, increasing isolation of habitat patches has a similar effect as warming, as it leads to decreasing diversity due to the extinction of predators on higher trophic levels. In this case it is caused by dispersal mortality of smaller and therefore less mobile species on lower trophic levels, meaning that an increasing fraction of their biomass production is lost to the inhospitable matrix surrounding the habitat patches as they become more isolated. It is further shown that increasing habitat isolation desynchronises population oscillations between the patches, which in itself helps species to persist by dampening fluctuations on the landscape level. However, this is counteracted by an increasing strength of local population oscillations fuelled by an indirect effect of dispersal mortality on the feeding interactions. Last, a study is presented that introduces a novel mechanism for supporting diversity in metacommunities. It builds on the self-organised formation of spatial biomass patterns in the landscape, which leads to the emergence of spatio-temporally varying selection pressures that keep local communities permanently out of equilibrium and force them to continuously adapt. Because this mechanism relies on the spatial extension of the metacommunity, it is also sensitive to habitat change.
In the third part of the thesis, the consequences of biodiversity for the functioning of ecosystems are explored. The studies focus on standing stock biomass, biomass production, and trophic transfer efficiency as ecosystem functions. It is first shown that increasing the diversity of animal communities increases the total rate of intra-guild predation. However, the total biomass stock of the animal communities increases nevertheless, which also increases their exploitative pressure on the underlying plant communities. Despite this, the plant communities can maintain their standing stock biomass due to a shift of the body size spectra of both animal and plant communities towards larger species with a lower specific respiration rate. In another study it is further demonstrated that the generally positive relationship between diversity and the above mentioned ecosystem functions becomes steeper when not only the feeding interactions but also the numerous non-trophic interactions (like predator interference or competition for space) between the species of an ecosystem are taken into account. Finally, two studies are presented that demonstrate the power of functional diversity as explanatory variable. It is interpreted as the range spanned by functional traits of the species that determine their interactions. This approach allows to mechanistically understand how the ecosystem functioning of food webs with multiple trophic levels is affected by all parts of the food web and why a high functional diversity is required for efficient transportation of energy from primary producers to the top predators.
The general discussion draws some synthesising conclusions, e.g. on the predictive power of ecosystem functioning to explain diversity, and provides an outlook on future research directions.
Large quantities of the antibiotic florfenicol are used in animal farming and aquaculture, contaminating the ecosystem with antibiotic residues and promoting antimicrobial resistance, ultimately leading to untreatable multidrug-resistant pathogens. Florfenicol-resistant bacteria often activate export mechanisms that result in resistance to various structurally unrelated antibiotics. We devised novel strategies for the enzymatic inactivation of florfenicol in different media, such as saltwater or milk. Using a combinatorial approach and selection, we optimized a hydrolase (EstDL136) for florfenicol cleavage. Reaction kinetics were followed by time-resolved NMR spectroscopy. Importantly, the hydrolase remained active in different media, such as saltwater or cow milk. Various environmentally-friendly application strategies for florfenicol inactivation were developed using the optimized hydrolase. As a potential filter device for cost-effective treatment of waste milk or aquacultural wastewater, the hydrolase was immobilized on Ni-NTA agarose or silica as carrier materials. In two further application examples, the hydrolase was used as cell extract or encapsulated with a semi-permeable membrane. This facilitated, for example, florfenicol inactivation in whole milk, which can help to treat waste milk from medicated cows, to be fed to calves without the risk of inducing antibiotic resistance. Enzymatic inactivation of antibiotics, in general, enables therapeutic intervention without promoting antibiotic resistance.
Stimuli-promoted in situ formation of hydrogels with thiol/thioester containing peptide precursors
(2022)
Hydrogels are potential synthetic ECM-like substitutes since they provide functional and structural similarities compared to soft tissues. They can be prepared by crosslinking of macromolecules or by polymerizing suitable precursors. The crosslinks are not necessarily covalent bonds, but could also be formed by physical interactions such as π-π interactions, hydrophobic interactions, or H-bonding. On demand in situ forming hydrogels have garnered increased interest especially for biomedical applications over preformed gels due to the relative ease of in vivo delivery and filling of cavities. The thiol-Michael addition reaction provides a straightforward and robust strategy for in situ gel formation with its fast reaction kinetics and ability to proceed under physiological conditions. The incorporation of a trigger function into a crosslinking system becomes even more interesting since gelling can be controlled with stimulus of choice. The use of small molar mass crosslinker precursors with active groups orthogonal to thiol-Michael reaction type electrophile provides the opportunity to implement an on-demand in situ crosslinking without compromising the fast reaction kinetics.
It was postulated that short peptide sequences due to the broad range structural-function relations available with the different constituent amino acids, can be exploited for the realisation of stimuli-promoted in situ covalent crosslinking and gelation applications. The advantages of this system over conventional polymer-polymer hydrogel systems are the ability tune and predict material property at the molecular level.
The main aim of this work was to develop a simplified and biologically-friendly stimuli-promoted in situ crosslinking and hydrogelation system using peptide mimetics as latent crosslinkers. The approach aims at using a single thiodepsipeptide sequence to achieve separate pH- and enzyme-promoted gelation systems with little modification to the thiodepsipeptide sequence. The realization of this aim required the completion of three milestones.
In the first place, after deciding on the thiol-Michael reaction as an effective in situ crosslinking strategy, a thiodepsipeptide, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH (TDP) with expected propensity towards pH-dependent thiol-thioester exchange (TTE) activation, was proposed as a suitable crosslinker precursor for pH-promoted gelation system. Prior to the synthesis of the proposed peptide-mimetic, knowledge of the thiol-Michael reactivity of the would-be activated thiol moiety SH-Leu, which is internally embedded in the thiodepsipeptide was required. In line with pKa requirements for a successful TTE, the reactivity of a more acidic thiol, SH-Phe was also investigated to aid the selection of the best thiol to be incorporated in the thioester bearing peptide based crosslinker precursor. Using ‘pseudo’ 2D-NMR investigations, it was found that only reactions involving SH-Leu yielded the expected thiol-Michael product, an observation that was attributed to the steric hindrance of the bulkier nature of SH-Phe. The fast reaction rates and complete acrylate/maleimide conversion obtained with SH-Leu at pH 7.2 and higher aided the direct elimination of SH-Phe as a potential thiol for the synthesis of the peptide mimetic.
Based on the initial studies, for the pH-promoted gelation system, the proposed Ac-Pro-Leu-Gly-SLeu-Leu-Gly-NEtSH was kept unmodified. The subtle difference in pKa values between SH-Leu (thioester thiol) and the terminal cysteamine thiol from theoretical conditions should be enough to effect a ‘pseudo’ intramolecular TTE. In polar protic solvents and under basic aqueous conditions, TDP successfully undergoes a ‘pseudo’ intramolecular TTE reaction to yield an α,ω-dithiol tripeptide, HSLeu-Leu-Gly-NEtSH. The pH dependence of thiolate ion generation by the cysteamine thiol aided the incorporation of the needed stimulus (pH) for the overall success of TTE (activation step) – thiol-Michael addition (crosslinking) strategy.
Secondly, with potential biomedical applications in focus, the susceptibility of TDP, like other thioesters, to intermolecular TTE reaction was probed with a group of thiols of varying thiol pKa values, since biological milieu characteristically contain peptide/protein thiols. L-cysteine, which is a biologically relevant thiol, and a small molecular weight thiol, methylthioglycolate both with relatively similar thiol pKa, values, led to an increase concentration of the dithiol crosslinker when reacted with TDP. In the presence of acidic thiols (p-NTP and 4MBA), a decrease in the dithiol concentration was observed, an observation that can be attributed to the inability of the TTE tetrahedral intermediate to dissociate into exchange products and is in line with pKa requirements for successful TTE reaction. These results additionally makes TDP more attractive and the potentially the first crosslinker precursor for applications in biologically relevant media.
Finally, the ability of TDP to promote pH-sensitive in situ gel formation was probed with maleimide functionalized 4-arm polyethylene glycol polymers in tris-buffered media of varying pHs. When a 1:1 thiol: maleimide molar ratio was used, TDP-PEG4MAL hydrogels formed within 3, 12 and 24 hours at pH values of 8.5, 8.0 and 7.5 respectively. However, gelation times of 3, 5 and 30 mins were observed for the same pH trend when the thiol: maleimide molar was increased to 2:1.
A direct correlation of thiol content with G’ of the gels at each pH could also be drawn by comparing gels with thiol: maleimide ratios of 1:1 to those with 2:1 thiol: maleimide mole ratios. This is supported by the fact that the storage modulus (G') is linearly dependent on the crosslinking density of the polymer. The values of initial G′ for all gels ranged between (200 – 5000 Pa), which falls in the range of elasticities of certain tissue microenvironments for example brain tissue 200 – 1000 Pa and adipose tissue (2500 – 3500 Pa).
Knowledge so far gained from the study on the ability to design and tune the exchange reaction of thioester containing peptide mimetic will give those working in the field further insight into the development of new sequences tailored towards specific applications.
TTE substrate design using peptide mimetic as presented in this work has revealed interesting new insights considering the state-of-the-art. Using the results obtained as reference, the strategy provides a possibility to extend the concept to the controlled delivery of active molecules needed for other robust and high yielding crosslinking reactions for biomedical applications. Application for this sequentially coupled functional system could be seen e.g. in the treatment of inflamed tissues associated with urinary tract like bladder infections for which pH levels above 7 were reported. By the inclusion of cell adhesion peptide motifs, the hydrogel network formed at this pH could act as a new support layer for the healing of damage epithelium as shown in interfacial gel formation experiments using TDP and PEG4MAL droplets.
The versatility of the thiodepsipeptide sequence, Ac-Pro-Leu-Gly-SLeu-Leu-Gly-(TDPo) was extended for the design and synthesis of a MMP-sensitive 4-arm PEG-TDPo conjugate. The purported cleavage of TDPo at the Gly-SLeu bond yields active thiol units for subsequent reaction of orthogonal Michael acceptor moieties. One of the advantages of stimuli-promoted in situ crosslinking systems using short peptides should be the ease of design of required peptide molecules due to the predictability of peptide functions their sequence structure. Consequently the functionalisation of a 4-arm PEG core with the collagenase active TDPo sequence yielded an MMP-sensitive 4-arm thiodepsipeptide-PEG conjugate (PEG4TDPo) substrate.
Cleavage studies using thiol flourometric assay in the presence of MMPs -2 and -9 confirmed the susceptibility of PEG4TDPo towards these enzymes. The resulting time-dependent increase in fluorescence intensity in the presence of thiol assay signifies the successful cleavage of TDPo at the Gly-SLeu bond as expected. It was observed that the cleavage studies with thiol flourometric assay introduces a sigmoid non-Michaelis-Menten type kinetic profile, hence making it difficult to accurately determine the enzyme cycling parameters, kcat and KM .
Gelation studies with PEG4MAL at 10 % wt. concentrations revealed faster gelation with MMP-2 than MMP-9 with 28 and 40 min gelation times respectively. Possible contributions by hydrolytic cleavage of PEG4TDPo has resulted in the gelation of PEG4MAL blank samples but only after 60 minutes of reaction. From theoretical considerations, the simultaneous gelation reaction would be expected to more negatively impact the enzymatic than hydrolytic cleavage. The exact contributions from hydrolytic cleavage of PEG4TDPo would however require additional studies.
In summary this new and simplified in situ crosslinking system using peptide-based crosslinker precursors with tuneable properties exhibited in situ crosslinking gelation kinetics on similar levels with already active dithiols reported. The advantageous on-demand functionality associated with its pH-sensitivity and physiological compatibility makes it a strong candidate worth further research as biomedical applications in general and on-demand material synthesis is concerned.
Results from MMP-promoted gelation system unveils a simple but unexplored approach for in situ synthesis of covalently crosslinked soft materials, that could lead to the development of an alternative pathway in addressing cancer metastasis by making use of MMP overexpression as a trigger. This goal has so far not being reach with MMP inhibitors despite the extensive work this regard.