Institutes
Refine
Year of publication
Document Type
- Article (320)
- Doctoral Thesis (179)
- Preprint (41)
Language
- English (540) (remove)
Has Fulltext
- yes (540)
Is part of the Bibliography
- no (540)
Keywords
- Podospora anserina (8)
- aging (8)
- SARS-CoV-2 (7)
- Cyanobacteria (5)
- Ecology (5)
- Membrane Proteins (5)
- Phylogeny (5)
- mitochondria (5)
- Acetogenesis (4)
- Biodiversity (4)
- Haloferax volcanii (4)
- Saccharomyces cerevisiae (4)
- Synechococcus (4)
- alternative splicing (4)
- bats (4)
- fungi (4)
- Acetogen (3)
- Bioenergetics (3)
- Biogeography (3)
- Biomarker (3)
- COVID19-NMR (3)
- Carotenoids (3)
- Evolution (3)
- Lipid and Fatty Acid Composition (3)
- Marine Diatoms (3)
- Membrane Transport (3)
- Microbiology (3)
- Oxidoreductases (3)
- Photooxidation (3)
- Pigmentation (3)
- Protein Structure (3)
- RNA (3)
- Solution NMR spectroscopy (3)
- Taxonomy (3)
- Thermophile (3)
- Transcriptomics (3)
- biodiversity (3)
- climate change (3)
- sleep (3)
- structural biology (3)
- zebrafish (3)
- 14CO2 Fixation (2)
- 5′-UTR (2)
- Acetogenic bacteria (2)
- Acinetobacter (2)
- Adhesion (2)
- Aloe (2)
- Amino Acid Pools (2)
- Archaea (2)
- Asphodelaceae (2)
- Bioaccumulation (2)
- Biomarkers (2)
- Biosynthesis (2)
- Bleaching Herbicides (2)
- Climate change (2)
- Community ecology (2)
- Conservation biology (2)
- Covid19-NMR (2)
- Crustacea (2)
- DNA Transformation (2)
- DNA uptake (2)
- Desiccation resistance (2)
- Dicarboxylic acids (2)
- Downy mildew (2)
- Ecological modelling (2)
- Ecotoxicogenomics (2)
- Electron Bifurcation (2)
- Electron Transfer (2)
- Electron Transport (2)
- Energy Conservation (2)
- Energy Metabolism (2)
- Energy conservation (2)
- Entomology (2)
- Enzyme Mechanisms (2)
- European beech (2)
- Host-parasite interaction (2)
- Iron-Sulfur Protein (2)
- Land cover (2)
- Light-sheet microscopy (2)
- MICOS (2)
- Magnetic compass (2)
- Maxent (2)
- Membrane Biogenesis (2)
- Metabolic Engineering (2)
- Metabolic engineering (2)
- Metabolism (2)
- Metalloenzymes (2)
- Methylorubrum extorquens (2)
- Methylorubrum extorquens AM1 (2)
- Microplastic (2)
- Mitochondria (2)
- Modification (2)
- Morphogenesis (2)
- Morphology (2)
- NMR (2)
- NMR spectroscopy (2)
- Non-invasive sampling (2)
- Oaks (2)
- Oomycetes (2)
- Oxidative stress (2)
- Peronosporaceae (2)
- Photosynthesis (2)
- Phycocyanin-Free Lamellae (2)
- Protein Translocation (2)
- Psychology (2)
- Risk assessment (2)
- Solution NMR-spectroscopy (2)
- Species distribution modelling (2)
- Synaptic transmission (2)
- Synchron Cultures (2)
- Thermus (2)
- Trypanosoma cruzi (2)
- UV-B Stress (2)
- Wood-Ljungdahl pathway (2)
- Wood–Ljungdahl pathway (2)
- Xenorhabdus (2)
- Zebrafish (2)
- angiogenesis (2)
- aroma (2)
- autophagy (2)
- bacteria (2)
- biodiversity protection (2)
- biosynthesis (2)
- carotenoid biosynthesis (2)
- climate (2)
- color (2)
- community composition (2)
- conservation (2)
- conservation funding (2)
- conservation genetics (2)
- conservation planning (2)
- cox2 (2)
- cristae (2)
- cryptochrome (2)
- decision making (2)
- development (2)
- environmental attitudes (2)
- environmental education (2)
- extremophile (2)
- gene expression (2)
- genomics (2)
- global change (2)
- heat stress (2)
- inclination compass (2)
- integrins (2)
- long non-coding RNA (2)
- metabarcoding (2)
- microglia (2)
- migration (2)
- morphology (2)
- nuclear magnetic resonance (NMR) (2)
- one new species (2)
- oomycetes (2)
- peroxisomes (2)
- phylogeny (2)
- population genetics (2)
- population genomics (2)
- post-2020 biodiversity targets (2)
- pre-mRNA (2)
- predation (2)
- prefrontal cortex (2)
- prostate carcinoma cells (2)
- strategic site selection (2)
- structure–activity relationships (2)
- tumor microenvironment (2)
- 14C- and 15N-Assimilation (1)
- 15N-Labelled Amino Acids (1)
- 16S rRNA gene (1)
- 18S rRNA gene (1)
- 2030 Agenda (1)
- 3-Hydroxybutyric acid (1)
- 5'-UTR (1)
- 5-Hydroxyaloin A (1)
- 5_SL4 (1)
- ABR (1)
- AChE (1)
- ADAM15 (1)
- ADCD (1)
- ALE (1)
- AMPK (1)
- ATG24 (1)
- ATP (1)
- Absorption Spectra (1)
- Acetobacterium (1)
- Acetogenic metabolism (1)
- Acid transporters (1)
- Active Particles (1)
- Adenosine (1)
- Aedes (1)
- Agent-based modeling (1)
- Aging (1)
- Aging Phenomenon (1)
- Aichi targets (1)
- Air Pollutants (1)
- Alien species (1)
- Allohormone pheromones (1)
- Alphaproteobacteria (1)
- Amino Acids (1)
- Amphibia (1)
- Amplexus (1)
- Anabaena flos-aquae (1)
- Anacystis (1)
- Anaerobes (1)
- Anaerobic bacteria (1)
- Androst-4-en-3,17-dione (1)
- Anion Transport System (1)
- Anthraquinones (1)
- Anthropocene (1)
- Antibiotic Resistance (1)
- Antibiotics and Metabolite Export (1)
- Antioxidants (1)
- Aphanomyces astaci (1)
- Apoptosis (1)
- Aposematism (1)
- Aquilegia (1)
- Arabidopsis thaliana (1)
- Arctic Ocean (1)
- Ascomycota (1)
- Assignment (1)
- Assimilation of 15N-Nitrate (1)
- Asymmetrie Reconstitution (1)
- Auditory midbrain (1)
- Autism Spectrum Disorder (1)
- Autism Spectrum disorder (1)
- Automobile Exhaust (1)
- B chromosome (1)
- Bacillariaphyceae (1)
- Bacillus (1)
- Background expression (1)
- Bacteria (1)
- Bacterial Metabolism (1)
- Bacterial genes (1)
- Bacterial physiology (1)
- Bacterial structural biology (1)
- Bacteriology (1)
- Baleen whales (1)
- Band 3 Protein (1)
- Bartonella henselae (1)
- Basidiomycota (1)
- Behaviour (1)
- Benin (1)
- Benthic environment (1)
- Benthos (1)
- Biochemistry (1)
- Biodiversity tools and pipelines (1)
- Bioenergetics/Electron Transfer Complex (1)
- Bioengineering (1)
- Biofuels (1)
- Biohydrogen (1)
- Biological anthropology (1)
- Bioreactor (1)
- Biosecurity (1)
- Biotechnology (1)
- Biotic interactions (1)
- Biotransformation (1)
- Body burden (1)
- Bogert’s rule (1)
- Bolivia (1)
- Bovidae (1)
- Brain-stimulus synchrony (1)
- Breeding glands (1)
- Brudenell River (1)
- Bungarus (1)
- Bungarus niger (1)
- Bungarus walli (1)
- Business strategy in drug development (1)
- Butyrate (1)
- CAZy (1)
- CLIP (1)
- CLP protease (1)
- CNV 16p11.2 (1)
- COVID-19 (1)
- CRISPR-Cas9 (1)
- CRISPR-Cas9 gene conversion (1)
- CXCL12 (1)
- CXCR4 (1)
- CaMPARI (1)
- Caffeate Respiration (1)
- Calathea (1)
- Calmodulin (1)
- Canada (1)
- Canis lupus (1)
- Canis lupus familiaris (1)
- Carbohydrates (1)
- Carbon capture (1)
- Carbon cycling (1)
- Cardiac regeneration (1)
- Cardiac remodeling (1)
- Carnivora (1)
- Carnivores (1)
- Carotene Isomerase (1)
- Carotenoid Desaturation (1)
- Castor bean tick (1)
- Catalase (1)
- Cation Proton Antiporter (1)
- Cell Wall (1)
- Cellular microbiology (1)
- Cellulase gene expression (1)
- Cercospora (1)
- Chagas disease (1)
- Chaperone Chaperonin (1)
- Chaperones (1)
- Chemical communication (1)
- Chemical dispersant (1)
- Chemical dispersants (1)
- Chemistry (1)
- Chemotaxonomy (1)
- Chironomus riparius (1)
- Chlorophyll (1)
- Chlorophyll Fluorescence (1)
- Chlorophyll Formation (1)
- Chlorophyll fluorescence (1)
- Chloroplast (1)
- Chlorosis (1)
- Chromatin (1)
- Chromones (1)
- Chrysops (1)
- Climate (1)
- Climate Change (1)
- Climate-change ecology (1)
- Climatic conditions (1)
- Closely related fungal species (1)
- ClpB (1)
- Coevolution (1)
- Colorectal Cancer (1)
- Community barcoding (1)
- Computational model (1)
- Conservation (1)
- Coronaries (1)
- Cortex (1)
- Cortical column (1)
- Costs (1)
- Crude oil (1)
- Crystal Structure (1)
- Cucumis sativus (Cucumber) (1)
- Cumate (1)
- D. magna (1)
- DCMU-Type Inhibitors (1)
- DCMU-Type Inhibitors Shade Adaptation (1)
- DEPDC5 (1)
- DIRAS2 (1)
- DNA Amplification Fingerprinting (1)
- DNA metabarcoding (1)
- DNA-Specific Labelling (1)
- Daboia russelii (1)
- Dark fermentation (1)
- Data standard (1)
- Data standards (1)
- Deep sea (1)
- Dehydration (medicine) (1)
- Dental Tissues (1)
- Depth (1)
- Development (1)
- Diatomophthora (1)
- Dicellomyces (1)
- Dimer Yield Ratio (1)
- Dimerization domain (1)
- Dioscorea (1)
- Diosgenin Production (1)
- Direct seeding (1)
- Discovery (1)
- Diseases (1)
- Dispersal capacity (1)
- Dissemination (1)
- Diversity (1)
- Drought (1)
- Drought reaction (1)
- Drug discovery (1)
- Drug therapy (1)
- Dynamics (1)
- E-NTPDase (1)
- ER (1)
- ERAL1 (1)
- EROD (1)
- Earth sciences (1)
- Earthworms (1)
- EcNhaA (1)
- Ech (1)
- Ecological niche modelling (1)
- Ecological requirements (1)
- Ecosystem Services (1)
- Ecotoxicology (1)
- Ecto-5'-nucleotidase (1)
- Ectrogella (1)
- Electron Microscopy (1)
- Electron transport chain (1)
- Electron-bifurcating hydrogenase (1)
- Electrophysiology (1)
- Elimination of Rho Factor (1)
- Embryo toxicity (1)
- Embryogenesis (1)
- Emerging insect model organisms (1)
- Endocrine disruptors (1)
- Endocrine-disrupting compounds (1)
- Endothelial (1)
- Endothelial-to-mesenchymal transition (1)
- Engineering (1)
- Entolomataceae (1)
- Entorrhizales (1)
- Envelope (1)
- Environmental factors (1)
- Environmental fate (1)
- Environmental partitioning (1)
- Environmental sciences (1)
- Environmental studies (1)
- Enzyme Induction (1)
- Enzyme Kinetics (1)
- Enzyme engineering (1)
- EphrinB2 (1)
- Equilibrium partitioning theory (1)
- Erythrocyte Membrane (1)
- Ethiopia (1)
- Ethylmalonyl-CoA (1)
- Eubacterium (1)
- Europe (1)
- European Beech (1)
- European Union (1)
- Evolutionary biology (1)
- Evolutionary developmental biology (1)
- Evolutionary genetics (1)
- Excretion (1)
- Extinction (1)
- Extracellular matrix (1)
- Extremophile (1)
- Extremophiles (1)
- F1Fo-ATP-synthase (1)
- FAD (1)
- FAD synthase (1)
- FAD1 (1)
- Fabaceae (1)
- Fabclavine (1)
- Fagaceae (1)
- Far UV (1)
- Felidae (1)
- Filamentous fungi (1)
- Flavoproteins (1)
- Fluorescence imaging (1)
- Folic Acid Antagonists (1)
- Foraminiferal (1)
- Freshwater (1)
- Freshwater Ecosystems (1)
- Freshwater invertebrate (1)
- Functional Ecology (1)
- Functional genomics (1)
- Functional traits (1)
- Fungal pan-genomes (1)
- G protein-coupled receptor (GPCR) (1)
- G3BP1 (1)
- GRAND-SLAM (1)
- Gal2 (1)
- Galakturonsäure (1)
- Gas Vacuoles (1)
- Gene sll0033 (1)
- Genetic variation (1)
- Genetic vectors (1)
- Genetics (1)
- Genome (1)
- Genome sequence (1)
- Genotoxicity (1)
- Genotyping and haplotyping (1)
- Geoffrey Burnstock (1)
- Geomagnetic field (1)
- Global warming (1)
- Glucose-6-phosphate- and 6-phosphogluconate dehydrogenase (1)
- Glycolate Oxidase (1)
- Glycophorin A dimerization (1)
- Graminicolous downy mildews (1)
- H+ transport (1)
- HARS2 (1)
- HCMV (1)
- HER (1)
- HWC database (1)
- Habitat transfer (1)
- Haematopota (1)
- Hazard assessment (1)
- Health care (1)
- Heart (1)
- Heat-Bleaching (of Plastids) (1)
- Hematophagous arthropods (1)
- Herbicide Resistance (1)
- Herbicide Resistant Mutants (1)
- Herbicide-Tolerant Mutants (1)
- Herbivores (1)
- Hi-C (1)
- High Performance Liquid (1)
- Hippocampal development (1)
- Hippocampus (1)
- History (1)
- Hominins (1)
- Host jump (1)
- Human impact (1)
- Hybridization (1)
- Hydrogen storage (1)
- Hydrogen-dependent CO2 reductase (1)
- Hydrogen-dependent CO2 reductase (HDCR) (1)
- Hydrogenase (1)
- Hypercolumn (1)
- Hypothermia (1)
- I50 Value (1)
- IDP (1)
- ITS (1)
- IUCN protection categories (1)
- In situ burning (1)
- In vivo electrophysiology (1)
- Inducible Promoter (1)
- Infectious diseases (1)
- Inferior colliculus (1)
- Influenza (1)
- Insularity (1)
- International survey (1)
- Intestinal bacterial community (1)
- Inthraszentin (1)
- InvaCost (1)
- Invasive species (1)
- Isoprenoids (1)
- Isozyme Pattern (1)
- Ixodes ricinus (1)
- Kinetics of Dimer Formation (1)
- Klebsiella (1)
- Kordyana (1)
- LARS2 (1)
- LASSO algorithm (1)
- LanI Protein (1)
- Lantibiotic (1)
- Lantibiotic Immunity (1)
- Larmor frequency (1)
- Larva (1)
- Latent Injury (1)
- Laurasiatheria (1)
- Leaf Peroxisomes (1)
- Leguminosae (1)
- Life-Satisfaction (1)
- Life-history (1)
- Lifespan (1)
- Light dark transition test (1)
- Light sheet-based fluorescence microscopy (1)
- Limnology (1)
- Limonene-3-hydroxylase (1)
- Lineage Through Time (1)
- Lipoprotein (1)
- Long-term potentiation (1)
- MARTINI force field (1)
- MEK inhibition (1)
- MMN (1)
- Macrobenthosda (1)
- Macroevolution (1)
- Macrotermes (1)
- Macrozoobenthos (1)
- Magnetic conditioning (1)
- Magnetic map (1)
- Marantaceae (1)
- Marine biodiversity (1)
- Marine ecosystem (1)
- Marine invertebrates (1)
- Mass spectrometry (1)
- Maternal Immune Activation (1)
- Mawson Bank (1)
- Mechanisms of disease (1)
- Mediterranean plants (1)
- Meliolales (1)
- Membrane Energetics (1)
- Membrane Enzymes (1)
- Membrane Protein Complex (1)
- MetVF (1)
- Metabolomics (1)
- Metagenomic shotgun sequencing (1)
- Metamorphosis (1)
- Methylene-THF reductase (1)
- Methylene-tetrahydrofolate reductase (1)
- Methylotroph (1)
- Methyltransferase (1)
- Mevalonic Acid (1)
- Microbiota (1)
- Microbotryales (1)
- Microenvironment (1)
- Microplastics (1)
- Microscopy (1)
- Mikroplastik (1)
- Mineralization (1)
- Mitochondrial Transport (1)
- Mitochondrial proteases (1)
- MjNhaP1 (1)
- Model (1)
- Molecular biology (1)
- Monoterpenoid (1)
- Monoterpenoid tolerance (1)
- Montane forest (1)
- Mount Kilimanjaro (1)
- Museum samples (1)
- Mutual information (1)
- Myocardial infarction (1)
- Myotis bechsteinii (1)
- NMR solution structure (1)
- NW Pacific (1)
- Na Gradient (1)
- Na+ transport (1)
- Naja (1)
- Nanoplastic (1)
- Natural Products (1)
- Natural products (1)
- Natural sounds (1)
- Nature Contributions to People (1)
- Nature Interest Scale (NIS) (1)
- Nature Valuation (1)
- Nature conservation (1)
- Nature's Contributions to People (1)
- Naturstoffe (1)
- Neocaridina palmata (1)
- Neotropic (1)
- Neural circuits (1)
- Neural map (1)
- Neurodevelopmental Psychiatric Disorders (1)
- Neuroligins (1)
- Neuronal Differentiation (1)
- Neurotoxicity (1)
- New host (1)
- New species (1)
- Niche (1)
- Nitrogen Metabolism (1)
- Noctuidae (1)
- Non-canonical terpenes (1)
- Non-ribosomal peptide synthetases (1)
- Non-structural protein (1)
- Norflurazon (1)
- Normative dimension (1)
- Nothopassalora (1)
- Nuclear Magnetic Resonance (1)
- Nucleic acid-binding domain (1)
- Nucleocapsid (1)
- Nucleus reuniens (1)
- Nyctalus leisleri (1)
- O-CAS assay (1)
- OXPHOS (1)
- Obituary (1)
- Oil spills (1)
- Olfactory Receptors (1)
- Olpidiopsis (1)
- Omp85-independent OMP Insertion (1)
- Optimal wiring (1)
- Optimization (1)
- Organic micropollutants (1)
- Organoids (1)
- Organophosphates (1)
- Orientation preference (1)
- Oxidation-Reduction (1)
- Oxidative Stress (1)
- Oxygen (1)
- Oxygen Evolution (1)
- Ozone (1)
- P 700 (1)
- P. anserina (1)
- P. maximowiczii Henry x P. nigra L. cv. Rochester (1)
- POTRA Domains (1)
- PURA (1)
- PaCRD1 (1)
- PaIAP (1)
- Panama (1)
- Panolis flammea (1)
- Parkinson (1)
- Parkinson’s disease (1)
- Particle toxicity (1)
- Passalora (1)
- Pathogenesis (1)
- Pathways (1)
- Pelagic (1)
- Peptide natural products (1)
- Pesticides (1)
- Pheromone Inhibitor (1)
- Pheromones (1)
- Phosphohydrolases (1)
- Photoinactivation (1)
- Photorhabdus (1)
- Photosynthetic CO2 Fixation (1)
- Photosynthetic Reaction Center (1)
- Photosystem II (1)
- Phvtoene Desaturase (1)
- Phvtofluene (1)
- Phylogenetics (1)
- Physical chemistry (1)
- Physiology (1)
- Phytoene (1)
- Pigment Composition (1)
- Pigment and Protein Content (1)
- Pink1 (1)
- Pinnotheres (1)
- Pinwheel (1)
- Planetary boundaries (1)
- Plant regeneration (1)
- Plant regeneration; community assembly; diversity (1)
- Plant sciences (1)
- Plant stress (1)
- Plastic pollution (1)
- Plastic response (1)
- Plasticity (1)
- Plastics (1)
- Plastid rRNA (1)
- Podocarpus National Park (1)
- Polyhedral Bodies (1)
- Polyketides (1)
- Polymer (1)
- Polypeptides (1)
- Population density (1)
- Population dynamics (1)
- Populus nigra L. cv. Loenen (1)
- Porin (1)
- Potato Tuber Slices (1)
- Potato Tuber Tissue (1)
- Prediction (1)
- Premature Leaf Drop (1)
- Prenyl pyrophosphates (1)
- Product reuptake (1)
- Protein Assembly (1)
- Protein Complexes (1)
- Protein DNA-Interaction (1)
- Protein Purification (1)
- Protein Shape (1)
- Protein Sorting (1)
- Protein drugability (1)
- Protein druggability (1)
- Proteomics (1)
- Pseudocercospora (1)
- Pseudomonas (1)
- Pseudomonas putida (1)
- Pure Cultures of Marine Diatoms (1)
- Purkinje cell (1)
- Pyrophosphatase (1)
- QuEChERS (1)
- Quality of life (1)
- Quantum Requirement (1)
- Quarantine (1)
- Quercus (1)
- Quercus frainetto (1)
- Quercus frainetto Ten. (Ungarische Eiche) (1)
- Quercus ilex L. (Steineiche) (1)
- Quercus pubescens (1)
- Quercus pubescens Willd. (Flaumeiche) (1)
- Quercus robur L. (Stieleiche) (1)
- Quercus rubra L. (Roteiche) (1)
- Quinolinate Phosphoribosyltransferase (1)
- Quinones (1)
- Qв Binding Protein (1)
- R-INLA (1)
- RBFOX1 (1)
- REM sleep (1)
- RMP1 (1)
- RNA Polymerase (1)
- RNA genome (1)
- RNA polymerase (1)
- RNA sequencing (1)
- RNA stability (1)
- RNA turnover (1)
- RNA-binding proteins (1)
- Radical Pair model (1)
- Radiotherapy (1)
- Range expansion (1)
- Recolonization (1)
- Regeneration (1)
- Regulation of D1 Protein (1)
- Reintroduction (1)
- Rep gene (1)
- Reproduction (1)
- Resilience (1)
- Respiration (1)
- Respiratory chain (1)
- Rheumatoid Arthritis (1)
- Rhodnius prolixus (1)
- Ribosomally synthesized and post-translationally modified peptides (1)
- Ribosomen, rRNA Prozessierung, snoRNA, Ribosomenbiogenesefaktoren (1)
- Rnf (1)
- Robert Koch Institute (1)
- Ross Sea (1)
- Russell´s Viper (1)
- S-azidoacyl-N-acetylcysteamine (1)
- S9 (1)
- SL1 (1)
- SL5b (1)
- SL5b + c (1)
- SL5c (1)
- SLAM-seq (1)
- SNF1 (1)
- SNP (1)
- SNP genotyping (1)
- SNPs (1)
- SPAD (1)
- SR proteins (1)
- SSA (1)
- Salinity (1)
- Scale-up (1)
- Schistosomiaisis (1)
- Schizokinen (1)
- Science–society interactions (1)
- Scrotifera (1)
- Sea water (1)
- Secondary metabolites (1)
- Secretin (1)
- Secretins (1)
- Secretion (1)
- Seed sowing experiment (1)
- Seedling establishment (1)
- Sensorimotor processing (1)
- Sensory processing (1)
- Sex Attractants (1)
- Shade Adaptation (1)
- Shallow water (1)
- Shores (1)
- Sign posts (1)
- Simuliidae (1)
- Smut fungi (1)
- Social sciences (1)
- Sodefrin precursor-like factor (1)
- Sodium Proton Exchange (1)
- Sodium Transport (1)
- Sodium transport (1)
- Solanum lycopersicum (1)
- Solid Supported Membrane (1)
- SpaI (1)
- Spatial navigation (1)
- Species richness (1)
- Spectral clustering algorithm (1)
- Sporisorium reilianum (1)
- Ste2p (1)
- Stewardship (1)
- Stewardship and dissemination (1)
- Streams (1)
- Streptomyces hydrogenans (1)
- Structural protein (1)
- Structured Illumination Microscopy (1)
- Subjective Well-Being (1)
- Subtilin (1)
- Summer drought (1)
- Super resolution (1)
- Super resolution fluorescence microscopy (1)
- Supervised machine learning (1)
- Surface range (1)
- Sustainability research (1)
- Sustainable chemistry (1)
- Svetamycin (1)
- Swimming (1)
- Swimming behavior (1)
- Symbiont evolution (1)
- Symbiosis (1)
- Synaptosomal preparation (1)
- Synovial Fibroblast (1)
- Synthesis gas (1)
- Systematics (1)
- TWNK (1)
- Tabanidae (1)
- Tabanus (1)
- Temperature preference (1)
- Terbutryn (1)
- Terpenes (1)
- Terpenoid (1)
- Testosterone (1)
- Tetrad Analysis (1)
- Thalassiosira (1)
- Thermoanaerobacter kivui (1)
- Thermoascus aurantiacus (1)
- Thermophiles (1)
- Thermophilic acetogenic bacteria (1)
- Thermus thermophilus (1)
- Thin Layer Chromatography (1)
- Thioesterase (1)
- Threatened species (1)
- Three-Dimensional Structure (1)
- Thylakoid Membrane (1)
- Thymidylate Low Requirement (1)
- Thymidylate Sensitivity (1)
- Thymidylate Synthetase (1)
- Thymidylate Uptake (1)
- Thymine Dimers (1)
- Tick-borne diseases (1)
- Tie2 (1)
- Tigray (1)
- Tocochromanol (1)
- TolC (1)
- Tools and pipelines (1)
- Tooth Development (1)
- Topology (1)
- Toxicity (1)
- Tragelaphus oryx (1)
- Transgenic organisms (1)
- Translational Psychiatry (1)
- Transport (1)
- Traumatic mating (1)
- Tree rings (1)
- Triatominae (1)
- Trichoptera (1)
- Trimethylamine biosynthesis (1)
- Tropical forest restoration (1)
- Tropical montane forest (1)
- Truffle (1)
- Trypanosoma rangeli (1)
- Tuber magnatum (1)
- Tylosis (1)
- Type IV Pili (1)
- UV-B Effects (1)
- UV/V cones (1)
- Ultrastructure (1)
- University students (1)
- Uptake (1)
- Urgent actions (1)
- Ustilaginales (1)
- Ustilaginomycotina (1)
- Ustilago maydis (1)
- Ustilagomaydis (1)
- V1 (1)
- VEGF (1)
- Variability (1)
- Vector-host-interaction (1)
- Viral infection (1)
- Visual cortex (1)
- Vitality monitoring (1)
- WL110547 (1)
- Water accommodated fractions (1)
- Weather conditions (1)
- West Africa (1)
- Western Kenya (1)
- Wood properties (1)
- X-ray crystallography (1)
- Xylem (1)
- Zea mays (1)
- Zebrafish eleutheroembryo (1)
- aIF (1)
- abiotic factors (1)
- abundance (1)
- acetogen (1)
- acetogenic metabolism (1)
- acetyl-CoA (1)
- acoustic features (1)
- acoustic stream (1)
- acquisition strategy (1)
- active sensing (1)
- activity budgetx (1)
- adaptive transgenerational plasticity (1)
- additive manufacturing (1)
- additives (1)
- adhesin (1)
- adipogenesis (1)
- alarm calls (1)
- algae (1)
- all-E Lycopene (1)
- alzheimer’s disease (1)
- amplicon sequencing (1)
- angipoietin (1)
- animal behaviour (1)
- animal movement (1)
- animal welfare (1)
- annual plants (1)
- anomaly zone (1)
- antibiotic resistance (1)
- antibiotics (1)
- antimicrobial resistance (1)
- antipredator (1)
- apex bird species (1)
- aptamers (1)
- arabinose (1)
- archaea (1)
- arid climate (1)
- articular chondrocytes (1)
- artificial docking domains (1)
- asgard group (1)
- assembly gaps (1)
- assisted migration (1)
- ataxia (1)
- attitudes towards species conservation (1)
- auditory cortex (1)
- automated radiotelemetry system (1)
- azido-fatty acids (1)
- bacillary angiomatosis (1)
- bacteria-host interaction (1)
- bacterial community (1)
- bacterial infection (1)
- barrier (1)
- behaviour (1)
- benchmarking (1)
- benthic fauna (1)
- bioacoustics (1)
- bioactivity testing (1)
- bioassays (1)
- biodiversity conservation (1)
- biodiversity in literature (1)
- bioenergetics (1)
- biofilm (1)
- bioinformatics (1)
- biological variables (1)
- biomarkers (1)
- biosonar (1)
- biotic factors (1)
- biotrophic parasites (1)
- birds (1)
- bitopic transmembrane α-helix (1)
- blood vessels (1)
- boundary patrolling (1)
- brain cancer (1)
- brain rhythms (1)
- brain waves (1)
- branching (1)
- breeding sites (1)
- cardiolipin (1)
- cardiovascular disease (1)
- carnivora (1)
- carnivores (1)
- carotenogenic pathways (1)
- carotenoid distribution (1)
- carotenoid pathway engineering (1)
- carotenoid structures (1)
- caudate (1)
- central place foraging (1)
- cerebellum (1)
- checklist (1)
- checkpoint inhibitors (1)
- chlorophyll fluorescence (1)
- chromosomes (1)
- click-chemistry (1)
- climatic variables (1)
- co-transcriptional regulation (1)
- coalescence (1)
- cobra (1)
- coevolution (1)
- communication (1)
- communication-mediating domains (1)
- community ecology (1)
- community mean (1)
- compass orientation (1)
- complete chloroplast genome (1)
- complexome profiling (1)
- computational literary studies (1)
- connection to nature (1)
- consortia (1)
- control theory (1)
- cooperation (1)
- cophylogeny (1)
- cospeciation (1)
- cotransformation (1)
- coupling (1)
- cpDNA (1)
- cross-species RNA-sequencing (1)
- crosslinking-mass spectrometry (1)
- crustacea (1)
- cryo-EM (1)
- cultural ecosystem services (1)
- custom (1)
- cyclooctyne (1)
- cytosolic free calcium (1)
- de novo Synthesis (1)
- de novo transcription (1)
- decomposition (1)
- deep learning (1)
- deep sea (1)
- deep-sea sediment (1)
- deletion mutant (1)
- demography (1)
- dendrite (1)
- dendritic branching (1)
- dendritic morphology (1)
- depth (1)
- dermosphere (1)
- diagnostics (1)
- diatoms (1)
- differentially regulated orthologs (1)
- differentiation diversity (1)
- digital student lab (1)
- dimer interface formation (1)
- discrete choice modeling (1)
- distribution (1)
- diurnal variation (1)
- docking domains (1)
- domain architecture evolution (1)
- downy mildew (1)
- drug design (1)
- easyPACId (1)
- ecological risk assessment (1)
- ecology and biodiversity (1)
- ecospat (1)
- ecosystem management (1)
- ecosystem services (1)
- ectomycorrhizal (1)
- ectrogella (1)
- effect monitoring (1)
- effectors (1)
- elapid snake (1)
- elephant (1)
- elevational gradient (1)
- endocrine disruption (1)
- endocrine-disrupting chemicals (1)
- endophytes (1)
- endothelium (1)
- energy (1)
- energy-converting hydrogenase (Ech) (1)
- engineering (1)
- envenoming (1)
- environmental DNA (1)
- environmental behavior (1)
- environmental factors (1)
- environmental gradients (1)
- environmental humanities (1)
- environmental knowledge (1)
- environmental pollution (1)
- eukaryotic biodiversity (1)
- evolution (1)
- evolutionary traceability (1)
- exon coalescence (1)
- exon concatenation (1)
- experiment (1)
- exposome (1)
- exposure (1)
- expression system (1)
- extracellular matrix (1)
- extreme frost (1)
- failure to diverge (1)
- fatty acid dependency (1)
- fatty acid desaturation (1)
- fatty acid metabolism (1)
- fence (1)
- fitness (1)
- flowering (1)
- foliar pathogens (1)
- food contact materials (1)
- foraging (1)
- foraging site fidelity (1)
- foraging site switching (1)
- forest management (1)
- freshwater crayfish (1)
- functional group (1)
- functional traits (1)
- fungal effectors (1)
- fungal pathogens (1)
- fungal phylogeny (1)
- fungal traits (1)
- fuzzy clustering (1)
- gamma oscillations (1)
- gas exchange (1)
- gene conversion (1)
- gene families (1)
- gene models (1)
- generalised additive models (1)
- genetic engineering (1)
- genome architecture (1)
- genome assembly (1)
- genome assembly and annotation (1)
- genomic diversity (1)
- genotype (1)
- genotyping (1)
- geoecology (1)
- geographical origin (1)
- giraffe behavior (1)
- glidobactins (1)
- global biomes (1)
- glucocorticoid receptor (1)
- glucocorticoid response (1)
- graded structure (1)
- grasslands (1)
- gravity (1)
- growth promotion (1)
- guanidine riboswitch (1)
- guided zoo tours (1)
- habitat heterogeneity (1)
- hands-on elements (1)
- heat (1)
- heat and drought (1)
- heat-shock protein (1)
- heathlands (1)
- hematopoietic stem cell (1)
- herbaria (1)
- herbivores (1)
- heteroplasmy (1)
- heterozygous cells (1)
- high temperature (1)
- high throughput screening (1)
- hippo (1)
- historical biodiversity (1)
- homeostasis (1)
- homologous gene expression (1)
- honey bee classification (1)
- honey bees (1)
- horizontal gene transfer (1)
- host specificity (1)
- host-switch (1)
- housing conditions (1)
- human footprint (1)
- human-wildlife conflict (1)
- hydroxamate (1)
- hyperparasitic fungi (1)
- hyperparasitism (1)
- hypoxia (1)
- in-vitro Assay (1)
- inbreeding (1)
- indel (1)
- individual interest (1)
- individuality (1)
- infectious diseases (1)
- infra-slow oscillation (1)
- integrate-and-fire (1)
- inter- seasonal predictability (1)
- interaction networks (1)
- interest in nature (1)
- intersexuality (1)
- invasive mammals (1)
- iron starvation (1)
- krait (1)
- lab motivation scale (LMS) (1)
- land use (1)
- landscape fragmentation (1)
- lantibiotic (1)
- large subunit maturation (1)
- lateral line (1)
- latitudinal gradient (1)
- learning technology (1)
- left ventricular hypertrophy (1)
- leukodystrophy (1)
- light (1)
- light-harvesting (1)
- lipid metabolism (1)
- lipoprotein (1)
- livelihood (1)
- liver cancer (1)
- local field potentials (1)
- long noncoding RNA (1)
- long sequencing reads (1)
- long-term protection (1)
- long36 term protection (1)
- mPFC (1)
- mPTP (1)
- mRNA (1)
- mTOR (1)
- machine learning (1)
- macroevolution (1)
- macrohabitat (1)
- magnetoreception (1)
- maladaptation (1)
- mathematical modeling (1)
- maturity (1)
- maximum likelihood (1)
- mean fruit body size (1)
- mechanics (1)
- medically relevant (1)
- meerkats (1)
- membrane protein (1)
- membrane trafficking (1)
- memory (1)
- metabolic disruptors (1)
- metabolomics (1)
- metazoans (1)
- microRNA (1)
- microbiome (1)
- microplastics (1)
- microsatellite (1)
- miracula (1)
- missing data (1)
- mitochondria localization (1)
- mitochondrial dysfunction (1)
- mitochondrial localization motif (1)
- mitohormesis (1)
- mitophagy (1)
- molecular phylogenetic analysis (1)
- monetary impacts (1)
- monocytes (1)
- morphology evaluation (1)
- moth indicator groups (1)
- mounting (1)
- movement (1)
- mt DNA (1)
- mtDNA haplotypes (1)
- multi-generation experiment (1)
- mushroom (1)
- mycorrhiza (1)
- myeloid angiogenic cells (1)
- natural behavior (1)
- natural products (1)
- naturalistic stimuli (1)
- nature connectedness (1)
- navigation (1)
- nematode diversity (1)
- network analysis (1)
- neural coding (1)
- neuro-vascular (1)
- neurobiology (1)
- neurodegeneration (1)
- neurodevelopment (1)
- neuroethology (1)
- neuromodulation (1)
- neuronal coherence (1)
- neurosimulation (1)
- nightly behavior (1)
- nisin binding (1)
- nocturnal activity (1)
- nomadism (1)
- non-destructive sampling (1)
- non-material contribution (1)
- non-ribosomal peptide syntheses (1)
- non-ribosomal peptide synthetase (1)
- non-target chemical analysis (1)
- non-timber forest products (NTFPs) (1)
- nonsense-mediated mRNA decay (1)
- nontarget (1)
- northern giraffe (1)
- novel natural products (1)
- obesogens (1)
- obligate pathogens (1)
- octanoic acid (1)
- oncomodulation (1)
- oomycete (1)
- open-source 3D bioprinting (1)
- organoids (1)
- orientation behavior (1)
- orthogroup (1)
- orthology (1)
- orthology assignment (1)
- outdoor education (1)
- oxygenic photosynthesis (1)
- pH Regulation (1)
- paleobiology (1)
- parabolic flight (1)
- paralogy (1)
- parasitism (1)
- parasitoid (1)
- parathyroid hormone 2 (1)
- pathogenicity (1)
- pathway (1)
- pathway complexity (1)
- pathway evolution (1)
- peptide-antimicrobial-Xenorhabdus peptide (1)
- phenology (1)
- phosphoketolase (1)
- phosphotransacetylase (1)
- photocycle (1)
- phylogenetic informativeness (1)
- phylogenetic profiles (1)
- phylogenetic profiling (1)
- physiological stress (1)
- planning and design (1)
- plant regeneration (1)
- plasma (1)
- plasmid (1)
- plasmid copy number (1)
- playback experiment (1)
- policies (1)
- politics and governance (1)
- pollinator crisis (1)
- polymers (1)
- polyploidy (1)
- population structure (1)
- postglacial colonisation (1)
- posture estimation (1)
- power law (1)
- precipitation (1)
- prediction error (1)
- priority natural areas (1)
- probe kit (1)
- propagating waves (1)
- proteasome inhibitors (1)
- protein folding (1)
- protein production (1)
- protein structure (1)
- proteobacteria (1)
- proteoliposomes, (1)
- proteomics (1)
- proton translocation (1)
- protoplast fusion (1)
- qH2 (1)
- quality control (1)
- quantitative disease resistance (1)
- quercus (1)
- raccoon dog (Nyctereutes procyonoides) (1)
- radical pair model (1)
- random forest (1)
- range boundary (1)
- range expansion (1)
- reaction mechanisms (1)
- receptor (1)
- regulation (1)
- reliability (1)
- repeat elements (1)
- repetition suppression (1)
- reptiles (1)
- resource losses (1)
- retrophylogenomics (1)
- ribosome (1)
- ribosomes, Arabiodpsis thaliana, pre-rRNA processing, snoRNA, (1)
- rock-climbing impact (1)
- root allocation strategy (1)
- root functional traits (1)
- roots (1)
- runs of homozygosity (1)
- sage downy mildew (1)
- saprobic and ectomycorrhizal basidiomycetes (1)
- saprotrophic (1)
- scale development (1)
- scale invariance (1)
- seafloor bathymetry (1)
- search (1)
- sediment (1)
- selection gradients (1)
- senescence (1)
- sensory (1)
- sensory acquisition (1)
- serine/arginine-rich proteins (1)
- shallow water (1)
- shroom (1)
- siderophore (1)
- siderophore-dependent iron uptake (1)
- signaling (1)
- silicate (1)
- simplified production (1)
- small angle x-ray scattering (1)
- small animals (1)
- small protein (1)
- small proteins (1)
- smut fungi (1)
- snake bite (1)
- social information (1)
- social isolation (1)
- socio-economic sectors (1)
- socio-economics (1)
- soil degradation (1)
- soil fungal communities (1)
- sound coding (1)
- spatial analysis (1)
- spatial modelling (1)
- special needs students (1)
- speciation (1)
- species delimitation (1)
- species distribution model (1)
- species richness (1)
- splicing (1)
- splicing regulation (1)
- stairway plot (1)
- stereolithography (1)
- stimulus repetition (1)
- stingless bee (1)
- stochastic factors (1)
- strained promoted cycloadditon (1)
- sub-Saharan Africa (1)
- sugar uptake (1)
- sun exposure (1)
- suricates (1)
- surround suppression (1)
- survival rate (1)
- sustainability (1)
- symbiont association patterns (1)
- systems knowledge (1)
- tRNA (1)
- tRackIT (1)
- tafazzin (1)
- target knowledge (1)
- taxonomy (1)
- teaching tool (1)
- technology acceptance model (TAM) (1)
- temperate forest (1)
- temperature (1)
- terrestrial mammal (1)
- text mining (1)
- thermal-melanism hypothesis (1)
- thiolation domain (1)
- threatened cliff plant species (1)
- tight junctions (1)
- topology (1)
- trait evolution (1)
- traits (1)
- transcription (1)
- transcriptome (1)
- transcriptome analysis (1)
- transdisciplinarity (1)
- transformation knowledge (1)
- transglutaminase 2 (1)
- translation initiation (1)
- transplant experiment (1)
- trimeric autotransporter adhesin (1)
- trisporic acids (1)
- tritrophic interaction (1)
- trophic interactions (1)
- tumor model (1)
- tumor-associated macrophages (1)
- ungulate (1)
- universal (1)
- university students (1)
- unselected segregation (1)
- validity (1)
- vascular integrity (1)
- vegetation (1)
- venomous snakes (1)
- video action classification (1)
- video observation (1)
- viruses (1)
- vocalization (1)
- vocalization production; (1)
- volatile (1)
- warming (1)
- water security (1)
- white truffle (1)
- wing geometric morphometrics (1)
- wolf (1)
- wwtr1 (1)
- xenology (1)
- xylose (1)
- yap1 (1)
- yeast (1)
- zinc finger (1)
- zoo (1)
- zoo biology (1)
- zoo education (1)
- zoo elephants (1)
- µ-protein (1)
- β-Barrel Proteins (1)
- β-oxidation (1)
- ζ-Carotene (1)
Institute
- Biowissenschaften (540)
- Senckenbergische Naturforschende Gesellschaft (33)
- Medizin (17)
- Biodiversität und Klima Forschungszentrum (BiK-F) (15)
- Biochemie, Chemie und Pharmazie (13)
- Buchmann Institut für Molekulare Lebenswissenschaften (BMLS) (13)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (13)
- Institut für Ökologie, Evolution und Diversität (11)
- MPI für Biophysik (8)
- Biochemie und Chemie (7)
Bei Autismus-Spektrum-Störungen (ASS) handelt es sich um genetisch komplexe Störungen mit hoher Erblichkeit. Als zugrundeliegender Pathomechanismus von ASS werden unter anderem Veränderungen der neuronalen Entwicklung diskutiert. Der Phänotyp von ASS ist definiert durch Einschränkungen in der sozialen Interaktion und Kommunikation sowie repetitives und stereotypes Verhalten. Genkopiepolymorphismen (englisch „copy number variations“/CNVs), also Deletionen oder Duplikationen einer chromosomalen Region, wurden wiederholt in Probanden mit ASS identifiziert. Hierbei ist in ASS die Region 16p11.2 mit am häufigsten von CNVs betroffen. Einige Gene aus diesem chromosomalen Abschnitt wurden bereits funktionell charakterisiert. Dennoch können die Befunde der bisherigen Einzelgenstudien nicht alle Aspekte erklären, die durch 16p11.2 CNVs hervorgerufen werden. Ziel dieser Studie war es daher, ein weiteres neuronal assoziiertes Kandidatengen dieser Region zu identifizieren und im Anschluss funktionell im Kontext der neuronalen Differenzierung zu charakterisieren.
Das SH-SY5Y Neuroblastom-Zellmodell wurde auf Transkriptom- und morphologischer Ebene auf seine Eignung als Modell für neuronale Differenzierung untersucht und bestätigt. Eine Analyse der Expressionen aller Gene der 16p11.2-Region zeigte, dass das Gen Quinolinat-Phosphoribosyltransferase (QPRT) eine vergleichsweise hohe Expression mit der stärksten und robustesten Regulierung über die Zeit aufwies. Eine de novo Deletion der 16p11.2-Region wurde in einem Patienten im Vergleich zu seinen Eltern validiert. In Patienten-spezifischen lymphoblastoiden Zelllinien derselben Familie konnten wir eine Gendosis-abhängige Expression von QPRT auf RNA-Ebene bestätigen. In SH-SY5Y-Zellen korrelierte die Expression von QPRT signifikant mit der Entwicklung von Neuriten während der Differenzierung. Um QPRT funktionell zu charakterisieren, benutzten wir drei verschiedene Methoden zur Reduktion der QPRT-Gendosis: (i) knock down (KD) durch siRNA, (ii) chemische Inhibition durch Phthalsäure und (iii) knock out (KO) über CRISPR/Cas9-Geneditierung. Eine Reduktion von QPRT durch siRNA führte zu einer schwachen Veränderung der neuronalen Morphologie differenzierter SH-SY5Y-Zellen. Die chemische Inhibition sowie der genetische KO von QPRT waren letal für differenzierende aber nicht für proliferierende Zellen. Eine Metabolitenanalyse zeigte keine Veränderungen des QPRT-assoziierten Tryptophanstoffwechsels. Gene, welche auf Transkriptomebene im Vergleich zwischen KO- und Kontrollzellen differenziell reguliert vorlagen, waren häufig an Prozessen der neuronalen Entwicklung sowie an der Bildung, Stabilität und Funktion synaptischer Strukturen beteiligt. Die Liste differenziell regulierter Gene enthielt außerdem überdurchschnittlich viele ASS-Risikogene und ko-regulierte Gengruppen waren assoziiert mit der Entwicklung des dorsolateralen präfrontalen Cortex, des Hippocampus sowie der Amygdala.
In dieser Studie zeigten wir einen kausalen Zusammenhang zwischen QPRT und der neuronalen Differenzierung in vitro sowie einen Einfluss von QPRT auf die Regulation von ASS-assoziierten Genen und Gen-Netzwerken. Funktionell standen diese Gene im Kontext mit synaptischen Vorgängen, welche durch Veränderungen zu einem Exzitations-Inhibitions-Ungleichgewicht und letztendlich zum Zelltod von Neuronen führen können. Unsere Ergebnisse heben in Summe die wichtige Rolle von QPRT in der Krankheitsentstehung von ASS, insbesondere in Trägern einer 16p11.2 Deletion, hervor.
This dissertation aimed to shed light on changes of the epigenetic landscape in heart and skeletal muscle tissue of the turquoise Killifish N. furzeri, a novel, short-lived animal model for aging research. The following results could be obtained:
1. A global trend towards closed chromatin conformation could be observed; histone markers for H3K27me3, H3K9me3 and H4K20me3 accumulated in skeletal muscle tissue from old N. furzeri. Markers for open chromatin conformation such as H3K4me3, H3K9ac and H4K16ac decreased in old skeletal muscle tissue. In old hearts from N. furzeri an accumulation of H3K27me3 could be detected while H3K9ac was found to increase with age as well. mRNA expression levels of methylating enzymes were higher in skeletal muscle tissue from old N. furzeri when compared to expression levels in skeletal muscle tissue from young N. furzeri.
2. The shift of epigenetic pattern was accompanied by a change of gene expression. Via mRNA sequencing in collaboration with the MPI, Bad Nauheim it could be shown that genes associated with cell cycle and DNA repair were lower expressed in skeletal muscle tissue from old N. furzeri than in tissue from young N. furzeri. Genes, associated with inflammatory signaling and glycolysis, displayed increased mRNA levels in skeletal muscle tissue from old N. furzeri. These results could be confirmed by Western blot and qRT-PCR analyses.
3. Markers for DNA damage and senescence increased in skeletal muscle tissue from old N. furzeri.
4. Cells derived from young and old N. furzeri skeletal muscle could be isolated and cultured for many passages. These cells were a mix of different cell types with properties and features of the native tissue. They could be used for treatment with drugs and/small compounds modulating the epigenetic landscape via specific interference with methylating enzymes.
5. DNA methylation and hydroxy-methylation were found to go in different directions in skeletal muscle and heart tissue from N. furzeri: while increasing in skeletal muscle tissue, a both DNA modifications declined in heart tissue with age.
6. In the heart of N. furzeri microRNA expression changes with age were assed with sequencing in collaboration with the FLI, Jena. It could be demonstrated that miRNA expression is age-dependent. Particular focus was on miR-29 and its target genes: miR-29 was highly upregulated in heart and skeletal muscle tissue, while target genes such as collagens and dnmts were reduced with age in the heart of N. furzeri.
7. Cardiac function remained stable with age and no accumulation of collagens could be found when comparing hearts of young and old N. furzeri despite the increase of markers for oxidative stress.
8. Cell culture experiments with human cardiac fibroblasts revealed that miR-29 is upregulated with increasing age of the donor. In addition to that, it could be shown that miR-29 is positively regulated by oxidative stress.
9. A zebrafish mutant with modified expression of miR-29 that was created in collaboration with the SNS, Pisa, presented a severe hypoxic phenotype and an altered mRNA expression profile compared to wild type control zebrafish. Cardiac dysfunction and hypertrophy were observed as well as an increase in DNA methylation and collagens.
Taken together, it could be shown that the aging process in skeletal muscle and heart tissue from N. furzeri leads to a series of changes on epigenetic levels. It remains to be elucidated whether these changes are result or cause for further changes of mRNA expression, protein levels and pathophysiology, yet the N. furzeri represents a promising research model for further aging studies.
Lizards of Paraguay: an integrative approach to solve taxonomic problems in central South America
(2018)
Paraguay is located in the center of South America with drier and warmer climatic conditions in the western part of the country, and more temperate and humid in the eastern region. Biogeographically, Paraguay is a key spot in South America, where several ecoregions converge. In my study, I sampled most of the ecoregions of Paraguay. The main objective of my work is to solve taxonomic problems, identified through genetic barcoding analyses, in the central region of South America. To achieve this objective, I used selected taxa of the Paraguayan Squamata as models taking into consideration the crucial geographic position of the country, plus the scarce available genetic data of Paraguayan reptiles.
The collecting activities were performed in the framework of a barcoding inventory project of the Paraguayan herpetofauna and carried out mostly in rural areas searching for animals in different types of habitats using active search as the sampling technique.
For genetics, the extraction of DNA was performed with DNeasy® Blood & Tissue Kit of Qiagen® for sets of few samples, and the fiber glass plate protocol for sets of 96 samples. I assessed the quality of sequences after amplification in agarose gel electrophoresis. The first marker sequenced was 16S mtDNA, used for barcoding analysis. A DNA barcode is a genetic identifier for a species. Once a taxonomic problem was detected, I generate more gene sequences to target the issue.
All the analyses to test phylogenetic hypotheses (based on single genes or concatenated datasets) were performed under Maximum Likelihood and Bayesian approaches. To root the phylogenetic trees, I chose the available taxon (or taxa) most closely related to the respective studied group as outgroups. For the general tree of Paraguayan Squamata, based on barcodes of 16S, I chose Sphenodon punctatus.
I generated a total of 142 sequences of 64 species of Squamata from Paraguay (Appendix I). The final alignment of 615 bp comprised 249 samples. The best substitution model for the Barcoding dataset based on the gene 16S was GTR+G, according to the BIC.
To complement molecular evidence generated with the ML grouping of 16S barcodes, I took a morphological approach based on voucher specimens collected during fieldwork (usually the same specimens that I used for genetic analysis), supplemented by the revision of museum collections.
Summarizing my results, samples of Colobosaura exhibit large genetic distances, and accordingly I revalidated Colobosaura kraepelini (Appendix II). Tropidurus of the spinulosus group show two clades and among them there is little genetic and morphological variation, I synonymized T. tarara and T. teyumirim with T. lagunablanca, and T. guarani with T. spinulosus (Appendix III). I detected the presence of candidate species of Homonota, and I restricted the name H. horrida for Argentina, and described two new species of Homonota (Appendices IV and V), and a new species of Phyllopezus also in the Family Phyllodactylidae (Appendix VI).
In this work I present the most comprehensive analysis of genetic samples of Squamata from Paraguay. The results obtained here will be useful to help to clarify further taxonomic issues regarding the squamate fauna from the central region of South America. Moreover, the data generated for this study will have a positive impact in a larger geographic context, beyond Paraguayan borders.
Regarding the conservation of the Paraguayan reptiles, and considering the taxonomic changes accomplished here, it is important to note that many species lack legal protection. In Paraguay, the major problem for conservation is habitat loss due to extensive crop farming. Thus, currently, the protected areas are the best strategy for conservation of biodiversity in the country. However, many such areas face legal problems (e.g., lack of official measurements, management plans, forest guards, infrastructure, etc.) so that the maintenance of their biodiversity over time is not guaranteed.
In conclusion, in this study I present contributions on the taxonomy of mostly lizards from Paraguay. Due to lack of samples, I was not able to deal with a deep taxonomic revision of the country's snakes. Based on my results, I can argue that analyses of Xenodontini and Pseudoboini are currently a pressing research issue. This barcoding project may continue since some colleagues in Paraguay are interested in collaboration. Given that the sequenced specimens are yet a small portion of the actual diversity of Paraguay, it will be of utmost importance to continue and expand these studies that will further improve our taxonomic knowledge. Furthermore, it is desirable to have Paraguayan scientists not only involved, but to see them taking the lead of high quality taxonomic research.
The metabolome of any live cell consists of several hundred, if not thousands of different molecules at any given moment, be it a relatively small bacterial cell or a whole multicellular organism. Although there are continuous attempts to differentiate between primary and secondary metabolites, the borders often blur in the eye of almost perfect interconvertability of all such matter. With chemistry and physics dominating this domain of biology it is an interdisciplinary endeavor to tackle the questions surrounding the workings of the metabolic pathways involved, searching for answers that ultimately help us to better understand life and find solutions to problems that affect us humans. One area of biochemistry that serves as a formidable example of the intertwined primary and secondary metabolic pathways are fatty acids, essential components of bacterial membranes, sources of energy and carbon but also important building blocks of several natural products. The second area to be mentioned is the metabolism of amino acids, the basic components of proteins and enzymes, which also serve as precursors to a diverse set of metabolites with many biological purposes.
This work focuses on these two areas of biochemistry, as several intermediates of their metabolism serve as building blocks for complex secondary metabolites whence many interesting and bioactive natural products are derived. The powerful and relatively novel tool of click-chemistry is employed to track azide-labeled precursors of primary and secondary metabolism in various bacterial strains to observe biochemistry at work and adds to the knowledge gained through other methods. The methods presented in this work serve the observation of fatty acid biosynthesis, degradation, modification and transport through direct ligation of azido fatty acids with cyclooctynes on one hand, leading to a revision of fatty acid transport in general. On the other hand a cleavable azide-reactive resin is devised to generally track the fate of azidated compounds through the myriads of metabolic pathways offered by entomopathogenic bacteria possessing a rich secondary metabolism. The resulting findings led to the identification of several antimicrobial peptides, amides and other compounds of which many had remained so far undetected in the strains that underwent investigation, underlining the worth of this method for future metabolomic research and beyond.
The role of the homeobox transcription factor Meis2b in zebrafish heart development and asymmetry
(2018)
Zebrafish heart development: The heart of the zebrafish is the first organ to form and function during embryonic development, and is composed by one atrium and one ventricle. Between 5-17 somites stage, the cardiomyocyte precursors form the bilateral cardiac fields in the anterior lateral plate mesoderm (ALMP); where the endocardial precursors are located anterior to the cardiac fields (Zeng, Wilm et al. 2007). Then, the pools of endocardial andmyocardial precursors fuse at the midline and form the heart disc; where atrial cardiomyocytes are located around, the ventricular cardiomyocytes are located in the centerof the heart disc, and the future endocardium is located in a ventral position relative to the cardiomyocytes (Bakkers 2011). After the heart disc is formed, the cardiomyocyte progenitors start to migrate and rotate asymmetrically to form the heart tube (de Campos-Baptista, Holtzman et al. 2008, Rohr, Otten et al. 2008, Smith, Chocron et al. 2008). This process is followed by a rightward bending of the heart tube, and the arterial and venous poles rotate at different speed and directions (a process known as heart looping) (Smith, Chocron et al. 2008). The heart looping process results in a ventricle located on the right side and a more posterior atrium located on the left side with respect to the midline; at this point the atrium and ventricle are separated by a fine segment called the atrioventricular canal, where the valves will be formed (Staudt and Stainier 2012). The second heart field (SHF) is a pool of cardiac progenitors that are specified later during the formation of the heart disc and until the heart looping stages. The SHF contributes withcells to the distal side of the ventricle, the outflow and inflow tracts, and is important for the specification of the cardiac conduction system (de Pater, Clijsters et al. 2009, Hami, Grimes et al. 2011, Zhou, Cashman et al. 2011, Witzel, Jungblut et al. 2012, Guner-Ataman, Paffett-Lugassy et al. 2013)....
Heat stress transcription factors (Hsfs) are required for transcriptional changes during heat stress (HS) thereby playing a crucial role in the heat stress response (HSR). The target genes of Hsfs include heat shock proteins (Hsps), other Hsfs and genes involved in protection of the cell from irreversible damages due to exposure to elevated temperatures. Among 27 Hsfs in Solanum lycopersicum, HsfA1a, HsfA2 and HsfB1 constitute a functional triad which regulates important aspects of the HSR. HsfA1a is constitutively expressed and described as the master regulator of stress response and thermotolerance. Activation of HsfA1a under elevated temperatures leads to the induction of HsfA2 and HsfB1 which further stimulate the transcription of HS-responsive genes by forming highly active complexes with HsfA1a. Despite the well-established role of these three Hsfs in tomato HSR, information about functional relevance of other Hsfs is currently missing.
The heat stress inducible HsfA7 belongs alongside with HsfA2 to a phylogenetically distinct clade. Thereby the two proteins share high homology and a functional redundancy has been assumed. However, HsfA7 function and contribution to stress responses have not been investigated into detail in any plant species.
Tomato HsfA7 protein accumulates already at moderately elevated temperatures (~35°C) while HsfA2 becomes dominant at higher temperatures (>40°C). HsfA7 pre-mRNA undergoes complex and temperature-dependent alternative splicing resulting in several transcripts that encode for three protein isoforms. HsfA7-I contains a functional nuclear export signal (NES) and shows nucleocytoplasmic shuttling while HsfA7-II and HsfA7-III have a truncated NES which leads to the strong nuclear retention of the protein. Differences in the nucleocytoplasmic equilibrium have a major impact on the stability of protein isoforms, as nuclear retention is associated with increased protein turnover. Consequently, HsfA7-I shows a higher stability and can be detected even after 24 hours of stress attenuation, while HsfA7-II is rapidly degraded. The degradation of these factors is mediated by the ubiquitin-proteasome pathway.
HsfA7 can physically interact with HsfA1a and HsfA3 and form co-activator (“superactivator”) complexes with a very high transcriptional activity as shown on different HS-inducible promoters. In order for the complex to be successfully transferred to the nucleus and confer its activity it needs a functional nuclear localization signal (NLS) of HsfA7. In contrast, the activator (AHA) motif of HsfA7 is not essential for its co-activator function. Interestingly, while interaction of HsfA7 with either HsfA3 or HsfA1a stabilizes HsfA7 isoforms, concomitantly this leads to an increased turnover of HsfA1a and HsfA3. In contrast, HsfA2 has a stabilizing effect on the master regulator HsfA1a.
Thus, HsfA7 knockout mutants generated by CRISPR/Cas9 gene editing, show increased HsfA1a levels and a stronger induction of HS-related genes at 35°C compared to wild-type plants and HsfA2 knockout mutants. Consequently, HsfA7 knockout seedlings exhibit increased thermotolerance as shown by the enhanced hypocotyl elongation under a prolonged mild stress treatment at 35°C. In summary, these results highlight the importance of HsfA7 in regulation of cellular responses at elevated temperatures. Under moderately elevated temperatures, the accumulation of HsfA7 and its subsequent interaction with HsfA1a, leads to increased turnover of the latter, thereby ensuring a milder transcriptional activation of temperature-responsive genes like Hsps. In turn, in response to further elevated temperatures, HsfA2 becomes the dominant stress-induced Hsf. HsfA2 forms co-activator complexes with HsfA1a which in contrast to HsfA7, allows the stabilization of the master regulator, leading to the stronger expression of HS-responsive genes required for survival. Thereby, this study uncovers a new regulatory mechanism, where the temperature-dependent competitive interaction of HsfA2 and HsfA7 with HsfA1a control the fate of the master regulator and consequently the activity of temperature-responsive networks.
Echolocation allows bats to orientate in darkness without using visual information. Bats emit spatially directed high frequency calls and infer spatial information from echoes coming from call reflections in objects (Simmons 2012; Moss and Surlykke 2001, 2010). The echoes provide momentary snapshots, which have to be integrated to create an acoustic image of the surroundings. The spatial resolution of the computed image increases with the quantity of received echoes. Thus, a high call rate is required for a detailed representation of the surroundings.
One important parameter that the bats extract from the echoes is an object’s distance. The distance is inferred from the echo delay, which represents the duration between call emission and echo arrival (Kössl et al. 2014). The echo delay decreases with decreasing distance and delay-tuned neurons have been characterized in the ascending auditory pathway, which runs from the inferior colliculus (Wenstrup et al. 2012; Macías et al. 2016; Wenstrup and Portfors 2011; Dear and Suga 1995) to the auditory cortex (Hagemann et al. 2010; Suga and O'Neill 1979; O'Neill and Suga 1982).
Electrophysiological studies usually characterize neuronal processing by using artificial and simplified versions of the echolocation signals as stimuli (Hagemann et al. 2010; Hagemann et al. 2011; Hechavarría and Kössl 2014; Hechavarría et al. 2013). The high controllability of artificial stimuli simplifies the inference of the neuronal mechanisms underlying distance processing. But, it remains largely unexplored how the neurons process delay information from echolocation sequences. The main purpose of the thesis is to investigate how natural echolocation sequences are processed in the brain of the bat Carollia perspicillata. Bats actively control the sensory information that it gathers during echolocation. This allows experimenters to easily identify and record the acoustic stimuli that are behaviorally relevant for orientation. For recording echolocation sequences, a bat was placed in the mass of a swinging pendulum (Kobler et al. 1985; Beetz et al. 2016b). During the swing the bat emitted echolocation calls that were reflected in surrounding objects. An ultrasound sensitive microphone traveling with the bat and positioned above the bat’s head recorded the echolocation sequence. The echolocation sequence carried delay information of an approach flight and was used as stimulus for neuronal recordings from the auditory cortex and inferior colliculus of the bats.
Presentation of high stimulus rates to other species, such as rats, guinea pigs, suppresses cortical neuron activity (Wehr and Zador 2005; Creutzfeldt et al. 1980). Therefore, I tested if neurons of bats are suppressed when they are stimulated with high acoustic rates represented in echolocation sequences (sequence situation). Additionally, the bats were stimulated with randomized call echo elements of the sequence and an interstimulus time interval of 400 ms (element situation). To quantify neuronal suppression induced by the sequence, I compared the response pattern to the sequence situation with the concatenated response patterns to the element situation. Surprisingly, although the bats should be adapted for processing high acoustic rates, their cortical neurons are vastly suppressed in the sequence situation (Beetz et al. 2016b). However, instead of being completely suppressed during the sequence situation, the neurons partially recover from suppression at a unit specific call echo element. Multi-electrode recordings from the cortex allow assessment of the representation of echo delays along the cortical surface. At the cortical level, delay-tuned neurons are topographically organized. Cortical suppression improves sharpness of neuronal tuning and decreases the blurriness of the topographic map. With neuronal recordings from the inferior colliculus, I tested whether the echolocation sequence also induced neuronal suppression at subcortical level. The sequence induced suppression was weaker in the inferior colliculus than in the cortex. The collicular response makes the neurons able to track the acoustic events in the echolocation sequence. Collicular suppression mainly improves the signal-to-noise ratio. In conclusion, the results demonstrate that cortical suppression is not necessarily a shortcoming for temporal processing of rapidly occurring stimuli as it has previously been interpreted.
Natural environments are usually composed of multiple objects. Thus, each echolocation call reflects off multiple objects resulting in multiple echoes following the calls. At present, it is largely unexplored how neurons process echolocation sequences containing echo information from more than one object (multi-object sequences). Therefore, I stimulated bats with a multi-object sequence which contained echo information from three objects. The objects were different distances away from each other. I tested the influence of each object on the neuronal tuning by stimulating the bats with different sequences created from filtering object specific echoes from the multi-object sequence. The cortex most reliably processes echo information from the nearest object whereas echo information from distant objects is not processed due to neuronal suppression. Collicular neurons process less selectively echo information from certain objects and respond to each echo.
For proper echolocation, bats have to distinguish between own biosonar signals and the signals coming from conspecifics. This can be quite challenging when many bats echolocate adjacent to each other. In behavioral experiments, the echolocation performance of C. perspicillata was tested in the presence of potentially interfering sounds. In the presence of acoustic noise, the bats increase the sensory acquisition rate which may increase the update rate of sensory processing. Neuronal recordings from the auditory cortex and inferior colliculus could strengthen the hypothesis. Although there were signs of acoustic interference or jamming at neuronal level, the neurons were not completely suppressed and responded to the rest of the echolocation sequence.
The fruit fly Drosophila melanogaster is one of the most important biological model organisms, but only the comparative approach with closely related species provides insights into the evolutionary diversification of insects. Of particular interest is the live imaging of fluorophores in developing embryos. It provides data for the analysis and comparison of the threedimensional morphogenesis as a function of time. However, for all species apart from Drosophila, for example the red flour beetle Tribolium castaneum, essentially no established standard operation procedures are available and the pool of data and resources is sparse. The goal of my PhD project was to address these limitations. I was able to accomplish the following milestones:
- Development of the hemisphere and cobweb mounting methods for the non-invasive imaging of Tribolium embryos in light sheet-based fluorescence microscopes and characterization of most crucial embryogenetic events.
- Comprehensive documentation of methods as protocols that describe (i) beetle rearing in the laboratory, (ii) preparation of embryos, (ii) calibration of light sheet-based fluorescence microscopes, (iv) recording over several days, (v) embryo retrieval as a quality control as well as (vi) data processing.
- Adaption of the methods to record and analyze embryonic morphogenesis of the Mediterranean fruit fly Ceratitis capitata and the two-spotted cricket Gryllus bimaculatus as well as integration of the data into an evolutionary context.
- Further development of the hemisphere method to allow the bead-based / landmark-based registration and fusion of three-dimensional images acquired along multiple directions to compensate the shadowing effect.
- Development of the BugCube, a web-based computer program that allows to share image data, which was recorded by using light sheet-based fluorescence microscopy, with colleagues.
- Invention and experimental proof-of-principle of the (i) AGameOfClones vector concept that creates homozygous transgenic insect lines systematically. Additionally, partial proof-of-principle of the (ii) AClashOfStrings vector concept that creates double homozygous transgenic insect lines systematically, as well as preliminary evaluation of the (iii) AStormOfRecords vector concept that creates triple homozygous transgenic insect lines systematically.
- Creation and performance screening of more than fifty transgenic Tribolium lines for the long-term imaging of embryogenesis in fluorescence microscopes, including the first Lifeact and histone subunit-based lines.
My primary results contribute significantly to the advanced fluorescence imaging approaches of insect species beyond Drosophila. The image data can be used to compare different strategies of embryonic morphogenesis and thus to interpret the respective phylogenetic context. My technological developments extend the methodological arsenal for insect model organisms considerably.
Within my perspective, I emphasize the importance of non-invasive long-term fluorescence live imaging to establish speciesspecific morphogenetic standards, discuss the feasibly of a morphologic ontology on the cellular level, suggest the ‘nested linearly decreasing phylogenetic relationship’ approach for evolutionary developmental biology, propose the live imaging of species hybrids to investigate speciation and finally outline how light sheet-based fluorescence microscopy contributes to the transition from on-demand to systematic data acquisition in developmental biology.
During my PhD project, I wrote a total of ten manuscripts, six of which were already published in peer-reviewed scientific journals. Additionally, I supervised four Master and two Bachelor projects whose scientific questions were inspired by the topic of my PhD work.
The continuous conversion of natural wildlife habitats into agricultural areas, as well as the fragmentation of the last wildlife refuges, is increasing the interface between people and wildlife. When wildlife negatively impacts on people and vice versa, we speak about human-wildlife conflicts (HWCs). This definition includes losses on both sides and takes into consideration the rooting of most of these conflicts between different groups of interest, such as advocates for nature conservation and economic groups. The centres of highest biodiversity are located in developing countries, which are also characterized by poverty. In African and Asian countries, people living in the vicinity of national parks and other conservation areas mostly receive only little support through the government or conservation organisations. Especially for those people who are dependent on agriculture, damage to fields and harvests can have catastrophic consequences. If the species causing damage is protected by national or even international law, the farmer is not allowed to use lethal methods, but has to approach the authority in charge. If this agency, however, cannot offer appropriate support, resentment, anger or even hate develops, and the support for wildlife conservation activities declines. For this reason, HWCs were declared as one of the most important conservation topics today, being particularly relevant for large and threatened species such as the African and Asian elephant, hippopotamus and the greater one-horned rhino, as well as for large predators. Up to today, no general assessment scheme has been recommended for damage caused by protected wildlife species.
In my study, HWCs in Asia and Africa are compared, focussing on all herbivorous species identified which damaged crops. For the French NGO Awely, des animaux et des hommes, I developed a detailed assessment scheme suitable for all terrestrial ecosystems, and any type of HWCs and any species (Chapter 2). This HWC assessment scheme was used in four different study areas located in two African countries (South Luangwa/Zambia (SL), Tarangire/Tanzania (TA)) and two Asian countries (Bardia/Nepal (BA) and Manas/India (MA)). This scheme ran for six consecutive years (2009 to 2014) for Zambia, Nepal and India and two years (2010 to 2011) for Tanzania. To carry out the assessments, I trained local HWC officers (Awely Red Caps) to assess HWCs by field observations (measurement of damage, identification of species through signs of presence, landscape attributes etc.) and interviews with aggrieved parties (socio economic data). Results of this assessment are presented in Chapters 2-4.
To determine whether elephants prefer or avoid specific crop species, two field experiments were carried out, one in SL and one in BA (Chapter 5 and 6). For this, two test plots were set up and damage by elephants (and other herbivores) were quantified.
Within this doctoral thesis, 3306 damage events of 7408 aggrieved parties were analysed. In three out of the four study areas (SL, BA, MA), elephants caused the highest number of damage events compared to all other wildlife species, however, in TA, most fields were damaged by zebra. Furthermore, the greater one-horned rhino, hippopotamus, wild boar, bushpig, deer and antelope, as well as primates, caused damage to fields and harvests. Damage to houses and other property were nearly exclusively caused by elephants.
With this doctoral thesis I was able to show that season, crop availability, type and the phenological stage of the crop played an important role for crop damaging behavior of herbivores (Chapter 2). Elephants especially damaged rice, maize and wheat and preferred all crop types in a mature stage of growth. In contrast, rhinos preferred wheat to rice and similar to antelope and deer, they preferred crops at earlier stages of growth, before ripening. Crop damage by wildlife species varied strongly in size; most damages fell below 40% of the total harvest per farmer, but in several cases (3 to 8% depending on the study area), harvests were completely destroyed. Interestingly, during times of low nutritional availability in the natural habitat (dry season), crop damages in all four study areas were significantly less than during other seasons.
In all four study areas, crop protection strategies, such as active guarding in the fields, chasing wildlife with noise or fire torches or erecting barriers, were used. In some cases protection strategies were combined. Analysis of data revealed that traditional protection strategies did not reduce the costs of damage (Chapter 3). In some cases, costs of damage, on protected fields were even higher than for unprotected fields. Only in MA did strategic and cohesive guarding significantly reduce crop damage by wildlife species.
Besides damage in the fields, elephants also caused damage to properties in the villages. In search for stored staple crops, they damaged houses, grain stores and kitchens. Such damage was analysed in three study areas (SL, BA, MA) (Chapter 4). Although property damage occurred less frequently compared to crop damage in the fields, the mean cost of this damage was found to be double in BA/MA and four times higher in SL, compared to the costs of crop damage in the fields. It is further remarkable that property damage significantly increased towards the dry season, when the harvest was brought into the villages.
The findings of this study underpin the assumption that wildlife herbivores, especially elephants, are lured to fields and crops because the highly nutritional food (crop) being readily available. Traditional crop protection is cost and labour intensive and does not reduce the costs of damage. For this reason, crop types, which are thought to be not consumed by elephants were systematically tested on their attractiveness in field experiments in SL and BA (Chapter 5 and 6). In SL, lemon grass, ginger and garlic were proven to be less attractive to African elephants than maize and in BA, basil, turmeric, chamomile, coriander, mint, citronella and lemon grass were found to be less attractive to Asian elephants than rice.
The results of this doctoral thesis are relevant for the management of wildlife conservation as they can lead to new approaches to the mitigation of HWCs in African and Asian countries. Finally, specific needs for more scientific research in this field have been identified.
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization
(2017)
The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobionts, with around 21% of all fungal species participating in lichen symbioses that can be facultative or obligate. Lichenization is furthermore evolutionary old, with fossil evidence for lichens reaching back 415 million years. For an individual fungal lineage, the Lecanoromycetes, the lichenization happened around 300 million years ago. This longstanding symbiotic relationship and the diversity of observed symbiotic dependency make them promising models to study the genomic consequences that follow the establishment of symbioses. Despite this, only little is known about the genomic effects of lichenization and extreme symbiotic dependency. To fill this gap we sequenced the hologenome of the lichen Lasallia pustulata, where the mycobiont could so far not been cultivated, suggesting that it might be more dependent on its symbionts.
As the poor culturability of lichen symbionts renders their genomes inaccessible to standard sequencing practices, we evaluated the extent to which different metagenome sequencing- and de novo assembly-strategies can be used to sequence and reconstruct the genomes of the individual symbionts. We find that the abundances of individual genomes present in the L. pustulata hologenome vary substantially, with the mycobiont being most abundant. Using in silico generated data sets and real Illumina sequencing data for L. pustulata we observe that the skewed abundances prevent a contiguous assembly of the underrepresented genomes when using only short-read sequencing. We conclude that short-read sequencing can offer first insights into lichen hologenomes. The fragmentation of the reconstructions hinders downstream analyses into the genomic consequences of lichenization though, as these are focused on identifying the gain and loss of genes.
We thus demonstrate a hybrid genome assembly strategy that is based on both short- and long-read sequencing. We show that this strategy is capable of creating highly contiguous genome reconstructions, not only for the L. pustulata mycobiont but also its photobiont Trebouxia sp., along with substantial amounts of the bacterial microbiome. A subsequent analysis of the microbiome of L. pustulata – performed over nine different samples collected in Germany and Italy – showed a stable taxonomic composition across the geographic range. We find that Acidobacteriaceae, which are known to thrive in nutrient poor habitats, are the dominant taxa. These would make them well adapted for the co-habitation with L. pustulata, which largely grows on rocks. Whether the Acidobacteriaceae are functionally involved in the lichen symbiosis is unclear so far.
As further comparative genomic studies rely on comprehensive genome annotations, we evaluate the completeness and fidelity of the gene annotations for the mycobiont L. pustulata as well as four further Lecanoromycetes. This reveals that un- and mis-annotated genes impact all evaluated genomes, with artificially joined genes and unannotated genes having the largest impact. In addition to these factors we find that the sequence composition – especially G/C-rich inverted repeats – lead to sequencing errors that interfere with the gene prediction. We minimize the effects of these artifacts through a rigorous curation.
Given the extremely sparse taxon sampling of available green alga genomes, we focus our search for the genomic footprints of lichenization on the mycobionts. We compare the genomes of the Lecanoromycetes to their closest relatives, the Eurotiomycetes and Dothideomycetes. This reveals that the last common ancestor of the Lecanoromycetes has lost around 10% of its genes after they split from the non-lichenized ancestor they share with the Eurotiomycetes. These losses are furthermore enriched, showing an excessive loss of genes involved with the degradation of polysaccharides. The loss of these genes fits a change from an ancestral saprotrophic lifestyle that depends on degrading complex plant matter, to the symbiotic lifestyle that relies on simpler nutrients provided by the photobionts. While the last common ancestor of the Lecanoromycetes additionally gained around 400 genes these could so far not be further characterized due to a lack of functionally annotated reference data.
As the mycobiont L. pustulata could so far not been grown in axenic culture, we initially expected to find an extensive genomic remodeling compared to the other mycobionts that easily grow in culture. We do not find evidence for this. Analyzing both the contraction of gene families and the loss of genes, we observe that L. pustulata and Umbilicaria muehlenbergii – its close relative that is easily grown in culture – share most of these. Furthermore, L. pustulata does not show an excessive loss of evolutionary old and well-conserved genes. These effects are mirrored on the functional level, as neither gene family contractions nor gene losses show a functional enrichment. This is partially due to the lack of functional reference data, analogous to the genes gained in the Lecanoromycetes, rendering their characterization hard. Thus, further studies on the genomic consequences of lichenization and differences in symbiotic dependence will have to be conducted, including larger taxon sets. This will be even more important for the photobionts, as the Chlorophyta are even more sparsely sampled today, hindering an effective functional and evolutionary study.