570 Biowissenschaften; Biologie
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- Orthologous Matrix (OMA) Project (2)
- Outcrossing (2)
- Outcrossing rate (2)
- Outdoor enclosure (2)
- PBPK (2)
- PC-3 cells (2)
- PEI coating (2)
- PKS (2)
- PUFA (2)
- Palaeogenetics (2)
- Paläoökologie (2)
- Parasit (2)
- Parasitoid wasp (2)
- Partial Little Square (2)
- Partnership (2)
- Paternity analysis (2)
- Pathway design (2)
- Periphyton (2)
- Personality (2)
- Pex1 (2)
- Pex6 (2)
- Pflanze (2)
- Pflanzengemeinschaften (2)
- Pflanzenwachstum (2)
- Pflanzenökologie (2)
- Phase variation (2)
- Phosphat (2)
- Photosynthesis (2)
- Phylogenetics (2)
- Phylogenie (2)
- Phylogenomics (2)
- Pichia pastoris (2)
- Pipistrellus nathusii (2)
- Plankton (2)
- Plant community model (2)
- Plant development (2)
- Plant-soil feedback (2)
- Plants (2)
- Plasma membrane (2)
- Poecilia formosa (2)
- Poecilia latipinna (2)
- Polyadenylierung (2)
- Polyelektrolyt-Multischichten (2)
- Polysaccharide (2)
- Population dynamics (2)
- Predator-prey interactions (2)
- Pregnancy (2)
- Priming (2)
- Promiscuous enzymes (2)
- Protein (2)
- Proteinaggregation (2)
- Proteins (2)
- Pseudomonas aeruginosa (2)
- Pseudomonas syringae (2)
- Puumala virus seroprevalence (2)
- QDs (2)
- QTL mapping (2)
- R Shiny (2)
- RNA (2)
- RNA interference (2)
- RNA virus (2)
- RNA-guided Cas9 (2)
- RUNX2 (2)
- Randomized-controlled trial (2)
- Raphidiopsis (2)
- Recombination (2)
- Redox marker (2)
- Redoxreaktion (2)
- Rhizophagus irregularis (2)
- Rice (2)
- Riesenvesikel (2)
- Rodent (2)
- Roridula gorgonias (2)
- Rotifera (2)
- RpoS (2)
- RubisCO (2)
- Russia (2)
- S-XRF (2)
- SELEX (2)
- SERS enhancement factor (2)
- SFON (2)
- SIMS techniques (2)
- SPB (2)
- SWL (2)
- Saccharomyces cerevisiae (2)
- Sailfin molly (2)
- Salmonella (2)
- Salmonella Typhimurium (2)
- Saprolegnia (2)
- Saprolegniaceae (2)
- Savannas (2)
- Savanne (2)
- Schwefel (2)
- Scopoletin (2)
- Seasonality (2)
- Sediment (2)
- Senescence (2)
- Sequenzierung der nächsten Generation (2)
- Serine cycle (2)
- Sexual selection (2)
- Siberian tree line (2)
- Sibirien (2)
- Simulation (2)
- Smpd1 (2)
- Soil function (2)
- Solanaceae (2)
- Solanum lycopersicum (2)
- Solanum tuberosum (2)
- Space use (2)
- Specific wood density (2)
- Strategic growth adjustment (2)
- Stress (2)
- Sundaland (2)
- Sus scrofa (2)
- Systems Biology (2)
- Säugetiere (2)
- TEM (2)
- TMS (2)
- TTR (2)
- Tailspike protein (2)
- Tanzania (2)
- Temperate forest (2)
- Tenebrio molitor larvae (2)
- Toll and Imd pathways (2)
- Tomato (2)
- Transcription factors (2)
- Transcriptional memory (2)
- Transcriptome assembly (2)
- Transporters (2)
- Tree allometry (2)
- Turkey (2)
- TusA (2)
- Type 2 Diabetes (2)
- UV radiation (2)
- Ulcerative colitis (2)
- Urbanization (2)
- Ursus arctos (2)
- Venom proteins (2)
- Verkhoyansk mountains (2)
- Virus (2)
- Walker A motif (2)
- Wastewater (2)
- Weakly electric fish (2)
- Weißstorch (2)
- Wildschwein (2)
- Wind (2)
- Wood specific gravity (2)
- Woody aboveground biomass (2)
- X-ray structure (2)
- XMRV (2)
- Xpr1 (2)
- Yap1/Wwtr1 (Taz) (2)
- Zebrafish (2)
- Zellweger (2)
- Zellweger syndrome spectrum disorder (ZSSD) (2)
- Zinypr-1 (2)
- Zytoskelett (2)
- aberrations (2)
- accelerometer (2)
- acclimation (2)
- acid mine drainage (2)
- acoustic communication (2)
- actin polymerization (2)
- activated carbon (2)
- activator–inhibitor models (2)
- adaptive introgression (2)
- adaptive processes (2)
- adaptive radiation (2)
- adiponectin (2)
- adiposity (2)
- age (2)
- agricultural landscape (2)
- agrin (2)
- agro-infiltration (2)
- agroecology (2)
- aldehyde oxidoreductase (2)
- alignment (2)
- alignment sensitivity / specificity (2)
- alkylphospholipids (2)
- all-cause mortality (2)
- allocation (2)
- alphaherpesvirus (2)
- alternative splicing (2)
- amino acid (2)
- amino acids (2)
- amphibians (2)
- animal cognition (2)
- animal migration (2)
- anthropogenic environment (2)
- anthropogenic food subsidies (2)
- anthropometric measures (2)
- anti-oxidative response (2)
- antibody producing cell selection (2)
- antioxidant capacity (2)
- anxiety-like behavior (2)
- aphids (2)
- apis mellifera (2)
- apple (2)
- aquatic ecosystems (2)
- aqueous dispersion (2)
- aqueous-solution (2)
- arable land (2)
- arable weeds (2)
- arbuscular mycorrhizal symbiosis (2)
- archival DNA (2)
- area-based conservation (2)
- arsenic (2)
- arthropod (2)
- artificial light at night (ALAN) (2)
- ascorbate peroxidase (2)
- assembly (2)
- assembly processes (2)
- assembly rules (2)
- atomic force microscopy (2)
- autocorrelation (2)
- automated radio telemetry (2)
- axillary bud (2)
- baltic sea (2)
- basal body (2)
- base excision repair (incision activity) (2)
- bat fatalities (2)
- behavioral plasticity (2)
- behavioral type (2)
- behaviour (2)
- behavioural syndrome (2)
- beta diversity (2)
- bias (2)
- bifurcation (2)
- bifurcation theory (2)
- biodiversity conservation (2)
- biodiversity decline (2)
- biodiversity exploratories (2)
- biodiversity facets (2)
- biofortification (2)
- biogenic amine (2)
- biological age (2)
- biological control (2)
- biological invasions (2)
- biological soil crusts (2)
- biomarker detection (2)
- biomaterials (2)
- biomimetic sensors (2)
- biophysics (2)
- biosensors (2)
- biosignatures (2)
- biostimulant (2)
- biosynthesis (2)
- biotic filtering (2)
- biotin sulfoxide reductase (2)
- bird migration (2)
- bisphosphonates (2)
- body composition (2)
- body proportions (2)
- bone mineral density (2)
- bone pathologies (2)
- brackish waters (2)
- brain insulin signaling (2)
- branched chain amino acids (2)
- branching (2)
- breeding (2)
- buffer zones (2)
- bush encroachment (2)
- cTBS (2)
- cadmium-free (2)
- caffeine (2)
- calcination (2)
- calcite (2)
- calcium (2)
- calcium carbonate inclusions (2)
- calcium influx (2)
- canalization (2)
- cancer epidemiology (2)
- capture enrichment (2)
- carbohydrates (2)
- carbon dots (2)
- carbon isotopes (2)
- carbon labeling (2)
- cardiac development (2)
- cardiomyocyte (2)
- cardiomyogenic differentiation (2)
- carotenoid biosynthesis (2)
- carrion ecology (2)
- cascading effects (2)
- catalase (2)
- cave fish (2)
- cell shape (2)
- cells (2)
- cellular bioenergetics (2)
- cellular bioimaging (2)
- cellular signalling (2)
- cellulose polymeric organic matter (2)
- cerami-des (2)
- ceramides (2)
- cereal leaf beetle (2)
- cereal meals (2)
- child growth (2)
- chimeric transcription factors (2)
- chlamydomonas (2)
- chlorophyll a (2)
- chloroplast (2)
- chronic diseases (2)
- chytridiomycota (2)
- cis-regulatory evolution (2)
- climate adaptation (2)
- climate dynamics (2)
- climate extremes (2)
- climate warming (2)
- co-expression (2)
- co-limitation (2)
- codon usage (2)
- coefficient (2)
- coffee by-products (2)
- cold stress (2)
- collagen (2)
- colony viability (2)
- common‐garden experiment (2)
- community composition (2)
- community model (2)
- community structure (2)
- community theory (2)
- competition–defense trade‐off (2)
- comprehensive analysis (2)
- concepts (2)
- confocal microscopy (2)
- conformational change (2)
- conformational rearrangement (2)
- congeneric species (2)
- conscripts (2)
- constitutive activity (2)
- constraint-based modeling (2)
- converting factor (2)
- copper complex (2)
- copper(II) (2)
- copper-related disorders (2)
- cord blood (2)
- core shell UCNP (2)
- cori cycle (2)
- cortisol (2)
- counting (2)
- coviability analysis (2)
- crop diversity (2)
- cropping system (2)
- cross-species capture (2)
- cryolithology (2)
- cryptomycota (2)
- cyanobacterial bloom (2)
- cyanobacterial sucrose-phosphatase (2)
- cyclic AMP (2)
- cytochrome c (2)
- cytoplasmic polyadenylation (2)
- cytosine methylation (2)
- cytosolic tRNA thiolation (2)
- cytotoxicity (2)
- dark virus (2)
- data integration (2)
- ddRAD (2)
- de novo genome assembly (2)
- dead Cas9 (2)
- decline (2)
- defense against predation (2)
- defensive symbiosis (2)
- degraded DNA (2)
- dehydration (2)
- demographic noise (2)
- depressive-like behavior (2)
- desiccation (2)
- design of experiment (2)
- developing brain (2)
- developmental canalization (2)
- developmental dyslexia (2)
- developmental plasticity (2)
- diacylglycerol (2)
- dietary patterns (2)
- dietary restriction (2)
- differential expression analysis (2)
- digestive enzymes quantification (2)
- dimerization of 4-nitrothiophenol (2)
- dispersal filtering (2)
- diversity profiles (2)
- dominance effect (2)
- droughts (2)
- drug delivery (2)
- drug metabolism (2)
- drug release (2)
- dynamic equilibrium (2)
- eastern continental Asia (2)
- eavesdropping (2)
- echolocation (2)
- ecophysiology (2)
- ecosystem services provisioning (2)
- education (2)
- effectors (2)
- egg ratio (2)
- eicosapentaenoic acid (2)
- electric fish (2)
- electroencephalography (EEG) (2)
- electron paramagnetic resonance (2)
- electronic tool integration (2)
- emotional imagery (2)
- emotions (2)
- endocardium (2)
- endotoxin (2)
- energy expenditure (2)
- enrichment experiments (2)
- entropy (2)
- environmental DNA (2)
- environmental genomics (2)
- environmental noise (2)
- enzymology (2)
- epidemiology (2)
- epigenetic variation (2)
- epiphytes (2)
- epithionitrile (2)
- epitope prediction (2)
- epizoochory (2)
- equalizing and stabilizing mechanisms (2)
- error reduction (2)
- establishment (2)
- event coincidence analysis (2)
- evolutionary ecology (2)
- evolutionary rescue (2)
- exploitation (2)
- expression profile (2)
- extinction (2)
- extinction drivers (2)
- extra-cytoplasmic pockets (2)
- extracellular DNA (2)
- extracellular enzymes (2)
- extracellular matrix (2)
- extracellular signaling (2)
- eye-tracking (2)
- facilitation (2)
- fatty acid changes (2)
- feeding (2)
- feeding behaviour (2)
- fence interaction (2)
- fertilization (2)
- fetal origins hypothesis (2)
- fisheries (2)
- fitness gradient (2)
- fitness response (2)
- floating mat (2)
- flooded grasslands (2)
- floral scent (2)
- fluorescent probe (2)
- food frequency questionnaire (2)
- food web dynamics (2)
- food webs (2)
- forage availability (2)
- forage gaps (2)
- foraging (2)
- foraging behaviour (2)
- forebrain (2)
- forest management (2)
- forestREplot (2)
- formaldehyde assimilation (2)
- formate dehydrogenase (2)
- fractionation (2)
- fractionation factors (2)
- free zinc (2)
- freshwater algae (2)
- freshwater heterotrophic bacteria (2)
- functional complementation (2)
- functional inhibitors of acid sphin-gomyelinase (2)
- functional response (2)
- functional richness (2)
- fungal diversity (2)
- fungal pathogens (2)
- funktionelle Diversität (2)
- gamma diversity (2)
- gas-production (2)
- gene delivery (2)
- gene regulation (2)
- generalized dissimilarity modelling (2)
- genetic accommodation (2)
- genetic adaptation (2)
- genetic rescue (2)
- genetic screen (2)
- genetischer Screen (2)
- genome (2)
- genome scan (2)
- genomic prediction (2)
- geo-bio interaction (2)
- geographic distribution (2)
- glacial maximum (2)
- global and regional change (2)
- glucocorticoid receptor (2)
- glucose (2)
- glucosinolate hydrolysis (2)
- glutathione (2)
- glutathione peroxidase (2)
- glycine cleavage system (2)
- governance (2)
- gross primary production (2)
- groundwater (2)
- groundwater recharge (2)
- growth behavior (2)
- growth restriction (2)
- guard cell (2)
- gwas (2)
- habitat (2)
- habitat selection (2)
- habitat use (2)
- habituation (2)
- hantavirus (2)
- heart regeneration (2)
- heat (2)
- heat shock protein (2)
- heliozoa (2)
- hepcidin-25 (2)
- hilly loes plateau (2)
- histone modification (2)
- holding capability (2)
- holding isometric muscle action (HIMA) (2)
- holocene (2)
- honey bees (2)
- hoverflies (2)
- human aldehyde oxidase (2)
- human endotoxemia (2)
- human excised skin (2)
- human introduction (2)
- human-wildlife conflict (2)
- hybridoma (2)
- hydrogels (2)
- hyena (2)
- hyperoxia (2)
- hypertension (2)
- hyperthermia (2)
- hypoxia (2)
- identification (2)
- immunoassay (2)
- immunogenicity (2)
- in silico (2)
- in vitro intestinal model (2)
- in-vitro-synthesis (2)
- inbreeding depression (2)
- indirect facilitation (2)
- individual based modeling (2)
- individual-based modeling (2)
- infancy (2)
- infiltration (2)
- inhibition (2)
- inner-mongolia (2)
- insects (2)
- integrated assessments (2)
- inter-brain synchronization (2)
- inter-muscle-brain synchronization (2)
- interpersonal muscle action (2)
- interspecific interactions (2)
- intestinal mucins (2)
- intestinal zinc resorption (2)
- intra-organ-communication (2)
- intraguild predation (2)
- intraspecific variation (2)
- invasibility (2)
- invasion success (2)
- invasive species (2)
- ion mobility spectrometry (2)
- ion-exchange chromatography (2)
- ionic liquid (2)
- ionic strength (2)
- ionogel (2)
- iron-sulfur clusters (2)
- island biogeography (2)
- island disharmony (2)
- island syndromes (2)
- islands (2)
- isomerization (2)
- jasmonate (2)
- kelp (2)
- l-cysteine desulfurase (2)
- lake monitoring (2)
- lake periphyton (2)
- land sharing vs. land sparing (2)
- land use change (2)
- land-use change (2)
- landscape diversity (2)
- landscape generator (2)
- landscape homogenization (2)
- late pleistocene (2)
- later health (2)
- lichens (2)
- life cycle (2)
- life‐history traits (2)
- ligand exchange (2)
- light adaptation (2)
- light variability (2)
- limits (2)
- lipid classes (2)
- lipid limitation thresholds (2)
- lipid membranes (2)
- lipidomics (2)
- lipid–lipid interactions (2)
- lipoplexes (2)
- loci (2)
- lokale Anpassung (2)
- longitudinal (2)
- low-energy electrons (2)
- luminescence (2)
- lysosomal hydrolases (2)
- lysosomal storage disorders (2)
- lysosome (2)
- mRNA degradation (2)
- magnitude estimation (2)
- maintenance (2)
- maintenance of functional diversity (2)
- maintenance of genomic integrity (2)
- major histocompatibility complex (2)
- male Daphnia (2)
- maltooligosaccharides (2)
- mammalian-cells (2)
- manganese (2)
- manual muscle test (2)
- many-to-one genotype–phenotype map (2)
- mapping (2)
- mass conservation (2)
- mass index (2)
- mate-pairs (2)
- mathematical modelling (2)
- mathematical precursor (2)
- maturation (2)
- meal timing (2)
- mechanical (2)
- mechanical strength (2)
- mechanisms (2)
- mechanomyography (MMG) (2)
- mediated delivery (2)
- membrane biophysics (2)
- membrane fusion (2)
- membrane microdomains (2)
- membrane protein (2)
- membrane stabilization (2)
- memory (2)
- mercaptocarboxylic acids (2)
- mesenchymal stem cells (2)
- mesophyll cell (2)
- messenger-rna polyadenylation (2)
- meta-analysis (2)
- metabolic syndrome (2)
- metabolic-profiling (2)
- metabolische Netzwerke (2)
- metagenome (2)
- metagenomic analysis (2)
- metagenomics 2.0 (2)
- metal complex (2)
- metal peptide (2)
- metallopeptide (2)
- metalloprotein (2)
- methane (2)
- methane oxidation (2)
- methylotrophy (2)
- microarrays (2)
- microbial activity (2)
- microbial communities (2)
- microbiome (2)
- microbiota (2)
- microclimate (2)
- microcomputed tomography (2)
- microeukaryotes (2)
- microfluidics (2)
- microstructure (2)
- microtubule-organization (2)
- mining lakes (2)
- mitochondrial genome (mtDNA) (2)
- mitogenomes (2)
- mixed cultures (2)
- model (2)
- model integration (2)
- model limitations (2)
- models (2)
- modern coexistence theory (2)
- mojave desert (2)
- molecular dynamics simulations (2)
- molecular evolution (2)
- molecular species identification (2)
- molecularly imprinted polymers (2)
- molybdoenzyme (2)
- molybdopterin synthase (2)
- morphology (2)
- mouse (2)
- movement speed (2)
- mowing (2)
- mucus layer (2)
- multidrug resistance (2)
- multiple sclerosis (2)
- multishell (2)
- multivalence (2)
- multi‐ year flooding cycle (2)
- musicality (2)
- mutation (2)
- mutual information (2)
- myocardial infarction (2)
- myocardium (2)
- myoglobin (2)
- n-alkanes (2)
- n-oxide reductase (2)
- nachhaltige Landnutzung (2)
- nanoelectrodes (2)
- nanogels (2)
- native American ancestry (2)
- nature conservation (2)
- necrobiome (2)
- neophilia (2)
- neophobia (2)
- net primary productivity (2)
- network analysis (2)
- network reconstruction (2)
- neurodegeneration (2)
- neurodegenerative diseases (2)
- neuroendocrine (2)
- neuromuscular adaptation (2)
- niche and fitness differences (2)
- niche width (2)
- nickel (2)
- nitrile (2)
- nitrogen fixation (2)
- nitrogen limitation (2)
- nitrous-oxide (2)
- noise color (2)
- non-linear dynamics (2)
- nonlinear waves (2)
- nuclear pore complex (2)
- nucleolus (2)
- nucleoporins (2)
- nucleus-associated body (2)
- number knowledge (2)
- nutrient (2)
- nutrient availability (2)
- nutrient spike (2)
- nutrient transport (2)
- octopamine (2)
- odd chain fatty acids (2)
- oil palm (2)
- omics (2)
- ontogeny (2)
- ordinary differential equation (2)
- organ size (2)
- organic compounds adsorption (2)
- organic matter (2)
- organic–inorganic hybrid (2)
- organisches Material (2)
- osmotic-pressure (2)
- osteoporosis (2)
- other-race effect (2)
- outbreeding depression (2)
- overhunting (2)
- overweight (2)
- oxidase (2)
- oxidative stress tolerance (2)
- pH (2)
- pace-of-life syndrome (2)
- paleoenvironmental records (2)
- parameter estimation (2)
- parameters (2)
- paraquat (2)
- parasites (2)
- parasitoid (2)
- parchment (2)
- parentage (2)
- partial correlation (2)
- participatory research (2)
- pathogens (2)
- pathway engineering (2)
- pattern formation (2)
- performance (2)
- perialpine lakes (2)
- periphyton (2)
- periplasmic nitrate reductase (2)
- phagocytosis (2)
- phase transfer (2)
- phenotypic phase plane (2)
- phenotyping (2)
- phloem (2)
- phloem proteins (2)
- phonotaxis (2)
- phosphate (2)
- phosphatidylserine (2)
- phosphoglucan (2)
- photoresponse (2)
- physical and physiological dormancy (2)
- physiology (2)
- phytoplankton host (2)
- plant Mediator (2)
- plant adaptation (2)
- plant clonality (2)
- plant ecology (2)
- plant invasion (2)
- plant macro-fossils (2)
- plant macrofossil data (2)
- plant naturalization (2)
- plant strategies (2)
- plant–soil feedback (2)
- plasma measurements (2)
- plastic-associated biofilms (2)
- plastid transformation (2)
- plastidial phosphorylase (2)
- platelets (2)
- playback (2)
- pleasant and unpleasant imagery (2)
- polarization (2)
- poly(ADP-ribosyl)ation (2)
- poly(a)-binding protein (2)
- polyadenylation (2)
- polyamide (2)
- polyethylene (2)
- polymer degradation (2)
- polyphenols (2)
- polysulfide (2)
- population delimitation (2)
- population genetics (2)
- population viability analysis (2)
- population-specific risk marker (2)
- positive selection (2)
- postglacial recolonization (2)
- potential-functions (2)
- pre-school (2)
- preadaptation (2)
- precuneus (2)
- predator (2)
- predator–prey cycles (2)
- pregnancy (2)
- preterm infants (2)
- primary metabolism (2)
- prior knowledge (2)
- probiotics (2)
- production (2)
- progenitor cells (2)
- proline (2)
- promiscuous (2)
- properties (2)
- prostaglandin E2 (2)
- protein aggregation (2)
- protein restriction (2)
- protein-carbohydrate interactions (2)
- protein-protein interaction (2)
- proteostasis (2)
- provitamin A (2)
- psychosocial stress (2)
- pubertal timing (2)
- public health (2)
- pulse perturbation (2)
- purifying selection (2)
- purity (2)
- pushing isometric muscle action (PIMA) (2)
- pyridoxal-50-phosphate (2)
- pyruvate (2)
- quality (2)
- quantification (2)
- quantum dots (2)
- questioning solutions (2)
- racemization (2)
- radiocarbon (2)
- radiocarbon dating (2)
- rain event depth (2)
- random forest (2)
- range size (2)
- rat (2)
- reaction norms (2)
- reciprocal transplant experiment (2)
- recombinant inbred line population (2)
- redfield ratio (2)
- redox (2)
- redox polymer (2)
- reference material (2)
- regime shift (2)
- regulate gene expression (2)
- reliability (2)
- repetition (2)
- repetitive elements (2)
- reproducibility (2)
- reserve design (2)
- resistin (2)
- resonance energy transfer (2)
- resource-tracking (2)
- respiration (2)
- responses (2)
- reveals (2)
- reversed-phase chromatography (2)
- reversible shape-memory actuator (2)
- rhizopods (2)
- rhodobacter-capsulatus (2)
- rhythm perception (2)
- rhythmic grouping (2)
- risk management cycle (2)
- robustness (2)
- rodent (2)
- root morphology (2)
- rooting depth (2)
- salicylic-acid (2)
- saliva (2)
- sarcopenia (2)
- scaffolding (2)
- scale-dependency (2)
- scaled mass index (2)
- scaling (2)
- school mathematics (2)
- seawater (2)
- secondary metabolites (2)
- secular changes (2)
- seed mass (2)
- selection (2)
- selenium (2)
- selenoneine (2)
- selfing syndrome (2)
- semi-closed mitosis (2)
- senescence (2)
- sequence dependence (2)
- sequence-structure-function relationship (2)
- sequencing error (2)
- serine palmitoyltransferase (2)
- serum (2)
- sex (2)
- sexual selection (2)
- sexual species (2)
- shoot apical meristem (2)
- shrub size (2)
- shrub-encroachment (2)
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The study of biological interaction networks is a central theme in systems biology. Here, we investigate common as well as differentiating principles of molecular interaction networks associated with different levels of molecular organization. They include metabolic pathway maps, protein-protein interaction networks as well as kinase interaction networks. First, we present an integrated analysis of metabolic pathway maps and protein-protein interaction networks (PIN). It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzyme complexes. Inspecting high-throughput PIN data, it has been shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In this study, we expanded this line of research to include comparisons of the respective underlying network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and hence might be essential for the structural integrity of several biosynthetic systems. Besides metabolic aspects of PINs, we investigated the characteristic topological properties of protein interactions involved in signaling and regulatory functions mediated by kinase interactions. Characteristic topological differences between PINs associated with metabolism, and those describing phosphorylation networks were revealed and shown to reflect the different modes of biological operation of both network types. The construction of phosphorylation networks is based on the identification of specific kinase-target relations including the determination of the actual phosphorylation sites (P-sites). The computational prediction of P-sites as well as the identification of involved kinases still suffers from insufficient accuracies and specificities of the underlying prediction algorithms, and the experimental identification in a genome-scale manner is not (yet) doable. Computational prediction methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding P-sites. However the recognition of such motifs by the respective kinases is a spatial event. Therefore, we characterized the spatial distributions of amino acid residue types around P-sites and extracted signature 3D-profiles. We then tested the added value of spatial information on the prediction performance. When compared to sequence-only based predictors, a consistent performance gain was obtained. The availability of reliable training data of experimentally determined P-sites is critical for the development of computational prediction methods. As part of this thesis, we provide an assessment of false-positive rates of phosphoproteomic data.
Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics
(2008)
Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40% of TSP for Pal and 20% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.
Adenylates are metabolites with essential function in metabolism and signaling in all living organisms. As Cofactors, they enable thermodynamically unfavorable reactions to be catalyzed enzymatically within cells. Outside the cell, adenylates are involved in signalling processes in animals and emerging evidence suggests similar signaling mechanisms in the plants’ apoplast. Presumably, apoplastic apyrases are involved in this signaling by hydrolyzing the signal mediating molecules ATP and ADP to AMP. This PhD thesis focused on the role of adenylates on metabolism and development of potato (Solanum tuberosum) by using reverse genetics and biochemical approaches. To study the short and long term effect of cellular ATP and the adenylate energy charge on potato tuber metabolism, an apyrase from Escherichia coli targeted into the amyloplast was expressed inducibly and constitutively. Both approaches led to the identification of adaptations to reduced ATP/energy charge levels on the molecular and developmental level. These comprised a reduction of metabolites and pathway fluxes that require significant amounts of ATP, like amino acid or starch synthesis, and an activation of processes that produce ATP, like respiration and an immense increase in the surface-to-volume ratio. To identify extracellular enzymes involved in adenylate conversion, green fluorescent protein and activity localization studies in potato tissue were carried out. It was found that extracellular ATP is imported into the cell by an apoplastic enzyme complement consisting of apyrase, unspecific phosphatase, adenosine nucleosidase and an adenine transport system. By changing the expression of a potato specific apyrase via transgenic approaches, it was found that this enzyme has strong impact on plant and particular tuber development in potato. Whereas metabolite levels were hardly altered, transcript profiling of tubers with reduced apyrase activity revealed a significant upregulation of genes coding for extensins, which are associated with polar growth. The results are discussed in context of adaptive responses of plants to changes in the adenylate levels and the proposed role of apyrase in apoplastic purinergic signaling and ATP salvaging. In summary, this thesis provides insight into adenylate regulated processes within and outside non-photosynthetic plant cells.
In order to function properly, organisms have a complex control mechanism, in which a given gene is expressed at a particular time and place. One way to achieve this control is to regulate the initiation of transcription. This step requires the assembly of several components, i.e., a basal/general machinery common to all expressed genes, and a specific/regulatory machinery, which differs among genes and is the responsible for proper gene expression in response to environmental or developmental signals. This specific machinery is composed of transcription factors (TFs), which can be grouped into evolutionarily related gene families that possess characteristic protein domains. In this work we have exploited the presence of protein domains to create rules that serve for the identification and classification of TFs. We have modelled such rules as a bipartite graph, where families and protein domains are represented as nodes. Connections between nodes represent that a protein domain should (required rule) or should not (forbidden rule) be present in a protein to be assigned into a TF family. Following this approach we have identified putative complete sets of TFs in plant species, whose genome is completely sequenced: Cyanidioschyzon merolae (red algae), Chlamydomonas reinhardtii (green alga), Ostreococcus tauri (green alga), Physcomitrella patens (moss), Arabidopsis thaliana (thale cress), Populus trichocarpa (black cottonwood) and Oryza sativa (rice). The identification of the complete sets of TFs in the above-mentioned species, as well as additional information and reference literature are available at http://plntfdb.bio.uni-potsdam.de/. The availability of such sets allowed us performing detailed evolutionary studies at different levels, from a single family to all TF families in different organisms in a comparative genomics context. Notably, we uncovered preferential expansions in different lineages, paving the way to discover the specific biological roles of these proteins under different conditions. For the basic leucine zipper (bZIP) family of TFs we were able to infer that in the most recent common ancestor (MRCA) of all green plants there were at least four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. Currently, following the approach described above, up to 57 TF and 11 TR families can be identified, which are among the most numerous transcription regulatory families in plants. Three families of putative TFs predate the split between rhodophyta (red algae) and chlorophyta (green algae), i.e., G2-like, PLATZ, and RWPRK, and may have been of particular importance for the evolution of eukaryotic photosynthetic organisms. Nine additional families, i.e., ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP, and WRKY, predate the split between green algae and streptophytes. The identification of putative complete list of TFs has also allowed the delineation of lineage-specific regulatory families. The families SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA significantly differ in size between algae and land plants. The SBP family of TFs is significantly larger in C. reinhardtii, compared to land plants, and appears to have been lost in the prasinophyte O. tauri. The families bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA preferentially expanded with the colonisation of land, and might have played an important role in this great moment in evolution. Later, after the split of bryophytes and tracheophytes, the families MADS, AP2-EREBP, NAC, AUX/IAA, PHD and HRT have significantly larger numbers in the lineage leading to seed plants. We identified 23 families that are restricted to land plants and that might have played an important role in the colonization of this new habitat. Based on the list of TFs in different species we have started to develop high-throughput experimental platforms (in rice and C. reinhardtii) to monitor gene expression changes of TF genes under different genetic, developmental or environmental conditions. In this work we present the monitoring of Arabidopsis thaliana TFs during the onset of senescence, a process that leads to cell and tissue disintegration in order to redistribute nutrients (e.g. nitrogen) from leaves to reproductive organs. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. 76% of these TFs are down-regulated during senescence, the remaining are up-regulated. The identification of TFs in plants in a comparative genomics setup has proven fruitful for the understanding of evolutionary processes and contributes to the elucidation of complex developmental programs.
Understanding the interactions of predators and their prey and their responses to environmental changes is one of the striking features of ecological research. In this thesis, spring dynamics of phytoplankton and its consumers, zooplankton, were considered in dependence on the environmental conditions in a deep lake (Lake Constance) and a shallow marine water (mesocosms from Kiel Bight), using descriptive statistics, multiple regression models, and process-oriented dynamic simulation models. The development of the spring phytoplankton bloom, representing a dominant feature in the plankton dynamics in temperate and cold oceans and lakes, may depend on temperature, light, and mixing intensity, and the success of over-wintering phyto- and zooplankton. These factors are often correlated in the field. Unexpectedly, irradiance often dominated algal net growth rather than vertical mixing even in deep Lake Constance. Algal net losses from the euphotic layer to larger depth were induced by vertical mixing, but were compensated by the input from larger depth when algae were uniformly distributed over the water column. Dynamics of small, fast-growing algae were well predicted by abiotic variables, such as surface irradiance, vertical mixing intensity, and temperature. A simulation model additionally revealed that even in late winter, grazing may represent an important loss factor of phytoplankton during calm periods when losses due to mixing are small. The importance of losses by mixing and grazing changed rapidly as it depended on the variable mixing intensity. Higher temperature, lower global irradiance and enhanced mixing generated lower algal biomass and primary production in the dynamic simulation model. This suggests that potential consequences of climate change may partly counteract each other. The negative effect of higher temperatures on phytoplankton biomass was due to enhanced temperature-sensitive grazing losses. Comparing the results from deep Lake Constance to those of the shallow mesocosm experiments and simulations, confirmed the strong direct effect of light in contrast to temperature, and the importance of grazing already in early spring as soon as moderate algal biomasses developed. In Lake Constance, ciliates dominated the herbivorous zooplankton in spring. The start of ciliate net growth in spring was closely linked to that of edible algae, chlorophyll a and the vertical mixing intensity but independent of water temperature. The duration of ciliate dominance in spring was largely controlled by the highly variable onset of the phytoplankton bloom, and little by the less variable termination of the ciliate bloom by grazing of meta-zooplankton. During years with an extended spring bloom of algae and ciliates, they coexisted at relatively high biomasses over 15-30 generations, and internally forced species shifts were observed in both communities. Interception feeders alternated with filter feeders, and cryptomonads with non-cryptomonads in their relative importance. These dynamics were not captured by classical 1-predator-1-prey models which consistently predict pronounced predator-prey cycles or equilibria with either the predator or the prey dominating or suppressed. A multi-species predator-prey model with predator species differing in their food selectivity, and prey species in their edibility reproduced the observed patterns. Food-selectivity and edibility were related to the feeding and growth characteristics of the species, which represented ecological trade-offs. For example, the prey species with the highest edibility also had the highest maximum growth rate. Data and model revealed endogenous driven ongoing species alternations, which yielded a higher variability in species-specific biomasses than in total predator and prey biomass. This holds for a broad parameter space as long as the species differ functionally. A more sophisticated model approach enabled the simulation of a continuum of different functional types and adaptability of predator and prey communities to altered environmental conditions, and the maintenance of a rather low model complexity, i.e., low number of equations and free parameters. The community compositions were described by mean functional traits --- prey edibility and predator food-selectivity --- and their variances. The latter represent the functional diversity of the communities and thus, the potential for adaptation. Oscillations in the mean community trait values indicated species shifts. The community traits were related to growth and grazing characteristics representing similar trade-offs as in the multi-species model. The model reproduced the observed patterns, when nonlinear relationships between edibility and capacity, and edibility and food availability for the predator were chosen. A constant minimum amount of variance represented ongoing species invasions and thus, preserved a diversity which allows adaptation on a realistic time-span.
Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach. This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL). Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis. The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.
The haemolymph of the adult Colorado potato beetle, Lepinotarsa decemlineata Say, contains a high molecular weight (MW > 200,000) JH-III specific binding protein. The Kd value of the protein for racemic JH-III is 1.3 ± 0.2 × 10−7 M. It has a lower affinity for racemic JH-I and it does not bind JH-III-diol or JH-III-acid. The binding protein does discriminate between the enantiomers of synthetic, racemic JH-III as was determined by stereochemical anaysis of the bound and the free JH-III. Incubation of racemic JH-III with crude haemolymph results in preferential formation of (10S)-JH-III-acid, the unnatural configuration. The JH-esterase present in L. decemlineata haemolymph is not enantioselective. It is concluded that the most important function of the binding protein is that of a specific carrier, protecting the natural hormone against degradation by esterases. The carrier does not protect JH-I as efficiently as the lower homologue.
The site of confluence of the artery and the portal vein in the liver still appears to be controversial. Anatomical studies suggested a presinusoidal or an intrasinusoidal confluence in the first, second or even final third of the sinusoids. The objective of this investigation was to study the problem with functional biochemical techniques. Rat livers were perfused through the hepatic artery and simultaneously either in the orthograde direction from the portal vein to the hepatic vein or in the retrograde direction from the hepatic vein to the portal vein. Arterial how was linearly dependent on arterial pressure between 70 cm H2O and 120 cm H2O at a constant portal or hepatovenous pressure of 18 cm H2O. An arterial pressure of 100 cm H2O was required for the maintenance of a homogeneous orthograde perfusion of the whole parenchyma and of a physiologic ratio of arterial to portal how of about 1:3. Glucagon was infused either through the artery or the portal vein and hepatic vein, respectively, to a submaximally effective ''calculated'' sinusoidal concentration after mixing of 0.1 nmol/L. During orthograde perfusions, arterial and portal glucagon caused the same increases in glucose output. Yet during retrograde perfusions, hepatovenous glucagon elicited metabolic alterations equal to those in orthograde perfusions, whereas arterial glucagon effected changes strongly reduced to between 10% and 50%. Arterially infused trypan blue was distributed homogeneously in the parenchyma during orthograde perfusions, whereas it reached clearly smaller areas of parenchyma during retrograde perfusions. Finally, arterially applied acridine orange was taken up by all periportal hepatocytes in the proximal half of the acinus during orthograde perfusions but only by a much smaller portion of periportal cells in the proximal third of the acinus during retrograde perfusions. These findings suggest that in rat liver, the hepatic artery and the portal vein mix before and within the first third of the sinusoids, rather than in the middle or even last third.
The major aim of this thesis was to study the effect of nitrate on primary metabolism and in development of the model plant Arabidopsis thaliana. The present work has two separate topics. First, to investigate the GDH family, a small gene family at the interface between nitrogen and carbon metabolisms. Second, to investigate the mechanisms whereby nitrogen is regulating the transition to flowering time in Arabidopsis thaliana. To gain more insights into the regulation of primary metabolism by the functional characterization of the glutamate dehydrogenase (GDH) family, an enzyme putatively involved in the metabolism of amino acids and thus suggested to play different and essential roles in carbon and nitrogen metabolism in plants, knock out mutants and transgenic plants carrying RNA interference construct were generated and characterized. The effect of silencing GDH on carbon and nitrogen metabolisms was investigated, especially the level of carbohydrates and the amino acid pool were further analysed. It has been shown that GDH expression is regulated by light and/or sugar status therefore, phenotypic and metabolic analysis were developed in plants grown at different points of the diurnal rhythm and in response to an extended night period. In addition, we are interested in the effect of nutrient availability in the transition from vegetative growth to flowering and especially in nitrate as a metabolite that triggers widespread and coordinated changes in metabolism and development. Nutrient availability has a dramatic effect on flowering time, with a marked delay of flowering when nitrate is supplied (Stitt, 1999). The use of different mutants and transgenic plants impaired in flowering signalling pathways was crucial to evaluate the impact of different nitrate concentrations on flowering time and to better understand the interaction of nitrate-dependent signals with other main flowering signalling pathways. Plants were grown on glutamine as a constitutive source of nitrogen, and the nitrate supply varied. Low nitrate led to earlier flowering. The response to nitrate is accentuated in short days and in the CONSTANS deficient co2 mutant, whereas long days or overexpression of CONSTANS overrides the nitrate response. These results indicate that nitrates acts downstream of the known flowering signalling pathways for photoperiod, autonomy, vernalization and gibberellic acid. Global analyses of gene expression of two independent flowering systems, a light impaired mutant (co2tt4) and a constitutive over-expresser of the potent repressor of flowering (35S::FLC), were to be investigated under two different concentrations of nitrate in order to identify candidate genes that may be involved in the regulation of flowering time by nitrate.
Small livestock is an important resource for rural human populations in dry climates. How strongly will climate change affect the capacity of the rangeland? We used hierarchical modelling to scale quantitatively the growth of shrubs and annual plants, the main food of sheep and goats, to the landscape extent in the eastern Mediterranean region. Without grazing, productivity increased in a sigmoid way with mean annual precipitation. Grazing reduced productivity more strongly the drier the landscape. At a point just under the stocking capacity of the vegetation, productivity declined precipitously with more intense grazing due to a lack of seed production of annuals. We repeated simulations with precipitation patterns projected by two contrasting IPCC scenarios. Compared to results based on historic patterns, productivity and stocking capacity did not differ in most cases. Thus, grazing intensity remains the stronger impact on landscape productivity in this dry region even in the future.