Biowissenschaften
Refine
Document Type
- Article (121)
Language
- English (121)
Has Fulltext
- yes (121)
Is part of the Bibliography
- no (121)
Keywords
- Haloferax volcanii (6)
- aging (5)
- Biogeography (4)
- Podospora anserina (4)
- heat stress (4)
- Acinetobacter baumannii (3)
- Archaea (3)
- Biodiversity (3)
- Biohydrogen (3)
- genomics (3)
- hippocampus (3)
- mitochondria (3)
- quality control (3)
- ABC transporter (2)
- AJAP1 (2)
- Antarctica (2)
- Arabidopsis (2)
- Coenzyme A (2)
- Cortex (2)
- Ecological modelling (2)
- Formate dehydrogenase (2)
- Hydrogen production (2)
- Hydrogenase (2)
- Invasive species (2)
- Non-coding RNA (2)
- Operons (2)
- Pantothenate (2)
- Saccharomyces (2)
- Solanum lycopersicum (2)
- amyloid precursor protein (2)
- archaea (2)
- autophagy (2)
- connectedness to nature (2)
- connection to nature (2)
- deletion mutant (2)
- desiccation (2)
- mannitol (2)
- microbiome (2)
- microglia (2)
- peptide-loading complex (2)
- presynaptic active zone (2)
- regulation (2)
- ribosome (2)
- thermotolerance (2)
- 1-octanol (1)
- 2cpsdummy′-O-ribose-methylation (1)
- 3D printed stamp (1)
- A. thaliana (1)
- ABE fermentation (1)
- ADCD (1)
- ADP (1)
- AMPK (1)
- ATP (1)
- ATP synthase (1)
- ATPase (1)
- Acetobacterium woodii (1)
- Acetogenic bacteria (1)
- Acetyl-CoA (1)
- Acetylating acetaldehyde dehydrogenase (1)
- Adherence junctions (1)
- Adhesion (1)
- Aedes aegypti (1)
- Aedes albopictus (1)
- Agent-based modeling (1)
- Agroecology (1)
- Akaike information criterion (1)
- Anamorphic fungi (1)
- Angiogenesis (1)
- Animal physiology (1)
- Anisakid nematodes (1)
- Antisense RNA (1)
- Apis mellifera (1)
- Applied microbiology (1)
- Aquatic invertebrates (1)
- Arabidopsis thaliana (1)
- Arabidopsis thaliana metabolism (1)
- Ascomycota (1)
- Automation (1)
- BMP signaling (1)
- Basidiomycota (1)
- Bathydraconinae (1)
- Bayesian information criterion (1)
- Behavioural ecology (1)
- Behavioural methods (1)
- Benin (1)
- Benthos (1)
- Biochemistry (1)
- Biofuel (1)
- Biogeography of disease (1)
- Biological invasion (1)
- Biomonitoring (1)
- Bioreactor (1)
- Biosynthesis (1)
- Birds of prey (1)
- Blastocysts (1)
- Brassicales (1)
- C-value (1)
- CDC-42 (1)
- CLP protease (1)
- CLPXP protease (1)
- CO2 reduction (1)
- Canis lupus (1)
- Caprylic acid (1)
- Carbon capture (1)
- Carboxylic acid reductase (1)
- Cell differentiation (1)
- Cell migration (1)
- Cercospora (1)
- Chaenodraco wilsoni (1)
- Champsocephalus gunnari (1)
- Channichthyidae (1)
- Chemical communication (1)
- Chemical contamination (1)
- Chorion (1)
- Chorismate mutase-prephenate dehydratase (1)
- Chromosomes and gene expression (1)
- Chrysops (1)
- Climate (1)
- Climatic habitat suitability (1)
- Cochlea (1)
- Communication center (1)
- Compartmentalization (1)
- Conservation biology (1)
- Contact microradiography (1)
- Contracaecum (1)
- Core marking (1)
- Cre-lox system (1)
- Crustacea (1)
- Cytoskeleton (1)
- DNA transporter (1)
- Dark fermentation (1)
- Deep sea (1)
- Dehydration (medicine) (1)
- Developmental biology (1)
- Developmental biology and stem cells (1)
- Diptera (1)
- Diversity (1)
- Ecological niche modeling (1)
- Ecology (1)
- Ecophysiology (1)
- Ecotoxicological status class (1)
- Ectoparasites (1)
- Eltonian noise hypothesis (1)
- Embryos (1)
- Endoplasmic reticulum (1)
- Endothelial cells (1)
- Envelope (1)
- Environmental health (1)
- Environmental sciences (1)
- Evaluation matrix (1)
- Evolution (1)
- F1Fo-ATP-synthase (1)
- FAD (1)
- Fabaceae (1)
- Fatty acid synthase (1)
- Fatty alcohol (1)
- Feather mites (1)
- Feeding behavior (1)
- Fluorescent proteins (1)
- Fungi (1)
- Fusarium (1)
- GC content (1)
- GLUT2 (1)
- GLUT3 (1)
- Gammarus fossarum (1)
- Gammarus roeselii (1)
- Gene prediction (1)
- Generation time (1)
- Genome annotation (1)
- Genotyping (1)
- Gerlachea australis (1)
- Global (1)
- Global warming (1)
- Golgi (1)
- Great philippine eagle (1)
- Gymnodraco acuticeps (1)
- HER (1)
- HSBP (1)
- HSF (1)
- Haematopota (1)
- High content imaging (1)
- Hispaniola (1)
- Hominins (1)
- Host specificity (1)
- Hydrogen storage (1)
- Hydrogen-dependent CO2 reductase (1)
- Hydrogen-dependent CO2 reductase (HDCR) (1)
- Hydromorphology (1)
- Hydroxymandelate synthase (1)
- Hypothermia (1)
- INS (1)
- Image processing (1)
- In vitro assays (1)
- Indoles (1)
- Insects (1)
- Intraspecific divergence (1)
- Klebsiella oxytoca (1)
- LTP (1)
- LUCA (1)
- Lactation (1)
- Land cover (1)
- Leaderless transcript (1)
- Leaf clearing (1)
- Leguminosae (1)
- Lepidoptera (1)
- Life-history evolution (1)
- Light sheet-based fluorescence microscopy (1)
- Local adaptation (1)
- Localized defecation (1)
- Long-term live imaging (1)
- MHC (1)
- Macropus (1)
- Malpighiales (1)
- Mammary gland (1)
- Mandelic acid (1)
- Marine biology (1)
- Massive Analysis of cDNA Ends (MACE) (1)
- Mathematical models (1)
- Maxent (1)
- Metabolic engineering (1)
- Metabolomics (1)
- Micro CT (1)
- Microthlaspi erraticum (1)
- Microtubules (1)
- Midbrain (1)
- Mindanao hawk-eagle (1)
- Mitochondria (1)
- Model (1)
- Model complexity (1)
- Molecular biology (1)
- Molecular phylogeny (1)
- Mollusca (1)
- Mortality (1)
- Multidimensional imaging (1)
- Neopagetopsis ionah (1)
- Network analysis (1)
- Neurophysiology (1)
- Niche (1)
- Nisaetus pinskeri (1)
- Northern blot (1)
- Notch signaling (1)
- Nothopassalora (1)
- O-CAS assay (1)
- Octanoic acid (1)
- Optimization (1)
- P2Y13 receptor (1)
- PAR complex (1)
- PSII core phosphorylation (1)
- Pagetopsis macropterus (1)
- Palaeontology (1)
- Parachaenichthys charcoti (1)
- Parasites (1)
- Parasites of endangered species (1)
- Passalora (1)
- Pelagic (1)
- Petri net (1)
- Phenology (1)
- Phylogenetics (1)
- PilF (1)
- Pithecophaga jefferyi (1)
- Population density (1)
- Population dynamics (1)
- Potamopyrgus antipodarum (1)
- Proline (1)
- Promoter (1)
- Protein domains (1)
- Pseudocercospora (1)
- Pseudochaenichthys georgianus (1)
- Pseudoterranova (1)
- Pterolichoidea (1)
- Quantitative imaging (1)
- RMP1 (1)
- RNA polymerase (1)
- RNA sequencing (1)
- RNA-seq (1)
- Racovitzia glacialis (1)
- Rapid evolution (1)
- Rearing temperature (1)
- Reproducibility (1)
- Reproduction (1)
- Retrotransposon (1)
- Rnf complex (1)
- SNF1 (1)
- SPAdes (1)
- Saccharomyces cerevisiae (1)
- Scale-up (1)
- Schizokinen (1)
- Sea water (1)
- Shallow water (1)
- Shores (1)
- Short-chain fatty acids (1)
- Shrew-1 (1)
- Signal inhibition (1)
- Small nucleolar RNA (1)
- Social behaviour (1)
- Solanum lycopersicum L. (1)
- Solenidae (1)
- Species distribution modelling (1)
- Species richness (1)
- Spheroids (1)
- Splice variants (1)
- Standardization (1)
- Stem cells (1)
- Surface range (1)
- Swimming (1)
- Tabanidae (1)
- Tabanus (1)
- Thermal pollution (1)
- Thermoanaerobacter kivui (1)
- Thermophiles (1)
- Three-dimensional cell culture (1)
- Tiger mosquito (1)
- Tissue integrity (1)
- Tools and resources (1)
- Tortoise beetles (1)
- Trans-2-enoyl-CoA reductase (1)
- Transcriptome (1)
- Transcriptome analysis (1)
- Transgenesis (1)
- Transposable elements (1)
- Tribolium castaneum (1)
- Tuber aestivum (1)
- Tumor suppressor protein (1)
- Tyrosine prototrophy (1)
- UV-stress (1)
- UV/V cones (1)
- Urban ecology (1)
- Vector borne diseases (1)
- Vector mosquito (1)
- Vectorpathogen-host (1)
- Vein density (1)
- Vein networks (1)
- West Africa (1)
- Whales (1)
- Wnt (1)
- Wood–Ljungdahl pathway (1)
- Yeast (1)
- Yellow fever mosquito (1)
- Zebrafish (1)
- aIF (1)
- acetogenesis (1)
- acetogenic bacteria (1)
- acetyl-CoA (1)
- acoustic startle reflex (1)
- adaptive immunity (1)
- adult neurogenesis (1)
- alternative splicing (1)
- alzheimer’s disease (1)
- amplicon sequencing (1)
- animal migration (1)
- anti-oxidants (1)
- antigen presentation (1)
- antigen processing (1)
- aposematism (1)
- asexual fungi (1)
- asymmetry (1)
- auditory cortex (1)
- auditory processing (1)
- background noise (1)
- bacterial communities (1)
- behavioural ecology (1)
- betaine/choline/carnitine transporter (1)
- biodiversity loss (1)
- biofilm (1)
- biosynthetic gene clusters (1)
- bromeliads (1)
- brood (1)
- carnitine metabolism (1)
- carotenoids (1)
- chlorophyta (1)
- chloroplast phosphorylation network (1)
- chromosome number (1)
- climate (1)
- climate-change ecology (1)
- clostridia (1)
- coherence (1)
- cold tolerance (1)
- coloration (1)
- common transition pairs (1)
- compaction (1)
- comparative genomics (1)
- compass orientation (1)
- compatible solutes (1)
- computed tomography (1)
- connectedness to nature scale (1)
- connectedness to nature scale (CNS) (1)
- conservation (1)
- conservation biology (1)
- copyright (1)
- cortical flow (1)
- costs (1)
- coupling (1)
- cryptochrome (1)
- dRNA-Seq (1)
- database (1)
- dataset (1)
- dentate gyrus (1)
- development (1)
- drug screening system (1)
- education for sustainable development (ESD) (1)
- electron bifurcation (1)
- energy conservation (1)
- energy metabolism (1)
- environmental behavior (1)
- environmental factors (1)
- environmental knowledge (1)
- enzyme activity (1)
- eukaryotic system (1)
- evolution (1)
- flow cytometry (1)
- forest tree (1)
- formate dehydrogenase (1)
- freeze avoidance (1)
- frontal cortex (1)
- functional coupling (1)
- fungi (1)
- gap duration (1)
- gap-prepulse inhibition (1)
- gel retardation (1)
- gene conversion (1)
- gene expression (1)
- gene flow (1)
- gene loss (1)
- genomic base composition (1)
- geographic distributions (1)
- giraffe (1)
- glucose transport inhibitor (1)
- grisel syndrome (1)
- hardwood (1)
- heat shock protein (1)
- heat stress transcription factor (1)
- heterozygous cells (1)
- homeostasis (1)
- human host adaptation (1)
- human pathogen (1)
- hxt0 yeast strain (1)
- hybrid assembly (1)
- hybrid enrichment (1)
- hybridization (1)
- hydrogen production (1)
- hydrogen storage (1)
- hydrogenase (1)
- hydroxamate (1)
- illustrated inclusion of nature in self scale (IINS) (1)
- imaging protocol (1)
- inclination compass (1)
- inclusion of nature in self scale (INS) (1)
- incomplete lineage sorting (1)
- insect (1)
- insecticides (1)
- intellectual property (1)
- interaction networks (1)
- intracellular protein localization (1)
- invariant transition pairs (1)
- iron starvation (1)
- kangaroo (1)
- kinase protein interaction (1)
- large carnivores (1)
- larva (1)
- larvae (1)
- latitudinal gradient in species richness (1)
- learning difficulties (1)
- lichen secondary metabolites (1)
- ligand binding (1)
- light-stress (1)
- lipid peroxidation (1)
- local-field potentials (1)
- mPTP (1)
- magnesium transporters (1)
- magnetic resonance imaging (1)
- magnetoreception (1)
- maladaptation (1)
- mating type (1)
- melanization (1)
- membrane proteins (1)
- metabolic pathway (1)
- metagenome assembly (1)
- mitophagy (1)
- model verification (1)
- molecular phylogenetic analysis (1)
- molecular tug-of-war (1)
- morphogenesis (1)
- motif search (1)
- multilocus genotype (1)
- museum collections (1)
- mutational spectrum bias (1)
- n-Butanol (1)
- n-butanol (1)
- natural competence (1)
- nature relatedness scale (NR) (1)
- network reduction (1)
- network state changes (1)
- neurodegeneration (1)
- neuronal network (1)
- nicotinic acetylcholine receptors (1)
- non-ribosomal peptide synthetases (1)
- nontraumatic atlantoaxial rotatory subluxation (1)
- oakmoss (1)
- off-target reads (1)
- open access (1)
- organellar ploidy levels (1)
- ortholog search (1)
- oscillations (1)
- osmotic stress (1)
- peptide editing (1)
- peroxisomes (1)
- phenotypic analysis (1)
- phenotyping (1)
- phosphate starvation (1)
- photocycle (1)
- photosynthesis (1)
- photosystem II assembly and repair (1)
- phylogenetic conflict (1)
- phylogenetic profile (1)
- phylogenetic signal (1)
- phylogenomics (1)
- phylogeny (1)
- piracy (1)
- planar polarity (1)
- plant-microbe interactions (1)
- plastic response (1)
- plastome (1)
- ploidy (1)
- polyketide synthases (1)
- polyploidy (1)
- polytomy (1)
- population growth (1)
- posttranslational regulation of photosynthesis (1)
- pre-mRNA (1)
- prepulse inhibition (1)
- progenitor cell (1)
- protected areas (1)
- protoplast fusion (1)
- pseudouridylation (1)
- publishing (1)
- pupil diameter (1)
- pupillometry (1)
- qH2 (1)
- rRNA (1)
- radical pair model (1)
- radicals (1)
- razor clams (1)
- recolonization (1)
- relational values (1)
- respiratory chain (1)
- ribosomal proteins (1)
- ribosome biogenesis (1)
- royal jelly (1)
- sRNA (1)
- sRNA regulon (1)
- scale validation (1)
- sci-hub (1)
- seedling (1)
- senescence (1)
- sensory coding (1)
- sequence evolution (1)
- sequencing error (1)
- siderophore (1)
- signaling (1)
- singlet oxygen (1)
- small protein (1)
- small regulatory RNA (1)
- snoRNA (1)
- soil VOCs (1)
- soil degradation (1)
- soil fungal communities (1)
- special needs education (1)
- speciation (1)
- species richness (1)
- structure activity relationship (1)
- substrate-binding site (1)
- sustainable development goals (SDGs) (1)
- swarming (1)
- symbiosis (1)
- synapse (1)
- systems biology (1)
- tapasin (1)
- taxon sampling (1)
- terpene synthases (1)
- thermophile (1)
- thylakoid kinases (1)
- tinnitus (1)
- torticollis (1)
- transcription (1)
- transcription factor (1)
- transcriptome (1)
- transcriptomics (1)
- transient regulation (1)
- transition invariant (1)
- translation initiation (1)
- tree moss (1)
- trehalose (1)
- tropical fungi (1)
- twilight zone (1)
- two factor model of environmental values model (1)
- type IV pili (1)
- unselected segregation (1)
- volatile organic compounds (1)
- wax layer (1)
- winter survival (1)
- zinc finger protein (1)
- µ-protein (1)
Institute
- Biowissenschaften (94)
- Institut für Ökologie, Evolution und Diversität (31)
- Senckenbergische Naturforschende Gesellschaft (23)
- Exzellenzcluster Makromolekulare Komplexe (20)
- Biodiversität und Klima Forschungszentrum (BiK-F) (17)
- Biochemie und Chemie (5)
- Medizin (5)
- Center for Membrane Proteomics (CMP) (4)
- Informatik (4)
- Sonderforschungsbereiche / Forschungskollegs (2)
Climate change affects ecosystems worldwide and is threatening biodiversity. Insects, as ectotherm organisms, are strongly dependent on the thermal environment. Yet, little is known about the effects of summer heat and drought on insect diversity. In the Mediterranean climate zone, a region strongly affected by climate change, hot summers might have severe effects on insect communities. Especially the larval stage might be sensitive to thermal variation, as larvae—compared to other life stages—cannot avoid hot temperatures and drought by dormancy. Here we ask, whether inter-annual fluctuations in Mediterranean moth diversity can be explained by temperature (TLarv) and precipitation during larval development (HLarv). To address our question, we analyzed moth communities of a Mediterranean coastal forest during the last 20 years. For species with summer-developing larvae, species richness was significantly negatively correlated with TLarv, while the community composition was affected by both, TLarv and HLarv. Therefore, summer-developing larvae seem particularly sensitive to climate change, as hot summers might exceed the larval temperature optima and drought reduces food plant quality. Increasing frequency and severity of temperature and drought extremes due to climate change, therefore, might amplify insect decline in the future.
Biodiversity patterns of marine crustaceans are still unknown in many locations or might have been overlooked due to our knowledge gaps, despite increasing sampling and data sharing efforts during the last decades. By analysing big data extracted from open portals such as Ocean Biodiversity Information System (OBIS) and Global Biodiversity Information System (GBIF), we aim to revisit the distribution and biodiversity patterns of the highly speciose and abundant Crustacea in the Northwest Pacific (NWP) from shallowest depths to the deep sea. This study focussed on selected benthic and pelagic crustacean (sub) classes and their species richness, sampling effort, and expected species richness (ES50) using equal/sized hexagonal cells, 5° latitudinal bands, 500 m depth intervals were analyzed. Crustacean species richness was highest in the tropical Philippines as well as around the Japanese islands. Pelagic crustacean species richness peaked at 30° latitude and declined beyond that. Benthic taxa; however, depicted high levels of species richness across most of the latitudinal gradient, reaching its highest point at 45° latitude. Due to the prevalence of certain crustacean orders in the deep sea, benthic species richness showed a distribution pattern with two distinct peaks across bathymetric gradients; with highest species richness recorded at shallow-water depths and also at abyssal depths. The most important environmental drivers of benthic and pelagic crustacean species richness were primary productivity (positive correlation) and salinity (negative correlation). Our study provides first insights into biodiversity patterns of the highly diverse Crustacea in the NWP and highlights strong differences between benthic and pelagic taxa. The results presented here could help us to better understand whether benthic or pelagic taxa might respond differently to climate changes in the NWP based on their distinct physiological and biological characteristics. This information is crucial in establishing species management strategies and ecosystem restorations in both shallow water and deep-sea environments.
Background: In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.
Results: In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.
Conclusions: The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.
The ORCID iDs are missing for the second, fifth, and sixth authors. Please see the authors’ respective ORCID iDs here:
Author Christine Hertler’s ORCID iD is: 0000-0002-8252-9674 (https://orcid.org/0000-0002-8252-9674).
Author Jan Ole Berndt’s ORCID iD is: 0000-0001-7241-3291 (https://orcid.org/0000-0001-7241-3291).
Author Ingo J. Timm’s ORCID iD is: 0000-0002-3369-813X (https://orcid.org/0000-0002-3369-813X).
Understanding hominin expansions requires the comprehension of movement processes at different scales. In many models of hominin expansion these processes are viewed as being determined by large-scale effects, such as changes in climate and vegetation spanning continents and thousands or even millions of years. However, these large-scale patterns of expansions also need to be considered as possibly resulting from the accumulation of small-scale decisions of individual hominins. Moving on a continental scale may for instance involve crossing a water barrier. We present a generalized agent-based model for simulating the crossing of a water barrier where the agents represent the hominin individuals. The model can be configured to represent a variety of movement modes across water. Here, we compare four different behavioral scenarios in conjunction with a set of water barrier configurations, in which agents move in water by either paddling, drifting, swimming or rafting. We introduce the crossing-success-rate (CSR) to quantify the performance in water crossing. Our study suggests that more focus should be directed towards the exploration of behavioral models for hominins, as directionality may be a more powerful factor for crossing a barrier than environmental opportunities alone. A prerequisite for this is to perceive the opposite shore. Furthermore, to provide a comprehensive understanding of hominin expansions, the CSR allows for the integration of results obtained from small-scale simulations into large-scale models for hominin expansion.
Translation is an important step in gene expression. Initiation of translation is rate-limiting, and it is phylogenetically more diverse than elongation or termination. Bacteria contain only three initiation factors. In stark contrast, eukaryotes contain more than 10 (subunits of) initiation factors (eIFs). The genomes of archaea contain many genes that are annotated to encode archaeal homologs of eukaryotic initiation factors (aIFs). However, experimental characterization of aIFs is scarce and mostly restricted to very few species. To broaden the view, the protein–protein interaction network of aIFs in the halophilic archaeon Haloferax volcanii has been characterized. To this end, tagged versions of 14 aIFs were overproduced, affinity isolated, and the co-isolated binding partners were identified by peptide mass fingerprinting and MS/MS analyses. The aIF–aIF interaction network was resolved, and it was found to contain two interaction hubs, (1) the universally conserved factor aIF5B, and (2) a protein that has been annotated as the enzyme ribose-1,5-bisphosphate isomerase, which we propose to rename to aIF2Bα. Affinity isolation of aIFs also led to the co-isolation of many ribosomal proteins, but also transcription factors and subunits of the RNA polymerase (Rpo). To analyze a possible coupling of transcription and translation, seven tagged Rpo subunits were overproduced, affinity isolated, and co-isolated proteins were identified. The Rpo interaction network contained many transcription factors, but also many ribosomal proteins as well as the initiation factors aIF5B and aIF2Bα. These results showed that transcription and translation are coupled in haloarchaea, like in Escherichia coli. It seems that aIF5B and aIF2Bα are not only interaction hubs in the translation initiation network, but also key players in the transcription-translation coupling.
What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen
(2020)
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
Impact of biological education and gender on students' connection to nature and relational values
(2020)
The new concept of relational values (RVs) is gaining more and more attention in environmental research, but empirical analyses are still rare. However, this type of research is necessary because the RVs have an influence on environmental behavior. To evaluate the impact of biological education on attributing higher importance to RVs and connectedness to nature, we compared the connection to nature scores (using the inclusion of nature scale (INS) and connectedness to nature scale (CNS)) and RV scores of biologically interested high school students (n = 417) with first year (n = 593) and advanced biology (n = 223) students. While high school students showed significant lower connection to nature scores than university students, there was no significant difference in RVs between the test groups. These results suggest that there is a lack of factors in the university study of biology that can change RVs. The gender comparison of RVs and connection to nature showed a significant higher RV score for females while INS and CNS did not show a gender difference. Thus, the study makes an important contribution to the research, as it was able to prove that gender has an influence on a person's RVs but not on their connection to nature.
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2′-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
Predator-induced plasticity in life-history and antipredator traits during the larval period has been extensively studied in organisms with complex life-histories. However, it is unclear whether different levels of predation could induce warning signals in aposematic organisms. Here, we investigated whether predator-simulated handling affects warning coloration and life-history traits in the aposematic wood tiger moth larva, Arctia plantaginis. As juveniles, a larger orange patch on an otherwise black body signifies a more efficient warning signal against predators but this comes at the costs of conspicuousness and thermoregulation. Given this, one would expect that an increase in predation risk would induce flexible expression of the orange patch. Prior research in this system points to plastic effects being important as a response to environmental changes for life history traits, but we had yet to assess whether this was the case for predation risk, a key driver of this species evolution. Using a full-sib rearing design, in which individuals were reared in the presence and absence of a non-lethal simulated bird attack, we evaluated flexible responses of warning signal size (number of orange segments), growth, molting events, and development time in wood tiger moths. All measured traits except development time showed a significant response to predation. Larvae from the predation treatment developed a more melanized warning signal (smaller orange patch), reached a smaller body size, and molted more often. Our results suggest plasticity is indeed important in aposematic organisms, but in this case may be complicated by the trade-off between costly pigmentation and other life-history traits.