Biowissenschaften
Refine
Year of publication
Document Type
- Article (130)
Language
- English (130)
Has Fulltext
- yes (130)
Is part of the Bibliography
- no (130)
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)
Institute
- Biowissenschaften (102)
- Institut für Ökologie, Evolution und Diversität (32)
- Senckenbergische Naturforschende Gesellschaft (24)
- Exzellenzcluster Makromolekulare Komplexe (20)
- Biodiversität und Klima Forschungszentrum (BiK-F) (18)
- Biochemie und Chemie (5)
- Medizin (5)
- Center for Membrane Proteomics (CMP) (4)
- Informatik (4)
- Sonderforschungsbereiche / Forschungskollegs (2)
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.
Environmental niche modelling is an acclaimed method for estimating species’ present or future distributions. However, in marine environments the assembly of representative data from reliable and unbiased occurrences is challenging. Here, we aimed to model the environmental niche and distribution of marine, parasitic nematodes from the Pseudoterranova decipiens complex using the software Maxent. The distribution of these potentially zoonotic species is of interest, because they infect the muscle tissue of host species targeted by fisheries. To achieve the best possible model, we used two different approaches. The land distance (LD) model was based on abiotic data, whereas the definitive host distance (DHD) model included species-specific biotic data. To assess whether DHD is a suitable descriptor for Pseudoterranova spp., the niches of the parasites and their respective definitive hosts were analysed using ecospat. The performance of LD and DHD was compared based on the variables’ contribution to the model. The DHD-model clearly outperformed the LD-model. While the LD-model gave an estimate of the parasites’ niches, it only showed the potential distribution. The DHD-model produced an estimate of the species’ realised distribution and indicated that biotic variables can help to improve the modelling of data-poor, marine species.
Background: Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii.
Results: Three independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5′-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 % of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 %) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 %) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 % of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs).
Conclusion: This study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated.
Precise temporal coding is necessary for proper acoustic analysis. However, at cortical level, forward suppression appears to limit the ability of neurons to extract temporal information from natural sound sequences. Here we studied how temporal processing can be maintained in the bats’ cortex in the presence of suppression evoked by natural echolocation streams that are relevant to the bats’ behavior. We show that cortical neurons tuned to target-distance actually profit from forward suppression induced by natural echolocation sequences. These neurons can more precisely extract target distance information when they are stimulated with natural echolocation sequences than during stimulation with isolated call-echo pairs. We conclude that forward suppression does for time domain tuning what lateral inhibition does for selectivity forms such as auditory frequency tuning and visual orientation tuning. When talking about cortical processing, suppression should be seen as a mechanistic tool rather than a limiting element.
Heat stress transcription factors (HSFs) regulate transcriptional response to a large number of environmental influences, such as temperature fluctuations and chemical compound applications. Plant HSFs represent a large and diverse gene family. The HSF members vary substantially both in gene expression patterns and molecular functions. HEATSTER is a web resource for mining, annotating, and analyzing members of the different classes of HSFs in plants. A web-interface allows the identification and class assignment of HSFs, intuitive searches in the database and visualization of conserved motifs, and domains to classify novel HSFs.
The opportunistic pathogen Acinetobacter baumannii is able to grow on carnitine. The genes encoding the pathway for carnitine degradation to the intermediate malic acid are known but the transporter mediating carnitine uptake remained to be identified. The open reading frame HMPREF0010_01347 (aci01347) of Acinetobacter baumannii is annotated as a gene encoding a potential transporter of the betaine/choline/carnitine transporter (BCCT) family. To study the physiological function of Aci01347, the gene was deleted from A. baumannii ATCC 19606. The mutant was no longer able to grow on carnitine as sole carbon and energy source demonstrating the importance of this transporter for carnitine metabolism. Aci01347 was produced in Escherichia coli MKH13, a strain devoid of any compatible solute transporter, and the recombinant E. coli MKH13 strain was found to take up carnitine in an energy‐dependent fashion. Aci01347 also transported choline, a compound known to be accumulated under osmotic stress. Choline transport was osmolarity‐independent which is consistent with the absence of an extended C‐terminus found in osmo‐activated BCCT. We propose that the Aci01347 is the carnitine transporter mediating the first step in the growth of A. baumannii on carnitine.
Background: Approximately 90% of German surface waters do not meet the objectives of the European Water Framework Directive (EU-WFD). This is primarily due to deficits in water body structure and biological quality components, which in turn are negatively affected by chemical pollution. In this context, hydromorphological restoration measures have often been conducted to improve habitat and species diversity and, therefore, the ecological status of water bodies. However, habitat improvement is not necessarily accompanied by biota enhancement and thus by the improvement of the ecological status of rivers. To prioritize water management measures, decision criteria for the water management practice are necessary, which enable the prognosis, whether chemical pollution and its resulting effects or other factors, such as structural deficits of the water bodies, are the main cause for the failure to meet the objective of a good ecological status.
Results: To address this need, we applied the freshwater mudsnail Potamopyrgus antipodarum and the amphipod Gammarus fossarum in active monitoring campaigns and in laboratory experiments with combined water/sediment samples and analyzed water and sediment samples with in vitro assays quarterly over the course of 1 year to provide evidence and guideline to assess if chemical contamination is a relevant stress factor for the aquatic biodiversity in rivers of the Nidda catchment (Hessen, Germany). On the basis of these results, an ecotoxicological, WFD–compliant assessment system was developed which, in comparison with the ecological status classes of the EU-WFD, permits the identification of the probable causes for the failure to meet the objectives of the EU-WFD. From these findings, recommendations for action were derived for the implementation of priority measures in water management practice. For the rivers Nidda, Usa, and Horloff, we identified a need for action to improve water and sediment quality at all investigated sampling sites except for the reference sites in the headwaters. The ecotoxicological assessment system also highlighted that hydromorphological restoration measures on their own will not lead to a good ecological status of rivers, as long as water and sediment quality are deficient.
Conclusion: Hydromorphological restoration measures should be performed in conjunction with measures to reduce chemical contamination to achieve a good ecological status of the rivers Nidda, Usa, and Horloff.
Holocarpic oomycetes infecting freshwater diatoms are obligate endobiotic parasites reported from a wide range of habitats. So far, the taxonomy of and phylogeny of most species remains unresolved, since most have not been reported throughout the past decades and sequence data are available for only the four species, Aphanomycopsis bacillariacearum, Diatomophthora gillii, Ectrogella bacillariacearum, and the recently-discovered species Miracula moenusica. In the current study, a new freshwater diatom parasite resembling Ectrogella bacillariacearum in the sense of Scherffel was discovered from pennate diatoms (Ulnaria acus, Ulnaria ulna) collected from the small stream Einbúalækur on Víkurskarð, North Iceland and investigated for its life cycle and phylogenetic placement. In contrast to the original description, Scherffel reports an achlya-like spore discharge for Ectrogella bacillariacearum. The phylogenetic reconstruction and morphological characterisation in this study revealed that Scherffel’s E. bacillariacearum is largely unrelated to the epitype of the species and is a member of the early-diverging genus Miracula. Consequently, the new species is described as M. einbuarlaekurica in the present study. This adds a second freshwater member to the genus, demonstrating the high ecological adaptability of the genus, which thrives in both freshwater and marine ecosystems.
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.
Biosynthetic gene content of the "Perfume Lichens" Evernia prunastri and Pseudevernia furfuracea
(2019)
Lichen-forming fungi produce a vast number of unique natural products with a wide variety of biological activities and human uses. Although lichens have remarkable potential in natural product research and industry, the molecular mechanisms underlying the biosynthesis of lichen metabolites are poorly understood. Here we use genome mining and comparative genomics to assess biosynthetic gene clusters and their putative regulators in the genomes of two lichen-forming fungi, which have substantial commercial value in the perfume industry, Evernia prunastri and Pseudevernia furfuracea. We report a total of 80 biosynthetic gene clusters (polyketide synthases (PKS), non-ribosomal peptide synthetases and terpene synthases) in E. prunastri and 51 in P. furfuracea. We present an in-depth comparison of 11 clusters, which show high homology between the two species. A ketosynthase (KS) phylogeny shows that biosynthetic gene clusters from E. prunastri and P. furfuracea are widespread across the Fungi. The phylogeny includes 15 genomes of lichenized fungi and all fungal PKSs with known functions from the MIBiG database. Phylogenetically closely related KS domains predict not only similar PKS architecture but also similar cluster architecture. Our study highlights the untapped biosynthetic richness of lichen-forming fungi, provides new insights into lichen biosynthetic pathways and facilitates heterologous expression of lichen biosynthetic gene clusters.