@article{VogelBusslerFinnbergetal.2021, author = {Vogel, Sebastian and Bussler, Heinz and Finnberg, Sven and M{\"u}ller, J{\"o}rg and Stengel, Elisa and Thorn, Simon}, title = {Diversity and conservation of saproxylic beetles in 42 European tree species: an experimental approach using early successional stages of branches}, series = {Insect Conservation and Diversity}, volume = {14}, journal = {Insect Conservation and Diversity}, number = {1}, doi = {10.1111/icad.12442}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218401}, pages = {132 -- 143}, year = {2021}, abstract = {Tree species diversity is important to maintain saproxylic beetle diversity in managed forests. Yet, knowledge about the conservational importance of single tree species and implications for forest management and conservation practices are lacking. We exposed freshly cut branch-bundles of 42 tree species, representing tree species native and non-native to Europe, under sun-exposed and shaded conditions for 1 year. Afterwards, communities of saproxylic beetles were reared ex situ for 2 years. We tested for the impact of tree species and sun exposure on alpha-, beta-, and gamma-diversity as well as composition of saproxylic beetle communities. Furthermore, the number of colonised tree species by each saproxylic beetle species was determined. Tree species had a lower impact on saproxylic beetle communities compared to sun exposure. The diversity of saproxylic beetles varied strongly among tree species, with highest alpha- and gamma-diversity found in Quercus petraea. Red-listed saproxylic beetle species occurred ubiquitously among tree species. We found distinct differences in the community composition of broadleaved and coniferous tree species, native and non-native tree species as well as sun-exposed and shaded deadwood. Our study enhances the understanding of the importance of previously understudied and non-native tree species for the diversity of saproxylic beetles. To improve conservation practices for saproxylic beetles and especially red-listed species, we suggest a stronger incorporation of tree species diversity and sun exposure of into forest management strategies, including the enrichment of deadwood from native and with a specific focus on locally rare or silviculturally less important tree species.}, language = {en} } @article{HollenhorstJurastowNandigamaetal.2020, author = {Hollenhorst, Monika I. and Jurastow, Innokentij and Nandigama, Rajender and Appenzeller, Silke and Li, Lei and Vogel, J{\"o}rg and Wiederhold, Stephanie and Althaus, Mike and Empting, Martin and Altm{\"u}ller, Janine and Hirsch, Anna K. H. and Flockerzi, Veit and Canning, Brendan J. and Saliba, Antoine-Emmanuel and Krasteva-Christ, Gabriela}, title = {Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling}, series = {The FASEB Journal}, volume = {34}, journal = {The FASEB Journal}, number = {1}, doi = {10.1096/fj.201901314RR}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213516}, pages = {316 -- 332}, year = {2020}, abstract = {For protection from inhaled pathogens many strategies have evolved in the airways such as mucociliary clearance and cough. We have previously shown that protective respiratory reflexes to locally released bacterial bitter "taste" substances are most probably initiated by tracheal brush cells (BC). Our single-cell RNA-seq analysis of murine BC revealed high expression levels of cholinergic and bitter taste signaling transcripts (Tas2r108, Gnat3, Trpm5). We directly demonstrate the secretion of acetylcholine (ACh) from BC upon stimulation with the Tas2R agonist denatonium. Inhibition of the taste transduction cascade abolished the increase in [Ca\(^{2+}\)]\(_{i}\) in BC and subsequent ACh-release. ACh-release is regulated in an autocrine manner. While the muscarinic ACh-receptors M3R and M1R are activating, M2R is inhibitory. Paracrine effects of ACh released in response to denatonium included increased [Ca\(^{2+}\)]\(_{i}\) in ciliated cells. Stimulation by denatonium or with Pseudomonas quinolone signaling molecules led to an increase in mucociliary clearance in explanted tracheae that was Trpm5- and M3R-mediated. We show that ACh-release from BC via the bitter taste cascade leads to immediate paracrine protective responses that can be boosted in an autocrine manner. This mechanism represents the initial step for the activation of innate immune responses against pathogens in the airways.}, language = {en} } @article{HennessenMiethkeZaburannyietal.2020, author = {Hennessen, Fabienne and Miethke, Marcus and Zaburannyi, Nestor and Loose, Maria and Lukežič, Tadeja and Bernecker, Steffen and H{\"u}ttel, Stephan and Jansen, Rolf and Schmiedel, Judith and Fritzenwanker, Moritz and Imirzalioglu, Can and Vogel, J{\"o}rg and Westermann, Alexander J. and Hesterkamp, Thomas and Stadler, Marc and Wagenlehner, Florian and Petković, Hrvoje and Herrmann, Jennifer and M{\"u}ller, Rolf}, title = {Amidochelocardin overcomes resistance mechanisms exerted on tetracyclines and natural chelocardin}, series = {Antibiotics}, volume = {9}, journal = {Antibiotics}, number = {9}, issn = {2079-6382}, doi = {10.3390/antibiotics9090619}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213149}, year = {2020}, abstract = {The reassessment of known but neglected natural compounds is a vital strategy for providing novel lead structures urgently needed to overcome antimicrobial resistance. Scaffolds with resistance-breaking properties represent the most promising candidates for a successful translation into future therapeutics. Our study focuses on chelocardin, a member of the atypical tetracyclines, and its bioengineered derivative amidochelocardin, both showing broad-spectrum antibacterial activity within the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) panel. Further lead development of chelocardins requires extensive biological and chemical profiling to achieve favorable pharmaceutical properties and efficacy. This study shows that both molecules possess resistance-breaking properties enabling the escape from most common tetracycline resistance mechanisms. Further, we show that these compounds are potent candidates for treatment of urinary tract infections due to their in vitro activity against a large panel of multidrug-resistant uropathogenic clinical isolates. In addition, the mechanism of resistance to natural chelocardin was identified as relying on efflux processes, both in the chelocardin producer Amycolatopsis sulphurea and in the pathogen Klebsiella pneumoniae. Resistance development in Klebsiella led primarily to mutations in ramR, causing increased expression of the acrAB-tolC efflux pump. Most importantly, amidochelocardin overcomes this resistance mechanism, revealing not only the improved activity profile but also superior resistance-breaking properties of this novel antibacterial compound.}, language = {en} } @article{SchulteSchweinlinWestermannetal.2020, author = {Schulte, Leon N. and Schweinlin, Matthias and Westermann, Alexander J. and Janga, Harshavardhan and Santos, Sara C. and Appenzeller, Silke and Walles, Heike and Vogel, J{\"o}rg and Metzger, Marco}, title = {An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection}, series = {mBio}, volume = {11, 2020}, journal = {mBio}, number = {1}, doi = {10.1128/mBio.03348-19}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229428}, year = {2020}, abstract = {A major obstacle in infection biology is the limited ability to recapitulate human disease trajectories in traditional cell culture and animal models, which impedes the translation of basic research into clinics. Here, we introduce a three-dimensional (3D) intestinal tissue model to study human enteric infections at a level of detail that is not achieved by conventional two-dimensional monocultures. Our model comprises epithelial and endothelial layers, a primary intestinal collagen scaffold, and immune cells. Upon Salmonella infection, the model mimics human gastroenteritis, in that it restricts the pathogen to the epithelial compartment, an advantage over existing mouse models. Application of dual transcriptome sequencing to the Salmonella-infected model revealed the communication of epithelial, endothelial, monocytic, and natural killer cells among each other and with the pathogen. Our results suggest that Salmonella uses its type III secretion systems to manipulate STAT3-dependent inflammatory responses locally in the epithelium without accompanying alterations in the endothelial compartment. Our approach promises to reveal further human-specific infection strategies employed by Salmonella and other pathogens. IMPORTANCE Infection research routinely employs in vitro cell cultures or in vivo mouse models as surrogates of human hosts. Differences between murine and human immunity and the low level of complexity of traditional cell cultures, however, highlight the demand for alternative models that combine the in vivo-like properties of the human system with straightforward experimental perturbation. Here, we introduce a 3D tissue model comprising multiple cell types of the human intestinal barrier, a primary site of pathogen attack. During infection with the foodborne pathogen Salmonella enterica serovar Typhimurium, our model recapitulates human disease aspects, including pathogen restriction to the epithelial compartment, thereby deviating from the systemic infection in mice. Combination of our model with state-of-the-art genetics revealed Salmonella-mediated local manipulations of human immune responses, likely contributing to the establishment of the pathogen's infection niche. We propose the adoption of similar 3D tissue models to infection biology, to advance our understanding of molecular infection strategies employed by bacterial pathogens in their human host.}, language = {en} } @article{BauriedlGerovacHeidrichetal.2020, author = {Bauriedl, Saskia and Gerovac, Milan and Heidrich, Nadja and Bischler, Thorsten and Barquist, Lars and Vogel, J{\"o}rg and Schoen, Christoph}, title = {The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-16650-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230040}, year = {2020}, abstract = {FinO-domain proteins are a widespread family of bacterial RNA-binding proteins with regulatory functions. Their target spectrum ranges from a single RNA pair, in the case of plasmid-encoded FinO, to global RNA regulons, as with enterobacterial ProQ. To assess whether the FinO domain itself is intrinsically selective or promiscuous, we determine in vivo targets of Neisseria meningitidis, which consists of solely a FinO domain. UV-CLIP-seq identifies associations with 16 small non-coding sRNAs and 166 mRNAs. Meningococcal ProQ predominantly binds to highly structured regions and generally acts to stabilize its RNA targets. Loss of ProQ alters transcript levels of >250 genes, demonstrating that this minimal ProQ protein impacts gene expression globally. Phenotypic analyses indicate that ProQ promotes oxidative stress resistance and DNA damage repair. We conclude that FinO domain proteins recognize some abundant type of RNA shape and evolve RNA binding selectivity through acquisition of additional regions that constrain target recognition. FinO-domain proteins are bacterial RNA-binding proteins with a wide range of target specificities. Here, the authors employ UV CLIP-seq and show that minimal ProQ protein of Neisseria meningitidis binds to various small non-coding RNAs and mRNAs involved in virulence.}, language = {en} } @article{VogelGossnerMergneretal.2020, author = {Vogel, Sebastian and Gossner, Martin M. and Mergner, Ulrich and M{\"u}ller, J{\"o}rg and Thorn, Simon}, title = {Optimizing enrichment of deadwood for biodiversity by varying sun exposure and tree species: An experimental approach}, series = {Journal of Applied Ecology}, volume = {57}, journal = {Journal of Applied Ecology}, number = {10}, doi = {10.1111/1365-2664.13648}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214614}, pages = {2075 -- 2085}, year = {2020}, abstract = {The enrichment of deadwood is essential for the conservation of saproxylic biodiversity in managed forests. However, existing strategies focus on a cost-intensive increase of deadwood amount, while largely neglecting increasing deadwood diversity. Deadwood objects, that is logs and branches, from six tree species were experimentally sun exposed, canopy shaded and artificially shaded for 4 years, after which the alpha-, beta- and gamma-diversity of saproxylic beetles, wood-inhabiting fungi and spiders were analysed. Analyses of beta-diversity included the spatial distance between exposed deadwood objects. A random-drawing procedure was used to identify the combination of tree species and sun exposure that yielded the highest gamma-diversity at a minimum of exposed deadwood amount. In sun-exposed plots, species numbers in logs were higher than in shaded plots for all taxa, while in branches we observed the opposite for saproxylic beetles. Tree species affected the species numbers only of saproxylic beetles and wood-inhabiting fungi. The beta-diversity of saproxylic beetles and wood-inhabiting fungi among logs was influenced by sun exposure and tree species, but beta-diversity of spiders by sun exposure only. For all saproxylic taxa recorded in logs, differences between communities increased with increasing spatial distance. A combination of canopy-shaded Carpinus logs and sun-exposed Populus logs resulted in the highest species numbers of all investigated saproxylic taxa among all possible combinations of tree species and sun-exposure treatments. Synthesis and applications. We recommend incorporating the enrichment of different tree species and particularly the variation in sun exposure into existing strategies of deadwood enrichment. Based on the results of our study, we suggest to combine the logs of softwood broadleaf tree species (e.g. Carpinus, Populus), hardwood broadleaf tree species (e.g. Quercus) and coniferous tree species (e.g. Pinus) under different conditions of sun exposure and distribute them spatially in a landscape to maximize the beneficial effects on overall diversity.}, language = {en} } @article{MuellerUlyshenSeiboldetal.2020, author = {M{\"u}ller, J{\"o}rg and Ulyshen, Mike and Seibold, Sebastian and Cadotte, Marc and Chao, Anne and B{\"a}ssler, Claus and Vogel, Sebastian and Hagge, Jonas and Weiß, Ingmar and Baldrian, Petr and Tl{\´a}skal, Vojtěch and Thorn, Simon}, title = {Primary determinants of communities in deadwood vary among taxa but are regionally consistent}, series = {Oikos}, volume = {129}, journal = {Oikos}, number = {10}, doi = {10.1111/oik.07335}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228201}, pages = {1579 -- 1588}, year = {2020}, abstract = {The evolutionary split between gymnosperms and angiosperms has far-reaching implications for the current communities colonizing trees. The inherent characteristics of dead wood include its role as a spatially scattered habitat of plant tissue, transient in time. Thus, local assemblages in deadwood forming a food web in a necrobiome should be affected not only by dispersal ability but also by host tree identity, the decay stage and local abiotic conditions. However, experiments simultaneously manipulating these potential community drivers in deadwood are lacking. To disentangle the importance of spatial distance and microclimate, as well as host identity and decay stage as drivers of local assemblages, we conducted two consecutive experiments, a 2-tree species and 6-tree species experiment with 80 and 72 tree logs, respectively, located in canopy openings and under closed canopies of a montane and a lowland forest. We sampled saproxylic beetles, spiders, fungi and bacterial assemblages from logs. Variation partitioning for community metrics based on a unified framework of Hill numbers showed consistent results for both studies: host identity was most important for sporocarp-detected fungal assemblages, decay stage and host tree for DNA-detected fungal assemblages, microclimate and decay stage for beetles and spiders and decay stage for bacteria. Spatial distance was of minor importance for most taxa but showed the strongest effects for arthropods. The contrasting patterns among the taxa highlight the need for multi-taxon analyses in identifying the importance of abiotic and biotic drivers of community composition. Moreover, the consistent finding of microclimate as the primary driver for saproxylic beetles compared to host identity shows, for the first time that existing evolutionary host adaptions can be outcompeted by local climate conditions in deadwood.}, language = {en} } @article{Vogel2020, author = {Vogel, J{\"o}rg}, title = {An RNA biology perspective on species-specific programmable RNA antibiotics}, series = {Molecular Microbiology}, volume = {113}, journal = {Molecular Microbiology}, number = {3}, doi = {10.1111/mmi.14476}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214869}, pages = {550 -- 559}, year = {2020}, abstract = {Our body is colonized by a vast array of bacteria the sum of which forms our microbiota. The gut alone harbors >1,000 bacterial species. An understanding of their individual or synergistic contributions to human health and disease demands means to interfere with their functions on the species level. Most of the currently available antibiotics are broad-spectrum, thus too unspecific for a selective depletion of a single species of interest from the microbiota. Programmable RNA antibiotics in the form of short antisense oligonucleotides (ASOs) promise to achieve precision manipulation of bacterial communities. These ASOs are coupled to small peptides that carry them inside the bacteria to silence mRNAs of essential genes, for example, to target antibiotic-resistant pathogens as an alternative to standard antibiotics. There is already proof-of-principle with diverse bacteria, but many open questions remain with respect to true species specificity, potential off-targeting, choice of peptides for delivery, bacterial resistance mechanisms and the host response. While there is unlikely a one-fits-all solution for all microbiome species, I will discuss how recent progress in bacterial RNA biology may help to accelerate the development of programmable RNA antibiotics for microbiome editing and other applications.}, language = {en} } @article{ThornSeiboldLeverkusetal.2020, author = {Thorn, Simon and Seibold, Sebastian and Leverkus, Alexandro B and Michler, Thomas and M{\"u}ller, J{\"o}rg and Noss, Reed F and Stork, Nigel and Vogel, Sebastian and Lindenmayer, David B}, title = {The living dead: acknowledging life after tree death to stop forest degradation}, series = {Frontiers in Ecology and the Environment}, volume = {18}, journal = {Frontiers in Ecology and the Environment}, number = {9}, doi = {10.1002/fee.2252}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218575}, pages = {505 -- 512}, year = {2020}, abstract = {Global sustainability agendas focus primarily on halting deforestation, yet the biodiversity crisis resulting from the degradation of remaining forests is going largely unnoticed. Forest degradation occurs through the loss of key ecological structures, such as dying trees and deadwood, even in the absence of deforestation. One of the main drivers of forest degradation is limited awareness by policy makers and the public on the importance of these structures for supporting forest biodiversity and ecosystem function. Here, we outline management strategies to protect forest health and biodiversity by maintaining and promoting deadwood, and propose environmental education initiatives to improve the general awareness of the importance of deadwood. Finally, we call for major reforms to forest management to maintain and restore deadwood; large, old trees; and other key ecological structures.}, language = {en} } @article{MichauxHansenJennichesetal.2020, author = {Michaux, Charlotte and Hansen, Elisabeth E. and Jenniches, Laura and Gerovac, Milan and Barquist, Lars and Vogel, J{\"o}rg}, title = {Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {10}, journal = {Frontiers in Cellular and Infection Microbiology}, issn = {2235-2988}, doi = {10.3389/fcimb.2020.600325}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-217947}, year = {2020}, abstract = {Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40\% (E. faecalis) and 43\% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.}, language = {en} }