Biology subjects

Brauer, A.

Publications and source records attributed to Brauer, A..

12 recordsLinked to original sources

bioRxiv2026

L1CAMxCD3 bispecific antibodies exert potent anti-tumor effects in preclinical pancreatic cancer models with representation of the complex tumor microenvironment

Pancreatic ductal adenocarcinoma (PDAC) is characterized by an immunosuppressive tumor microenvironment (TME) with pancreatic myofibroblasts (PMF) and macrophages being two prominent cell populations essentially impairing tumor responses to (immuno)therapies. L1 cell adhesion molecule (L1CAM) is upregulated in PDAC cells in primary and metastatic tissues and associated with tumor progression and therapy resistance. Using L1CAM as tumor-associated antigen, two bispecific antibodies (bsAB) targeting L1CAM and CD3 were developed in the IgG-(L)-ScFv format and their anti-tumorigenic activity was investigated in different preclinical PDAC models. In 2D models, both L1-bsAB exerted L1CAM-specific anti-PDAC cell activity when co-cultured with activated CD8+ T cells. Strong anti-PDAC cell effects along with elevated release of T cell effector molecules were also observed upon co-culture with peripheral blood mononuclear cells (PMBC) from healthy donors and PDAC patients. Of note, both L1-bsAB were also effective in 3D PDAC cell spheroids and neither impaired by PMF nor macrophages. Finally, application of L1-bsAB on organotypic tissue slice cultures from PDAC tissues comprising the entire complex TME also induced PDAC cell apoptosis and release of T cell effector molecules. Overall, our results highlight relevant anti-PDAC cell activity of L1-bsAB in immunosuppressive contexts supporting their potential as immunotherapeutic strategy for PDAC.

cancer biology↗

bioRxiv2026

Eelgrass seeds host a distinct microbiome that isconsistent along a salinity gradient

Seagrasses are the only plants that flower and produce seeds in the marine environment, where they form vast meadows that fulfill important ecosystem functions. Yet, seagrass cover has declined in many coastal areas around the world and re-colonization is slow. Despite clonal growth, seed recruitment is essential for seagrass dispersal and regional genetic diversity. While the seed microbiome of several terrestrial plants has been shown to influence germination and seedling survival, the role of the seagrass seed microbiome is still unclear. We investigated the microbiome of eelgrass (Zostera marina) seeds, leaves and roots along the natural salinity gradient of the German North and Baltic Sea coasts. Despite this strong variability, Z. marina seeds harbor distinct prokaryotic and eukaryotic microbial communities compared to those on leaves and roots. Predicted microbial functions suggest roles in nutrient cycling and germination, which may be critical for recovery and restoration of seagrass ecosystems. Scientific significance statementSeagrass meadows are important but declining coastal ecosystems. Around the world, efforts are being made to restore seagrass meadows in order to halt the loss of biodiversity and maintain ecosystem function. With an evolutionary history on land, seagrasses have introduced unique features to the marine environment, such as seeds. In terrestrial plants, the seed microbiome has been shown to be important for seed germination and seedling health. Here we show that the northern hemisphere seagrass Zostera marina has a distinct seed microbiome, containing core bacterial and eukaryotic taxa and predicted functions that may play a role in seed germination and vertical microbiome transmission. Our results lay the foundation for future seagrass restoration efforts that seek to manipulate seed microbiomes to improve seedling survival. Data availability statementRaw DNA sequence data has been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB72211. Processed data and associated metadata will be made available on PANGEA via the German Federation for Biological data (GFBio.org).

microbiology↗

bioRxiv2024

The ecology of potentially pathogenic Vibrio spp. in a seagrass meadow ecosystem

Seagrass meadow ecosystems offer several valuable ecosystem services in coastal regions around the world. Recent studies have suggested that one such important service is reduction of pathogenic bacteria and specifically Vibrio spp. in adjacent waters. The specific mechanisms of pathogen reduction remain unclear, although increased sedimentation has been suggested as one likely process for pathogens to be quenched from the water column. Whether Vibrio spp. persist in the sediment or in other compartments of the seagrass meadow is currently not known, but it has been shown that marine surface biofilms can function as reservoirs of pathogenic vibrios. This general feature may also apply to seagrass and sediment surfaces. In this study, we investigated the relative abundance and community ecology of Vibrio spp. bacteria in Baltic Sea seagrass meadows using both culturing and culture-independent methods. While we did not detect a significant reduction of Vibrio spp., the highest relative abundances of Vibrio spp. were observed in the water column above unvegetated sites as compared to seagrass meadows. We also detected high relative abundances of Vibrio spp. on seagrass roots, supporting previous observations that marine surfaces are selectively colonized by Vibrio spp., implying that these habitats are important for the persistence and possibly release of Vibrio spp. into the water column. Our results emphasize the need to understand the interactions of pathogenic bacteria with coastal habitats, including interactions with host organisms such as seagrasses that provide biofilm microenvironments, in order to understand how diseases associated with these organisms develop.

ecology↗

bioRxiv2024

Isolation and characterization of a phage collection against Pseudomonas putida

The environmental bacterium Pseudomonas putida has a wide range of metabolic pathways and thus entails great promise both as cell factories in biotechnological production and for bioremediation approaches to degrade various aromatic pollutants. To thrive in the environment, P. putida has to be able to endure the constant threat posed by bacteriophages. Surprisingly, up until now, only a few phages have been isolated for the common laboratory strain P. putida KT2440, and no phage defence mechanisms have been characterized yet. Here, we introduce a novel Collection of Environmental Pseudomonas putida Phages from Estonia (CEPEST), consisting of 67 dsDNA phages that belong to 22 phage species and nine phage genera. We show that most of the phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require intact LPS for P. putida infection. Additionally, we demonstrate that cryptic prophages in the P. putida chromosome strongly protect against the infection of many phages, whereas the chromosomal toxin-antitoxin systems play no role in phage defence of P. putida.

microbiology↗

bioRxiv2022

High-throughput profiling of drug interactions in Gram-positive bacteria

Drug combinations present a powerful strategy to tackle antimicrobial resistance, but have not been systematically tested in many bacterial species. Here, we used an automated high-throughput setup to profile [~] 8000 combinations between 65 antibacterial drugs in three Gram-positive species: the model species, Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulate previously known drug interactions, but also identify ten times more interactions than previously reported in the pathogen S. aureus, including two synergies that were also effective in multi-drug resistant clinical S. aureus isolates in vitro and in vivo. Interactions were largely species-specific and mostly synergistic for drugs targeting the same cellular process, as observed also for Gram-negative species1. Yet, the dominating synergies are clearly distinct between Gram-negative and Gram-positive species, and are driven by different bottlenecks in drug uptake and vulnerabilities of their cell surface structures. To further explore interactions of commonly prescribed non-antibiotic drugs with antibiotics, we tested 2728 of such combinations in S. aureus, detecting a plethora of unexpected antagonisms that could compromise the efficacy of antimicrobial treatments in the age of polypharmacy. We uncovered even more synergies than antagonisms, some of which we could demonstrate as effective combinations in vivo against multi-drug resistant clinical isolates. Among them, we showed that the antiaggregant ticagrelor interferes with purine metabolism and changes the surface charge of S. aureus, leading to strong synergies with cationic antibiotics. Overall, this exemplifies the untapped potential of approved non-antibacterial drugs to be repurposed as antibiotic adjuvants. All data can be browsed through an interactive interface (https://apps.embl.de/combact/).

microbiology↗

bioRxiv2022

Sulfate reducing bacteria associated to diatoms during a spring phytoplankton bloom

Phytoplankton blooms fuel marine food webs with labile dissolved carbon, but also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration, yet are also sites of intense algal-bacterial interactions and provide diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in the North Sea. Particulate fractions larger than 10 {micro}m diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, which may have implications for algal-bacterial interactions and carbon export during blooms.

ecology↗

bioRxiv2022

Development of a dedicated Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides

Rhodotorula toruloides is a potential chassis to microbial cell factories as this yeast can metabolise different substrates into a diverse range of natural products, but the lack of efficient synthetic biology tools hinders its applicability. In this study, the modular, versatile and efficient Golden Gate DNA assembly system was adapted to the first basidiomycete, an oleaginous yeast R. toruloides (RtGGA). R. toruloides CCT 0783 was sequenced, and used for the RtGGA design. The DNA fragments were assembled with predesigned 4-nt overhangs and a library of standardized parts was created containing promoters, genes, terminators, insertional regions, and resistance genes. The library was combined to create cassettes for the characterization of promoters strength and to overexpress the carotenoid production pathway. A variety of reagents, plasmids, and strategies were used and the RtGGA proved to be robust. The RtGGA was used to build three versions of the carotenoid overexpression cassette were built by using different promoter combinations. The cassettes were transformed into R. toruloides and the three new strains were characterized. Total carotenoid concentration increased by 41%. The dedicated GGA platform fills a gap in the advanced genome engineering toolkit for R. toruloides, enabling the efficient design of complex metabolic pathways.

synthetic biology↗

bioRxiv2020

Pseudomonas putida chromosomal toxin-antitoxin systems carry neither clear fitness benefits nor big costs

Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance supports the hypothesis of TA systems being associated with stress adaptation. However, the deletion of TA genes has usually no fitness consequences, supporting the selfish elements hypothesis. Here, we aimed to evaluate the cost and benefits of chromosomal TA systems to Pseudomonas putida. We show that multiple TA systems do not confer fitness benefits to this bacterium as deletion of 13 TA loci does not influence stress tolerance, persistence and biofilm formation. Our results instead show that TA loci are costly and decrease the competitive fitness of P. putida. Still, the cost of multiple TA systems is low and detectable in certain conditions only. Construction of antitoxin deletion strains showed that only five TA systems code for toxic proteins, while other TA loci have evolved towards reduced toxicity and encode non-toxic or moderately potent proteins. Analysis of P. putida TA systems homologs among fully sequenced Pseudomonads suggests that the TA loci have been subjected to purifying selection and that TA systems spread among bacteria by horizontal gene transfer.

microbiology↗

bioRxiv2019

Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli

When nutrients run out, bacteria enter a dormant metabolic state. This low or undetectable metabolic activity helps bacteria to preserve their scant reserves for future, but also diminishes their ability to trace the environment for new growth-promoting substrates. However, neighboring microbial growth is a sure indicator of favorable environment and thus, can serve as a cue for exiting the dormancy. Here we report that for Escherichia coli this cue is the basic peptidoglycan unit (i.e. muropeptide). We show that several forms of muropeptides can stimulate growth resumption of dormant E. coli cells, but the sugar - peptide bond is crucial for activity. We also demonstrate that muropeptides from several different species can induce growth resumption of E. coli and also Pseudomonas aeruginosa. These results, together with the previous identification of muropeptides as germination signal for bacterial spores, makes muropeptides rather universal cue for bacterial growth.

microbiology↗

bioRxiv2019

Gene content of the fish-hunting cone snail Conus consors

BackgroundConus consors is a fish-hunting cone snail that lives in the tropical waters of the Indo-Pacific region. Cone snails have attracted scientific interest for the amazing potency of their venom, which consists of a complex mixture of small proteins known as conopeptides, many of which act as ion channel and receptor modulators with high selectivity.\n\nResultsWe have analysed publicly available transcriptomic sequences from 8 tissues of Conus consors and complemented the transcriptome data with the data from genomic DNA reads. We identified 17,715 full-length protein sequences from the transcriptome. In addition, we predicted 168 full-length or partial conopeptide sequences and characterized gene structures of several conopeptide superfamilies.

genomics↗

bioRxiv2018

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.

We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) generates a k-mer-based statistical model for predicting a given phenotype and (b) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa isolates (ciprofloxacin resistance) and 460 Clostridium difficile isolates (azithromycin resistance). The phenotype prediction models trained from these datasets performed with 88% accuracy on the K. pneumoniae test set, 88% on the P. aeruginosa test set and 96.5% on the C. difficile test set. Prediction accuracy was the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets.\n\nPhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (https://github.com/bioinfo-ut/PhenotypeSeeker/).\n\nSummaryPredicting phenotypic properties of bacterial isolates from their genomic sequences has numerous potential applications. A good example would be prediction of antimicrobial resistance and virulence phenotypes for use in medical diagnostics. We have developed a method that is able to predict phenotypes of interest from the genomic sequence of the isolate within seconds. The method uses statistical model that can be trained automatically on isolates with known phenotype. The method is implemented in Python programming language and can be run on low-end Linux server and/or on laptop computers.

bioinformatics↗

bioRxiv2017

Eelgrass leaf surface microbiomes are locally variable and highlycorrelated with epibiotic eukaryotes

Eelgrass (Zostera marina) is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes) as well as eukaryotic epibionts in-and outside lagoons on the German Baltic Sea coast. Bacterial microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both bacterial and eukaryotic community composition. Communities of bacterial and eukaryotic epibionts were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surface biofilms are a mosaic of the microbiomes of several eukaryotes, in addition to that of the eelgrass itself, and underlines that eukaryotic microbial diversity should be taken into account in order to explain microbiome assembly and dynamics in aquatic environments.

microbiology↗