Biology subjects

Behr, M.

Publications and source records attributed to Behr, M..

10 recordsLinked to original sources

bioRxiv2026

The 3D micro- and nanostructure of the apical extracellular matrix in Drosophila

The apical extracellular matrix (aECM) serves as a dynamic scaffold, orchestrating tissue growth, cellular communication, and wound repair, and thus functions as a powerful biomaterial. In this study, we explored the intricate three-dimensional landscape of the Drosophila larval aECM using advanced 3D Volume electron microscopy. This technique opens a window into understanding and mimicking the diversity of aECM surfaces and architectures of the exoskeletal cuticles. We reconstructed the striking forms of denticles, hairs, and sensory organs, including double sensilla and Keils organs, at the epidermal surface. Our reconstructions brought the larval tracheal system and the sponge-like felt chamber (Filzkorper) of the spiracles into sharp relief, revealing a labyrinth of tiny cavities surrounding a central tube that extends from the posterior opening to the tracheal lumen. When examining the ultrastructure of transport-active anal pad cells, we discovered an inverted pattern of cuticular pore-canal structures, which supports their suggested role in osmoregulation across the aECM. Our findings further suggest that ordinary epidermal cells weave an intricate network of pore canals, enabling the orchestration of material distribution throughout the entire aECM. Moreover, we reconstructed tendon cells and chordotonal organs that form a branching network of numerous filamentous intracuticular fibers that weave through the aECM, linking the exoskeleton to muscles and sensory organs. By thoroughly mapping the intricate ultrastructural features of the aECM, this study opens new avenues for exploring how its protective, mechanical, and sensory roles intertwine, inspiring the next generation of tailor-made biomimetic materials.

developmental biology↗

bioRxiv2025

Pantetheinamides that inhibit the growth of intracellular Salmonella Typhimurium

The metabolic adaptability of intracellular pathogens, such as the Gram-negative Salmonella enterica serovar Typhimurium (STm), enables their survival in nutrient-restricted host environments, while also presenting an opportunity for selective antimicrobial targeting. Herein, we report the synthesis and screening of a small pantetheinamide library aimed at inhibiting the proliferation of STm within macrophages. Two lead compounds exhibited selective activity against intracellular STm and reduced bacterial burden in a murine colitis model. Mechanistic studies suggest their primary mode of action to be the inhibition of coenzyme A (CoA) biosynthesis via the PanD-PanZ regulatory complex, which is absent in host cells. Importantly, resistance pressure to our compound was shown to be significantly stronger in nutrient-limited media compared to nutrient-rich media, supporting the targeting of nutrient stress as a strategy to delay resistance. This work highlights the value of inhibiting pathogen-specific metabolic vulnerabilities in combination with host defence mechanisms to develop novel antimicrobials.

microbiology↗

bioRxiv2024

A robust set of qPCR methods to evaluate adulteration in major spices and herbs

Spices and herbs are used in multiple forms by consumers and companies related to food or pharmaceuticals. Their intricate supply chains, high prices and limited productions make them susceptible to deceptive practises. However, robust methodology to detect multiple adulterants is still rarely available, preventing national control laboratories from enforcing European and national regulations. This article presents qPCR methods developed to identify adulterants in six commonly consumed spices and herbs, namely paprika, turmeric, saffron, cumin, oregano and black pepper. Each genuine sample was blended with the top five adulterants identified in the European Union-wide coordinated control plan on herbs and spices and existing literature. These SYBR Green qPCR methods enable specific detection of adulterants, and their sensitivities allow to differentiate inadvertent contamination from deliberate adulteration. Methods performances were evaluated both in binary mixtures and with complex adulteration pattern, validating their effectiveness in safeguarding the authenticity of these high values commodities. HighlightsO_LIAuthenticity of spices and herbs is at high risk of fraudulent malpractices. C_LIO_LIWe provide specific qPCR methods to detect prevalent adulterants. C_LIO_LITrueness of each method was systematically assessed. C_LIO_LISensitivity of methods meet ISO requirements for purity assessment. C_LIO_LIMethods versatility is evaluated with multi-adulterated samples. C_LI

molecular biology↗

bioRxiv2023

The proteolysis of ZP proteins is essential to control cell membrane structure and integrity of developing tubes

Membrane expansion integrates multiple forces to mediate precise tube growth and network formation. Defects lead to deformations, as found in diseases such as polycystic kidney diseases, aortic aneurysms, stenosis, and tortuosity. We identified a mechanism of sensing and responding to the membrane expansion of tracheal tubes. We show in Drosophila that Zona Pellucida domain proteins Piopio and Dumpy cooperate to integrate mechanical stress at cell membranes and luminal matrix. When tension appears at the apical membrane due to tracheal tube length expansion, Piopio undergoes ectodomain shedding by the Matriptase homolog Notopleural, which releases Piopio-mediated linkages between membranes and extracellular matrix. Failure of this process leads to deformations of the apical membrane and comprises tubular network function. We also show conserved ectodomain shedding by the human matriptase during TGF-{beta} signaling, both of which are required in the lung, providing novel approaches for in-depth analysis of pulmonary diseases caused by cell and tube shape changes.

developmental biology↗

bioRxiv2022

Loss of allosteric regulation in α-isopropylmalate synthase identified as an antimicrobial resistance mechanism

Despite our best efforts to discover new antimicrobials, bacteria have evolved mechanisms to become resistant. Resistance to antimicrobials can be attributed to innate, inducible, and acquired mechanisms. Mycobacterium abscessus is one of the most antimicrobial resistant bacteria and is known to cause chronic pulmonary infections within the cystic fibrosis community. Previously, we identified epetraborole as an inhibitor against M. abscessus with in vitro and in vivo activities and that the efficacy of epetraborole could be improved with the combination of the non-proteinogenic amino acid norvaline. Norvaline demonstrated activity against the M. abscessus epetraborole resistant mutants thus, limiting resistance to epetraborole in wild type populations. Here we show M. abscessus mutants with resistance to epetraborole can acquire resistance to norvaline in a leucyl-tRNA synthetase (LeuRS) editing-independent manner. After showing that the membrane hydrophobicity and efflux activity are not linked to norvaline resistance, whole-genome sequencing identified a mutation in the allosteric regulatory domain of -isopropylmalate synthase (-IPMS). We found that mutants with the -IPMSA555V variant incorporated less norvaline in the proteome and produced more leucine than the parental strain. Furthermore, we found that leucine can rescue growth inhibition from norvaline challenge in the parental strain. Our results demonstrate that M. abscessus can modulate its metabolism through mutations in an allosteric regulatory site to upregulate the biosynthesis of the natural LeuRS substrate and outcompete norvaline. These findings emphasize the antimicrobial resistant nature of M. abscessus and describe a unique mechanism of substrate-inhibitor competition. Significance StatementCystic fibrosis patients and individuals undergoing plastic surgery are at risk for acquiring chronic infections from Mycobacterium abscessus. Current antibiotics are not adequate and require increased drug discovery efforts to identify better treatments for these patients. The benzoxaborole, epetraborole has been shown by our group and others to be a promising candidate against M. abscessus but the emergence of resistance to epetraborole in a clinical trial for complicated urinary tract infections has hindered its development. Previously, we identified the combination of epetraborole and norvaline as a potential means to limit resistance against epetraborole. Our results here demonstrate that M. abscessus can acquire resistance to both epetraborole and norvaline. These results may help develop combination therapies to reduce the risk of resistance to benzoxaboroles and non-proteinogenic amino acids.

microbiology↗

bioRxiv2022

Discovery of benzophenanthridine derivatives with potent activity against multidrug resistant Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), the pathogen responsible for tuberculosis (TB), is the leading cause of bacterial disease-related death worldwide. Current antibiotic regimens for the treatment of TB remain dated and suffer from long treatment times as well as the development of drug-resistance. As such, the search for novel chemical modalities that have selective or potent anti-Mtb properties remains an urgent priority, particularly against multidrug resistant (MDR) Mtb strains. Herein, we design and synthesize 35 novel benzo[c]phenanthridine derivatives (BPD). The two most potent compounds, BPD-6 and BPD-9, accumulated within the bacterial cell and exhibited strong inhibitory activity (MIC90 [~] 2-10 M) against multiple Mycobacterium strains, while remaining inactive against a range of other Gram-negative and Gram-positive bacteria. BPD-6 and BPD-9 were also effective in reducing Mtb viability within infected macrophages. The two BPD compounds displayed comparable efficacy to rifampicin, a critical frontline antibiotic used for the prevention and treatment of TB. Importantly, BPD-6 and BPD-9 inhibited the growth of multiple MDR Mtb clinical isolates, suggesting a completely novel mechanism of action compared to existing frontline TB dugs. The discovery of BPDs provides novel chemical scaffolds for anti-TB drug discovery. TOC/GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/515485v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1536acaorg.highwire.dtl.DTLVardef@1881e83org.highwire.dtl.DTLVardef@18b2f58org.highwire.dtl.DTLVardef@d15f1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Identification of a microbial sub-community from the feral chicken gut that reduces Salmonella colonization and improves gut health in a gnotobiotic chicken model.

A complex microbial community in the gut generally prevent the colonization of enteric pathogens such as Salmonella. Because of the high complexity, several species or combination of species in the gut can confer colonization resistance. To gain a better understanding of the colonization resistance against Salmonella enterica, we isolated a library of 1,300 bacterial strains from feral chicken gut microbiota which represented a total of 51 species. Using a co-culture assay, we screened the representative species from this library and identified 30 species that inhibited Salmonella enterica Typhimurium. To improve the Salmonella inhibition capacity, from a pool of fast-growing species, we formulated 66 bacterial blends, each of which composed of 10 species. Bacterial blends were more efficient in inhibiting Salmonella as compared to individual species. The blend that showed maximum inhibition (Mix10) also inhibited other serotypes of Salmonella frequently found in poultry. The in vivo effect of Mix10 was examined in a gnotobiotic and conventional chicken model. The Mix10 consortium reduced Salmonella colonization, intestinal tissue damage and inflammation in both models. Cell free supernatant of Mix10 did not show Salmonella inhibition, indicating that Mix10 inhibits Salmonella through either nutritional competition or reinforcement of host immunity. Out of ten species, three species in Mix10 did not colonize while three species constituted more than 70% of the community. Two of these species represents previously uncultured bacteria. Our approach could be used as a high-throughput screening system to identify additional bacterial sub-communities that confer colonization resistance against enteric pathogens and its effect on the host. ImportanceSalmonella colonization in chicken and human infections originating from Salmonella- contaminated poultry is a significant problem. Poultry has been identified as the most common food linked to enteric pathogen outbreaks in the United States. Since multi-drug resistant Salmonella often colonize chicken and cause human infections, methods to control Salmonella colonization in poultry are needed. The method we describe here could form the basis of developing gut microbiota-derived bacterial blends as a microbial ecosystem therapeutic against Salmonella.

microbiology↗

bioRxiv2020

Learning epistatic polygenic phenotypes with Boolean interactions

Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1, a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

bioinformatics↗

bioRxiv2020

The antimicrobial activity of the macrophage metabolite itaconate is synergistic with acidity.

The production of itaconate by macrophages was only discovered in 2011. A rapidly increasing number of studies have since revealed essential biological roles for itaconate, ranging from antimicrobial to immunomodulator. Itaconate has been estimated to reach low-millimolar concentrations in activated macrophages, including those within infected lungs and brains, whereas itaconates MIC towards several bacterial strains were measured to be in the low-to-mid-millimolar range, casting some doubts on the antibacterial role of itaconate in vivo. Several of these investigations, in particular those measuring MIC values of itaconate or itaconic acid, have however tended to ignore the high acidity of this small diacid (pKas 3.85 and 5.45), thereby potentially biasing the MIC measurements. We report herein that: 1) at high concentration, itaconic acid can significantly reduce the pH of growth media; 2) the antibacterial activity of itaconate increases in a synergistic manner with acidity; 3) this synergistic effect is not simply due to increased permeability of monoanionic itaconate; 4) considering that the MIC of itaconate is many fold lower under acidic conditions for all strains tested, itaconate may serve an antimicrobial role, particularly in acidic vesicles such as the phagolysosome; and 5) differential growth behavior in the presence of disodium itaconate versus itaconic acid may serve to rapidly screen bacterial strains for their ability to metabolize itaconate. Our results further support the hypothesis that inhibitors of itaconate degradation in bacteria may provide a new strategy to treat infections.

microbiology↗

bioRxiv2019

treeSeg: Testing for Dependence on Tree Structures

Tree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently this is addressed on an ad hoc basis, usually requiring the user to decide on an appropriate number of clusters to prune out of the tree to be tested against the response variable. Here we present a statistical method with statistical guarantees that tests for association between the response variable and a fixed tree structure across all levels of the tree hierarchy with high power, while accounting for the overall false positive error rate. This enhances the robustness and reproducibility of such findings. Significance StatementTree like structures are abundant in the empirical sciences as they can summarize high dimensional data and show latent structure among many samples in a single framework. Prominent examples include phylogenetic trees or hierarchical clustering derived from genetic data. Currently users employ ad hoc methods to test for association between a given tree and a response variable, which reduces reproducibility and robustness. In this paper, we introduce treeSeg, a simple to use and widely applicable methodology with high power for testing between all levels of hierarchy for a given tree and the response while accounting for the overall false positive rate. Our method allows for precise uncertainty quantification and therefore increases interpretability and reproducibility of such studies across many fields of science.

bioinformatics↗