Biology subjects

Auer, M.

Publications and source records attributed to Auer, M..

18 recordsLinked to original sources

bioRxiv2026

Self-organized hemanoids derived from human iPSCs create a niche that produces definitive extraembryonic hematopoiesis.

Manufacturing red blood cells (RBCs) from human induced pluripotent stem cells (iPSCs) can improve our understanding of embryonic erythropoiesis, foster innovative treatments for RBC-related diseases, and ultimately address clinical blood supply shortages. However, existing systems face low efficiency, enucleation failure, and uncertainty about the develop-mental wave of cultured RBCs. We successfully used self-organized hemanoids to improve iPSC-derived RBC generation. Based on the hypothesis that cellular interactions and 3D organization promote hematopoietic cell fate, we aimed to thoroughly characterize hemanoids. We visualized the spatiotemporal emergence of hematopoiesis by generating a CD43-GFP reporter iPSC line. Imaging and spatial transcriptomics analysis provided de-tailed insight into the hemanoid architecture, identifying stromal cells and hepatoblasts as potential erythropoiesis-supportive elements. The developmental stage mirrors extraembryonic hematopoiesis. Given the difficulties of accessing these early stages in vivo, our system offers a platform not only for further clinical translation but also for exploring hu-man embryonic blood wave dynamics.

developmental biology↗

bioRxiv2026

Volume EM reveals three-dimensional architecture of the desmosome in epithelial cells and tissue models

Desmosomes are a type of cell-cell adhesive junction present in cardiac tissue and epithelial tissues such as the epidermis. These intercellular junctions anchor to the intermediate filament cytoskeleton, providing mechanical integrity to the tissues in which they reside. Our understanding of desmosome architecture has largely been influenced by observations of two-dimensional images obtained through conventional electron microscopy. Here, using focused ion beam scanning electron microscopy, we report the three-dimensional ultrastructure of desmosomes in A431 and S1 human mammary epithelial cells. We also reveal differences in desmosome ultrastructure at homo- and heterotypic junctions of human nasal airway epithelial cells. Quantitative analyses of these volume EM datasets reveal variations in desmosome size, shape, and organization. Importantly, we report the presence of discontinuities or "holes" within the desmosome outer dense plaque, a novel feature that is observed in either one or both halves of a desmosome. This study provides the first comprehensive description of the epithelial desmosome as a three-dimensional structure, and emphasizes the need to investigate the effects of dynamic morphogenetic processes and disease states on desmosome ultrastructure.

cell biology↗

bioRxiv2023

Estradiol propionate reduction of nuclear size in prostate cancer lines lacking DHRS7suggests DHRS7 absence as a biomarker for the effectiveness of estrogen therapy

Increased nuclear size correlates with lower survival rates for prostate cancer and is a hallmark of late-stage androgen-insensitive tumors. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a marker for prostate cancer grading because it is lost in late-stage androgen-insensitive tumors. Here we find that loss of DHRS7 from the early-stage LNCaP prostate cancer cell line increases nuclear size, potentially explaining the nuclear size increase observed in higher-grade prostate tumors. Exogenous expression of DHRS7 in the late-stage PC3 prostate cancer cell line correspondingly decreases nuclear size. We separately tested 80 compounds from the Microsource Spectrum library for their ability to restore normal nuclear size to PC3 cells, finding estradiol propionate had the same effect as re-expression of DHRS7 in the PC3 cells. However, the drug had no effect on LNCaP cells or PC3 cells re-expressing DHRS7. We speculate that reported beneficial effects of estrogens in late-stage prostate cancer may target a pathway which is only active in cells lacking DHRS7 that have increased nuclear size and propose DHRS7 as a potential biomarker for the likely effectiveness of estrogen-based treatments.

cancer biology↗

bioRxiv2023

Origin of biogeographically distinct ecotypes during laboratory evolution

Resource partitioning within microbial communities is central to their incredible productivity, including over 1 gigaton of annual methane emissions through syntrophic interactions1. Here, we show how isogenic strains of a sulfate reducing bacterium (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification over 300-1,000 generations in a purely planktonic environmental2-4 context giving rise to coexisting ecotypes that could partition resources and improve overall stability, cooperativity, and productivity in a simulated subsurface environment. We discovered that mutations in just 15 Dv and 7 Mm genes gave rise to ecotypes within each species that were spatially enriched between sediment and planktonic phases over the course of only a few generations after transferring the evolved populations to a fluidized bed reactor (FBR). While lactate utilization by Dv in the attached community was significantly greater, the resulting H2 was partially consumed by low affinity hydrogenases in Mm within the same attached phase. The unutilized H2 was scavenged by high affinity hydrogenases in the planktonic phase Mm, generating copious amounts of methane and higher ratio of Mm to Dv. Our findings show how a handful of mutations that arise in one environmental context can drive resource partitioning by ecologically differentiated variants in another environmental context, whose interplay synergistically improves productivity of the entire mutualistic community.

microbiology↗

bioRxiv2022

Nanoscaled discovery of a shunt rifamycin from Salinispora arenicola using a three-colour GFP-tagged Staphylococcus aureus macrophage infection assay.

Antimicrobial resistance has emerged as an urgent global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent. Staphylococcus aureus is a major human and animal pathogen, responsible for high levels of morbidity and mortality worldwide. The intracellular survival of S. aureus in macrophages contributes to immune evasion, dissemination, and resilience to antibiotic treatment. Here, we present a confocal fluorescence imaging assay for monitoring macrophage infection by GFP-tagged Staphylococcus aureus as a front-line tool to identify antibiotic leads. The assay was employed in combination with nanoscaled chemical analyses to facilitate the discovery of a novel, active rifamycin analogue. Our findings indicate a promising new approach to the identification of anti-microbial compounds with macrophage intracellular activity. The novel antibiotic identified here may represent a useful addition to our armoury in tackling the silent pandemic of antimicrobial resistance.

cell biology↗

bioRxiv2022

Neural underpinnings of action adaptation in the subthalamic nucleus.

Adapting our actions to changing goals and environments is central to intelligent behavior. There is substantial evidence that the basal ganglia play a crucial role in reinforcing actions that have led to favorable outcomes. However, little is known about the neural mechanisms underlying action adaptation following unfavorable outcomes when change is warranted. Here, we recorded electrophysiological activity and applied bursts of electrical stimulation to the subthalamic nucleus (STN), a core area of the basal ganglia, in patients with Parkinsons disease using deep brain stimulation electrodes. During a task where patients continuously had to adapt their force depending on changing action-value associations, decreases in STN beta (13-30 Hz) activity in two critical time windows were associated with poorer outcomes and stronger action adaptation. STN stimulation reduced beta activity and led to stronger action adaptation if applied within the time windows when STN activity reflected action evaluation and adaptation. These results suggest that dynamic modulation of STN activity facilitates adaptive behavior.

neuroscience↗

bioRxiv2021

Biofilm Interaction Mapping and Analysis (BIMA): A tool for deconstructing interspecific interactions in co-culture biofilms

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition and invasion) between colony forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and thirteen other species of pseudomonas isolated from non-contaminated soil. The metabolites and genes associated with both active co-culture growth and inhibitory growth were investigated using mass spectrometry based metabolomics and mutant fitness profiling of a DNA-barcoded mutant library. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and metabolomics. IMPORTANCEThe Biofilm Interaction Mapping and Analysis (BIMA) methodology provides a way to rapidly screen for positive and negative interspecific interactions, followed by an analysis of the genes and metabolites that may be involved. Knowledge of these may offer opportunities for engineered strains with improved function in biotechnology systems. P. stutzeri, an organism with wide-spread utilization in consortia based biotechnologies, was used to demonstrate the utility of this approach. Where little is known about the factors influencing biofilm based interactions, elucidation of the genes and metabolites involved allows for better control of the system for improved function or yield.

microbiology↗

bioRxiv2021

Fasting reverses drug-resistance in hepatocellular carcinoma through p53-dependent metabolic synergism

Cancer cells voraciously consume nutrients to support their growth, exposing a metabolic vulnerability that can be therapeutically exploited. Here we show in hepatocellular carcinoma (HCC) cells, xenografts, and in patient-derived HCC organoids that fasting can synergistically sensitize resistant HCC to sorafenib. Mechanistically, sorafenib acts non-canonically as an inhibitor of mitochondrial respiration, causing resistant cells to depend on glycolysis for survival. Fasting, through reduction in glucose and impeded AKT/mTOR-signaling, prevents this Warburg shift. Regulating glucose transporter and pro-apoptotic protein expression, p53 is necessary and sufficient for the sorafenib-sensitizing effect of fasting. p53 is also crucial for fasting-mediated improvement of sorafenib efficacy in an orthotopic HCC mouse model. Together, our data suggest intermittent fasting and sorafenib as rational combination therapy for HCC with intact p53 signaling. As HCC therapy is currently severely limited by resistance, these results should instigate clinical studies aimed at improving therapy response in advanced-stage, and possibly even early-stage, HCC. HIGHLIGHTSO_LIFasting sensitizes resistant HCC xenografts and patient-derived organoids to sorafenib C_LIO_LISorafenib-mediated Warburg shift is prevented by glucose limitation upon fasting C_LIO_LIFasting synergistically improves sorafenib efficacy in non-resistant models C_LIO_LIp53 is required for synergism by regulating glucose uptake and apoptosis C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/430545v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1c0bf9org.highwire.dtl.DTLVardef@15638b4org.highwire.dtl.DTLVardef@1a4b322org.highwire.dtl.DTLVardef@1ec863a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels

RNA-protein interactions are central to all gene expression processes and contribute to variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as incurable. Here we developed a fluorescent on-bead screening platform: RNA pull-down-Confocal Nanoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7s primary target is an mRNA of -Synuclein, which contributes to aetiology of Parkinsons disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of -Synuclein. This opens up new therapeutic avenues towards treatment of Parkinsons disease as well as provides novel methodology to search for RNA-protein interaction modulators.

molecular biology↗

bioRxiv2020

PyBindingCurve, simulation and curve fitting to complex binding systems at equilibrium.

Understanding multicomponent binding interactions in protein-ligand, protein-protein and competition systems is essential for fundamental biology and drug discovery. Hand deriving equations quickly becomes unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain complexity. To address this problem and allow easy access to simulation, plotting and parameter fitting to complex systems at equilibrium, we present the Python package PyBindingCurve. We apply this software to explore homodimer and heterodimer formation culminating in the discovery that under certain conditions, homodimers are easier to break with an inhibitor than heterodimers and may also be more readily depleted. This is a potentially valuable and overlooked phenomenon of great importance to drug discovery. PyBindingCurve may be expanded to operate on any equilibrium binding system and allows definition of custom systems using a simple syntax. PyBindingCurve is available under the MIT license at: https://github.com/stevenshave/pybindingcurve as Python source code accompanied by examples and as an easily installable package within the Python Package Index.

biophysics↗

bioRxiv2020

Chemical-Genetic Interrogation of Nuclear Size Control Reveals Cancer-Specific Effects on Cell Migration and Invasion

Lower survival rates for many cancer types correlate with increases or decreases in nuclear size/scaling in a tumor-type/tissue-specific manner. Postulating that nuclear size changes confer a fitness advantage on tumor cells, we screened for FDA/EMA-approved compounds that reverse tumor nuclear size changes in cell lines from three such tumor types: prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous lung cancer. We found distinct, largely non-overlapping sets of compounds that either rectify or exacerbate nuclear size changes for each tumor type. Nuclear size phenotypes across cell lines clustered particular classes of compounds including serotonin uptake inhibitors, cyclo-oxygenase inhibitors, beta-adrenergic receptor agonists, monoamine oxidase inhibitors, and Na+/K+ ATPase inhibitors. Nearly all compounds selected for further investigation inhibited cell migration and/or invasion, suggesting that targeting nuclear size control pathways in chemotherapy regimens could improve patient survival.

cancer biology↗

bioRxiv2019

Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution

Cryo-electron tomography maps often exhibit considerable noise and anisotropic resolution, due to the low-dose requirements and the missing wedge in Fourier space. These spurious features are visually unappealing and, more importantly, prevent an automated segmentation of geometric shapes, requiring a highly subjective, labor-intensive manual tracing. We developed a novel computational strategy for objectively denoising and correcting missing-wedge artifacts in the special but important case of repetitive basic shapes, such as filamentous structures. In this approach, we use the template and a non-negative "location map" to constrain the deconvolution scheme, allowing us to recover, to a considerable degree, the information lost in the missing wedge. We applied our method to data of actin-filament bundles of inner-ear stereocilia, which are critical in hearing transduction processes, and found a good overlap with the experimental map and with manual tracing. In addition, we demonstrate that our method can also be used for membrane detection.

biophysics↗

bioRxiv2019

Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication

As obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High throughput siRNA screens provide a systematic approach for the identification of novel host-virus interactions. Here, we report a large-scale screen for host factors important for human cytomegalovirus (HCMV), consisting of 6,881 siRNAs. We identified 47 proviral factors and 68 antiviral factors involved in a wide range of cellular processes including the mediator complex, proteasome function and mRNA splicing. Focused characterisation of one of the hits, asparagine synthetase (ASNS), demonstrated a strict requirement for asparagine for HCMV replication which leads to an early block in virus replication before the onset of DNA amplification. This effect is specific to HCMV, as knockdown of ASNS had little effect on herpes simplex virus-1 or influenza A virus replication, suggesting the restriction is not simply due to a failure in protein production. Remarkably, virus replication could be completely rescued seven days post-infection with addition of exogenous asparagine, indicating that while virus replication is restricted at an early stage, it maintains the capacity for full replication days after initial infection. This study represents the most comprehensive siRNA screen for the identification of host factors involved in HCMV replication and identifies the non-essential amino acid, asparagine as a critical factor in regulating HCMV virus replication. These results have implications for control of viral latency and the clinical treatment of HCMV in patients.\n\nImportanceHCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals have been developed for use against HCMV since the licensing of ganciclovir, and of these, the same viral genes are often targeted, reducing the usefulness of these drugs against resistant strains. An alternative approach is to target host genes essential for virus replication. Here we demonstrate that HCMV replication is highly dependent on levels of the amino acid asparagine and knockdown of a critical enzyme involved in asparagine synthesis results in severe attenuation of virus replication. These results suggest that reducing asparagine levels through dietary restriction or chemotherapeutic treatment could limit HCMV replication in patients.

microbiology↗

bioRxiv2019

3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography

Outer hair cells in the mammalian cochlea display a unique type of voltage-induced mechanical movement, termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the outer hair cell (OHC) lateral wall, and it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles that endow the SSC with a previously unrealized anisotropic structural rigidity. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections spaced at regular intervals. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features.

biophysics↗

bioRxiv2018

Electron cryo-tomography of vestibular hair-cell stereocilia

High-resolution imaging of hair-cell stereocilia of the inner ear has contributed substantially to our understanding of auditory and vestibular function. To provide three-dimensional views of the structure of stereocilia cytoskeleton and membranes, we developed a method for rapidly freezing unfixed stereocilia on electron microscopy grids, which allowed subsequent 3D imaging by electron cryo-tomography. Structures of stereocilia tips, shafts, and tapers were revealed, demonstrating that the actin paracrystal was not perfectly ordered. This sample-preparation and imaging procedure will allow for examination of structural features of stereocilia in a near-native state.

neuroscience↗

bioRxiv2018

Cryo-Electron tomography 3D structure and nanoscale model of Arabidopsis thaliana cell wall

Using cryo-electron tomography of vitrified sections of one month-old Arabidopsis thaliana inflorescence stem tissue, we visualized primary and secondary cell walls of xylem tissue. Extensive quantitative and statistical analysis of segmented 3D tomographic data allowed geometrically idealized 3D-CAD model building of prototypic microfibrils, cross-links, and their supramolecular microfibril 3D organization. We propose a prototypic microfibril model where a cellulose core is heavily decorated by a thin sheath of hemicellulose with infrequent but sturdy hemicellulose-based cross-links. Such prototypic microfibrils then adopt a rather unexpected 3D supramolecular organization of high order and complexity. We discuss a possible new role for lignin in plant cell walls at low concentrations with lignin not acting as a matrix but rather as a reinforcement of microfibrils and cross-links. Extensive computational simulations of mechanical properties further revealed that this 3D organization of the cell wall is not optimized for load bearing but instead for flexibility and ductility.\n\nOne Sentence SummaryCryo-electron tomography and mechanical simulations revealed cell wall 3D architecture, optimized for flexibility/ductility.

plant biology↗

bioRxiv2018

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labelled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging. UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2 and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme. As a sensitive, quantitative, flexible and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.

biochemistry↗

bioRxiv2017

Detecting Drug-Target Binding In Cells Using Fluorescence Activated Cell Sorting Coupled With Mass Spectrometry Analysis

The assessment of drug-target engagement for determining the efficacy of a compound inside cells remains challenging, particularly for difficult target proteins. Existing techniques are more suited to soluble protein targets. Difficult target proteins include those with challenging in vitro solubility, stability or purification properties that preclude target isolation. Here, we report a novel technique that measures intracellular compound-target complex formation, as well as cellular permeability, specificity and cytotoxicity - the Toxicity-Affinity-Permeability-Selectivity (TAPS) technique. The TAPS assay is exemplified here using human kynurenine 3-monooxygenase (KMO), a challenging intracellular membrane protein target of significant current interest. TAPS confirmed target binding of known KMO inhibitors inside cells. We conclude that the TAPS assay can be used to facilitate intracellular hit validation on most, if not all intracellular drug targets.

pharmacology and toxicology↗