Biology subjects

Moeller, A.

Publications and source records attributed to Moeller, A..

At least 19 recordsLinked to original sources

bioRxiv2026

MaSkel and napari-MaSkel: fast morphological skeleton feature extraction from segmentation masks

Summary: Existing workflows for extracting morphological features from network-like biomedical structures often require several heterogeneous tools, which can limit integration and reproducibility. We present MaSkel and napari-MaSkel, open-source Python tools that provide GUI- and CLI-based workflows for 2D and 3D skeletonization and graph-based feature extraction, using a substantially accelerated implementation of the widely used Lee94 thinning algorithm. Availability and Implementation: MaSkel and napari-MaSkel are open-source Python packages available under the MIT license on PyPI and GitHub: https://github.com/bionetslab/maskel/, https://github.com/bionetslab/napari-maskel/. Documentation: https://bionetslab.github.io/maskel/, https://bionetslab.github.io/napari-maskel/. Benchmarking and validation: https://github.com/bionetslab/maskel-evaluations.

bioinformatics↗

bioRxiv2026

Cholesterol transport cycle of human ABCA2

Cholesterol is a key component of cellular membranes and is critical for brain function, particularly axon myelination. Among the 48 human ATP-binding cassette (ABC) transporters, ABCA2 exhibits the highest expression in the brain and is involved in cholesterol metabolism, primarily in oligodendrocytes. Notably, ABCA2 has been associated with myelin sheath integrity and maintenance, as well as Alzheimer's disease. Here, we report cryo-EM structures of human ABCA2 that reveal critical endogenous lipid-binding sites unique to ABCA2. Our five distinct conformations include a previously uncharacterized intermediate between the closed and apo states of ABCA subfamily transporters. Most importantly, we elucidated the cholesterol transport mechanism of ABCA2, which involves novel interdependent rotations of the exocytoplasmic domains (ECDs) and regulatory domains (RDs). Our structural findings provide a new perspective on ABCA transporter function and highlight the role of ABCA2 in facilitating efficient cholesterol recycling and transport in the brain.

molecular biology↗

bioRxiv2026

Translational Opportunity of Engineered IFNγ-eEVs Through Targeted Inhibition of JAK/STAT1 Signaling, Mimicking IVIg Therapy

Immunoglobulin (Ig) replacement therapies (IgRT) including intravenous (IVIg) and subcutaneous (SCIg), are pooled IgG preparations widely used to restore humoral immunity and to suppress pathological inflammation in autoimmune and inflammatory disorders. Despite broad clinical use, the mechanisms underlying their immunomodulatory effects remain incompletely defined. Here, we identify extracellular vesicle (EV)-associated cytokines as mediators of IVIg activity. Multiplex bead-based flow cytometry revealed that EVs isolated by size exclusion followed by ultracentrifugation from IVIg were CD63 positive but depleted of platelet-derived and HLA markers relative to EVs from unprocessed human plasma. Luminex profiling demonstrated substantial reduction of pro-inflammatory cytokines in IVIg EVs. Notably, although IVIg EVs contained abundant IFN{gamma}, they failed to activate IFNGR/JAK/STAT1 signaling. Instead, prolonged exposure to IVIg EVs suppressed subsequent IFN{gamma}-induced STAT1 activation. Engineered IFN{gamma}-coated EVs (IFN{gamma}-eEVs) recapitulated both activating and inhibitory effects indicating context-dependent signaling bias. Critically, cold ethanol precipitation, a key step in IVIg manufacturing, selectively abrogated the activating function of IFN{gamma}-eEVs while preserving their inhibitory capacity. These findings define a previously unrecognized mechanism where IVIg processing generates EVs that bias IFN{gamma} signaling toward suppression. EV-associated cytokines therefore represent a generalizable pathway through which IVIg exerts anti-inflammatory effects across immune-mediated diseases.

bioengineering↗

bioRxiv2026

Dietary and gut microbial variation among urban and rural populations of house mice (Mus musculus domesticus)

Urbanization can result in shifts in abiotic and biotic factors, including temperature, pollution, habitat type, pathogens, and diet, among others. These shifts can, in turn, shape the ecological and evolutionary trajectory of urban wildlife. The gut microbiota has the potential to mediate host-environment interactions, especially in the context of diet and disease, and thus may be a useful lens for understanding the impacts of urbanization. House mice (Mus musculus domesticus) are a cosmopolitan human commensal with a wealth of genomic and metagenomic resources. Here, we investigate patterns of variation in diet and gut microbial diversity, community composition, and function using a paired urban-rural sampling design in house mice from three metro regions in the eastern United States. First, using stable isotope analysis, we found that habitat--urban versus rural--was a major driver of variation in {delta}15N, suggesting a diet richer in animal proteins in cities. Next, using short-read sequencing of the 16S rRNA gene, we found that urban mice have lower gut microbial taxonomic diversity than their rural counterparts. We also found that community composition varied among urban and rural habitats, with differences largely reflecting shifts among closely related taxa. In particular, Prevotellaceae, a family known to be responsive to dietary quality, was differentially abundant, with lower abundance in urban habitats. Finally, we found differentiation in a few predicted microbial functions across habitat, primarily related to metabolism. Together, data across three independent sampling regions provide strong evidence that urbanization has the potential to shape the diet and the microbiome of house mice.

microbiology↗

bioRxiv2026

A dual sensor regulates P-glycoproteins structural plasticity

P-glycoprotein is an efflux pump with an exceptionally broad substrate profile which drives its profound clinical impact. Despite its biological importance, it remains obscure how P-glycoprotein achieves its polyspecificity and how substrate binding and the lipid environment stimulate its activity. Structural data highlight the importance of transmembrane helices 4 and 10, which surround the binding pocket, and identify them as key players in substrate recognition. Here, we used cryo-EM to study P-glycoprotein in detergent and nanodiscs to strategically leverage environment- and substrate-dependent phenotypes. This approach allowed us to decipher unexpected and distinct roles of transmembrane helices 4 and 10, which structurally explain differences in ATPase activity. Our data highlights helix 4 as an environment sensor and helix 10 as the key player in substrate recognition constituting a dual regulation mechanism for the functional plasticity of P-glycoprotein, and visualizes the intricate interplay between a membrane protein and its environment.

molecular biology↗

bioRxiv2025

Ultrastructural organization and dynamics of TIRAP filaments

TIRAP (MAL) is an essential adaptor protein in Toll-like receptor (TLR) signaling, bridging activated receptors to downstream effectors such as MyD88 to initiate pro-inflammatory responses. Assembly of TLR signaling complexes is driven by homotypic interactions between Toll/interleukin-1 receptor (TIR) domains. Although previous studies demonstrated that isolated TIR domains of TIRAP can form filaments in vitro, the structural organization and membrane-dependent regulation of full-length TIRAP remained poorly understood. Here, we report a 3.3 [A] cryo-electron microscopy (cryo-EM) structure of full-length human TIRAP filaments combined with the first super-resolution imaging of TIRAP assemblies at the plasma membrane of cells. Using complementary lipid-binding assays on supported lipid bilayers (SLBs) and functional live-cell nanopatterning analysis, we identify a critical role of the N-terminal phosphoinositide-binding motif (PBM) in governing filament geometry and assembly dynamics, plasma membrane partitioning, and effector coupling capacity. Collectively, our multimodal analysis provides a comprehensive structure-function framework of TIRAP, highlighting the intricate features of the PBM as a regulator controlling spatiotemporally defined filament assembly and efficient signal induction at the plasma membrane.

biophysics↗

bioRxiv2025

Disentangling covariate effects on single cell-resolved epigenomes with DeepDive

Understanding the effects of individual biological factors from single cell-resolved epigenomic data is hindered by multicollinearity, particularly in human cohorts. We introduce DeepDive, a novel deep learning framework designed to systematically disentangle known and unknown sources of variation in single-nucleus ATAC-seq data. DeepDive accurately reconstructs chromatin accessibility, outperforms state-of-the-art methods with incomplete covariate information, and robustly recovers true biological signals from even highly entangled covariates, unlocking counter-factual, what-if, analyses. Applying DeepDive to pancreatic islet cells, we perform counter-factual analyses to prioritize covariates associated with a type 2 diabetes-linked beta cell subtype and nominate transcription regulators. DeepDive offers a powerful and unbiased tool for mechanistic discovery in complex human disease cohorts.

bioinformatics↗

bioRxiv2025

Quantifying distribution shifts in single-cell data with scXMatch

A basic task that frequently arises when analyzing single-cell data is to assess if there is a global distribution shift between the data profiles of cells from two different conditions. Widely used approaches to address this task such as visual inspection of two-dimensional representations or clustering-based workflows lack a solid statistical underpinning and are notoriously unstable and prone to confirmation bias. To promote more rigorous analysis, we here present the scverse-compatible Python tool scXMatch. scXMatch is based on a non-parametric graph-based test to quantify distribution shifts in arbitrary data spaces for which a suitable distance measure is available. We evaluated scXMatch on single-cell gene expression, chromatin accessibility, and imaging-derived cell morphology data, showing that it can robustly detect distribution shifts for different types of single-cell data. scXMatch thus aims to set a new standard in the single-cell biology field, replacing easy-to-manipulate semi-manual distribution shift quantification workflows by principled statistical testing.

bioinformatics↗

bioRxiv2025

Mechanistic Plasticity of the RabGEFs Mon1-Ccz1 and Fuzzy-Inturned

Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies thus reveal a function of RMC1/Bulli in the complex as mediator of membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.

biochemistry↗

bioRxiv2025

Oxytocin receptor and HER2 interactions in breast cancer

Breast cancer affects women globally, with HER2 being one of the most aggressive subtypes. Despite advances in HER2-targeted therapies, many patients fail to respond to such treatments. In search of alternative therapeutic targets, we investigated the role of the oxytocin (OT) and oxytocin receptor (OTR) signalling system in HER2+ breast cancer. Survival analysis of HER2 subtype breast cancer patients revealed high OTR expression correlating with significantly improved relapse-free survival. OTR overexpression or knockdown in HER2+ SK-BR-3 cells decreased or increased cell viability, respectively. HER2 was downregulated in OTR-overexpressing cells, which could contribute to the decreased Pertuzumab efficacy. Importantly, HER2 was internalised upon OT treatment and interacted with OTR to form OTR-HER2 complexes. OT treatment furthermore induced a transient inhibition of HER2 phosphorylation without affecting the total HER2 protein levels. In addition, OT inhibited ERK1/2 phosphorylation but enhanced Akt phosphorylation, linked to increased cell viability. In summary, this work describes a novel HER2-OTR interaction and mechanism, expanding our understanding of HER2 cancer biology that might lead to new prognostic and therapeutic opportunities centred around the OT/OTR signalling system for patients suffering from HER2+ breast cancer.

cancer biology↗

bioRxiv2024

High-accuracy prediction of 5-year progression-free melanoma survival using spatial proteomics and few-shot learning on primary tissue

Emerging techniques in imaging-based spatial proteomics (ISP) enable in-depth insights into the architecture and protein abundance of tissue(s). Explainable machine learning (xML) models promise to yield substantial advances in ISP data-based diagnosis and prognosis. However, a clinical application of these new possibilities predicting the course of a tumor has not been suggested yet. Here, we use a few-shot learning workflow on histological multi-antigen images to predict 5-year progression-free survival (PFS) in melanoma. We address the problem of a relatively small cohort (n = 22), by utilizing a pre-trained convolutional neural network (CNN) model, which we further pre-train on a proxy task for which more samples were available (n = 39) before fine-tuning for PFS prediction. Our approach yielded a model achieving an accuracy of more than 90%, outperforming baseline models trained on clinical data by around 10%. Using an xML technique, we identified immune infiltration and proteins associated with tumor progression as crucial predictors. This indicated that our models PFS predictions are not only highly accurate but also grounded in a relevant biological background.

bioinformatics↗

bioRxiv2024

The ABC transporter MsbA in a dozen environments

High-resolution structure determination of membrane proteins typically requires isolation from the native lipid bilayer and reconstitution into artificial membrane mimics. For this purpose, numerous detergents, amphipols, polymers and membrane scaffold proteins are available. The choice of the specific membrane substitute can strongly affect the proteins specific activity, stability and conformational spectrum, potentially leading to errors or misinterpretation during analysis. The bacterial ATP-binding cassette transporter MsbA is a prominent example of such environment-specific bias, resulting in apparent conformational and activity responses. Here, we present a systematic analysis of the conformational spectrum of MsbA, stabilized in a dozen environments, using cryo-EM. Our data show pronounced structural feedback of the ABC transporter to the respective membrane mimetics. Detergents generally favour a conformation with wide separation of the nucleotide-binding domains, while nanodiscs induce the narrow conformation. Notably, only three of the dozen tested environments allow MsbA to sample the functional conformational spectrum, enabling full movement of the nucleotide-binding domains between narrow and wide inward-facing conformations. We expect this study to serve as a blueprint for other membrane proteins, even where the structural reaction to the hydrophobic environment is not directly visible but still critical for the proteins function.

molecular biology↗

bioRxiv2024

Sex-specific competitive social feedback amplifies the role of early life contingency in male mice

Contingency (or luck) in early life plays an important role in shaping individuals development. When individuals live within larger societies, social experiences may cause the importance of early contingencies to be magnified or dampened. Here we test the hypothesis that competition magnifies the importance of early contingency in a sex-specific manner by comparing the developmental trajectories of genetically identical, free-living mice who either experienced high levels of territorial competition (males) or did not (females). We show that male territoriality results in a competitive feedback loop that magnifies the importance of early contingency and pushes individuals onto divergent, self-reinforcing life trajectories, while the same process appears absent in females. Our results indicate that the strength of sexual selection may be self-limiting, as within-sex competition increases the importance of early life contingency, thereby reducing the ability of selection to lead to evolution. They also demonstrate the potential for contingency to lead to dramatic differences in life outcomes, even in the absence of any underlying differences in ability ( merit).

evolutionary biology↗

bioRxiv2024

The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins.

The levels of sphingolipids are crucial determinants of neurodegenerative disorders. Therefore, sphingolipid levels have to be tightly regulated. The Orm protein family and ceramides act as inhibitors in the rate-limiting step of sphingolipid biosynthesis - the condensation of L-serine and palmitoyl-CoA. The two yeast isoforms Orm1 and Orm2 form a complex with the serine palmitoyltransferase (SPT). While the sequences of the Orm proteins are highly similar, however, Orm1 and Orm2 are differentially regulated in yeast cells. The mechanistic details of the differential regulation remain elusive. To elucidate the regulatory mechanism, we determined the cryo-electron microscopy structure of the SPT complex containing Orm2. Through in vitro activity assays and a newly developed plasmid coverage assay combined with targeted lipidomics, we demonstrate that the SPT complex with Orm2 exhibits lower activity in comparison to the complex containing Orm1. This collectively suggests a higher inhibitory potential of Orm2, despite the remarkably similar structures of the Orm1- and Orm2 containing complexes. The high conservation of the SPT from yeast to man implies that the three human ORMDL isoforms could also have different regulatory capacities, which might be essential to understanding their role in sphingolipid-mediated neurodegenerative disorders. HighlightsO_LICryo-EM structures of serine palmitoyltransferase with Orm2 from S. cerevisiae C_LIO_LICeramide-mediated inhibition on SPT activity is conserved amongst SPTs C_LIO_LIThe two yeast Orm isoforms have different regulatory capacity C_LI

biochemistry↗

bioRxiv2023

Structure of the yeast ceramide synthase

Ceramides play a pivotal role as essential lipids, serving as foundational components for complex sphingolipids and potent signaling molecules. Ceramides are the products of the N-acylation of a sphingoid base and a CoA-activated fatty acid. This reaction is catalyzed by the enzymes of the evolutionarily conserved ceramide synthase (CerS) family. Yet, the precise structural details and catalytic mechanisms of CerSs have remained elusive. Here, we employed cryo-EM single particle analysis to unravel the structure of the yeast ceramide synthase complex in both an active and a fumonisin B1 inhibited state. Our findings shed light on the complexs architecture, revealing a dimer of Lip1 subunits bound to the two catalytic subunits, Lag1 and Lac1. Each catalytic subunit forms a hydrophobic crevice that is accessible from both the cytosolic site as well as from the intermembrane space of the endoplasmic reticulum (ER). Within this cavity, we identify amino acids forming the active center and a sphingoid base, one of the substrates of the complex. Together, this suggests a pre-loaded state of the CerS. Additionally, the fumonisin B1 bound structure reveals the inhibitory mechanism by blocking the cytosolic acyl-CoA binding site.

biochemistry↗

bioRxiv2023

Structure of the endosomal CORVET tethering complex

Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solved the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discovered that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane packaging defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function. One-Sentence SummaryUsing cryo-EM, we solved the structure of the CORVET tethering complex and explained how it promotes endosome fusion.

biochemistry↗

bioRxiv2023

Cryo-EM structure of cell-free synthesized human histamine H2 receptor coupled to heterotrimeric Gs protein in lipid nanodisc environment

Here we describe the cryo-electron microscopy structure of the human histamine 2 receptor (H2R) in an active conformation with bound histamine and in complex with Gs heterotrimeric protein at an overall resolution of 3.4 [A]. The complex was generated by cotranslational insertion into preformed nanodisc membranes using cell-free synthesis in E. coli lysates. It is the first structure obtained by this detergent-free strategy and the first GPCR/Gs complex structure in lipid environment. Structural comparison with the inactive conformation of H2R and the inactive and Gq-coupled active state of H1R together with structure-guided functional experiments reveal molecular insights into the specificity of ligand binding and G protein coupling for this receptor family. We demonstrate lipid-modulated folding of cell-free synthesized H2R, its agonist-dependent internalization and its interaction with endogenously synthesized H1R and H2R in HEK293 cells by applying a recently developed nanotransfer technique.

molecular biology↗

bioRxiv2023

Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis

Magnesium chelatase is a conserved enzyme complex responsible for the first committed step of chlorophyll biosynthesis in photosynthetic organisms, which is the addition of magnesium to the chlorophyll precursor, protoporphyrin IX. The complex is composed of the catalytic subunit ChlH, the bridging subunit ChlD, and the subunit ChlI, which serves as the motor that drives the entire complex. Although the enzyme is well-characterized functionally, high-resolution structures are available only for individual subunits. Hence, the full assembly and the molecular mechanism of the enzyme complex remains unknown. Here, we used cryo-EM, supported by biochemical analysis and mass photometry, to determine structures of the ChlI motor subunit of magnesium chelatase under turnover conditions in the presence of ATP. Our data reveal the molecular details of ChlI oligomerization and conformational dynamics upon ATP binding and hydrolysis. These findings provide new insights into the mechanistic function of ChlI and its implications for the entire magnesium chelatase complex machinery.

biophysics↗