Biology subjects

Mueller, H.

Publications and source records attributed to Mueller, H..

12 recordsLinked to original sources

bioRxiv2026

A Crossed Laser Phase Plate for CryoEM

The laser phase plate (LPP) enables phase-contrast imaging in cryogenic electron microscopy (cryoEM), enhancing image contrast without compromising high-resolution information. Here we report the implementation of a crossed laser phase plate (xLPP) comprising two optical cavities oriented orthogonally, installed in a ThermoFisher Scientific Krios G4 microscope equipped with a newly designed transfer lens module. We demonstrate the expected, strong contrast enhancement and stable, additive phase shifts of 90{degrees}, with a contrast transfer function (CTF) that closely matches theory. Single-particle analysis (SPA) of apoferritin, a standard benchmark sample, reached a resolution of 1.79 [A], demonstrating the system is capable of acquiring high-resolution cryoEM data. When imaging thick E. coli cells ([~]350 nm), the xLPP enhances contrast and increases low-frequency template-matching signal. Together, these results establish the feasibility of the xLPP and highlight its potential for high-contrast, high-resolution cryoEM imaging of biological systems.

biophysics↗

bioRxiv2026

PRMT5 inhibitors actively promote metastatic progression of lung adenocarcinoma

Epigenetic changes are a major driver of cancer progression, placing considerable focus on epigenetic regulators as therapeutic targets. Protein arginine methyltransferase 5 (PRMT5) is one such regulator, and numerous PRMT5 inhibitors (PRMT5i) in clinical trials. Despite this, the mechanisms and consequences of PRMT5i-resistance are unknown. Here, we demonstrate that aggressive cancer progression is an inbuilt feature of PRMT5i-resistance acquisition in lung adenocarcinoma (LUAD). Independently-generated resistant cell lines gain dedifferentiation signatures that typify late-stage disease and show increased metastatic potential in vivo. We establish that these state shifts are a direct consequence of PRMT5i action; treatment induces rapid and widespread chromatin rewiring, enabling derepression of late-stage disease states that are stably established in resistant cells. Notably, treatment of lung tumor-bearing mice drives rapid disease advancement without decreasing tumor burden, showing that drug-induced disease progression supersedes any benefits from PRMT5 inhibition in vivo. Furthermore, analyses of human cell lines and patient cohorts supports the notion of PRMT5 inhibition-mediated dedifferentiation. Collectively our data show that PRMT5i can actively promote self-resistance and disease progression in different tumor types. This raises serious concerns for the use of PRMT5i in patients, arguing that clinical studies should consider the possibility of drug-induced plasticity, resistance, and disease advancement.

cancer biology↗

bioRxiv2025

Multi-modal atlas of lifestyle interventions reveals malleability of ageing-linked molecular features

Extending human healthspan requires understanding how lifestyle interventions impact molecular systems across tissues and time. Here, we present the TirolGESUND Lifestyle Atlas (ClinicalTrials.gov: NCT05678426), a longitudinal, multi-modal resource profiling 156 healthy women (aged 30-60 years) undergoing 6-month intermittent fasting (n=114) or smoking cessation (n=42) interventions. Participants were sampled up to four times across seven tissues and fluids, generating >3,450 biospecimens with harmonised DNA methylation, metabolomics, microbiome, and immune profiling, alongside skin histology, barrier measurements, and rich clinical metadata. We demonstrate the utility of this dataset through: (i) multi-omics-wide association studies linking traits to molecular features; (ii) integrative factor modelling revealing coordinated cross-tissue signatures; (iii) epigenetic-biomarker cross-omic associations, and (iv) CpG-level variance decomposition mapping stable, individual-specific, tissue-restricted, and intervention-responsive methylation patterns. We further show that ageing-linked features are selectively malleable: highly compliant intermittent fasting participants exhibited attenuated or even age-opposing molecular trajectories within six months. The atlas enables unprecedented within-cohort comparisons across omic layers and tissues, supporting discovery of context-dependent biomarkers, cross-system coordination, and intervention responsiveness. Data are available via an interactive portal, with sensitive data under controlled access (https://eutops.github.io/lifestyle-atlas/). This resource provides a foundation for exploring biomarker association and multi-tissue epigenetics, enabling hypothesis generation and benchmarking for systems biology and human healthspan research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/673115v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@fec2d9org.highwire.dtl.DTLVardef@1aa5d13org.highwire.dtl.DTLVardef@1c4a6f2org.highwire.dtl.DTLVardef@1ac62fb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMulti-tissue multi-modal profiling of two clinically-relevant lifestyle interventions in 156 women aged 30-60 C_LIO_LIIntermittent fasting modifies ageing-linked molecular features in an age-opposing direction C_LIO_LICross-tissue epigenetic biomarker mapping links immunity, metabolism, and microbiome C_LIO_LITissue-specific epigenetic plasticity maps reveal candidate meQTLs, C_LIO_LIData sharing and interactive portal enable broad reuse for hypothesis generation and exploration C_LI

systems biology↗

bioRxiv2025

Skin development and metamorphic re-arrangement in Arthroleptella villiersi Hewitt, 1935 reveals distinct heterochronic patterns in anurans with different life histories

BackgroundThe evolvability of ontogenetic trajectories, driven by modular developmental processes and their evolutionary repatterning, plays a crucial role in the diversity of animal diversity. Anurans offer a model for exploring how developmental repatterning, including the loss of larval features and heterochronic shifts of metamorphic processes lead to the diversity of, often terrestrialized, life histories. Ancestrally, anurans exhibit an aquatic larva (tadpoles) that differs tremendously from their semi-terrestrial adult forms. The transition from this tadpole to the adult is a thyroid hormone-dependent metamorphosis that results in the rearrangement of almost all organ systems. One of the organ systems that experiences the most extensive rearrangements is the skin. Is the ancestral pattern of metamorphic skin rearrangement altered in anurans with a completely terrestrial tadpole phase? ResultsSkin development and metamorphic rearrangement in the terrestrial tadpole of Arthroleptella villiersi is investigated based on histological sections. It follows the major pattern observed in anurans with an aquatic tadpole phase and correlates with thyroid gland maturation. Neuromasts develop and are present during a short developmental time. Both, metamorphic skin rearrangement and neuromast degeneration correlate with histological thyroid gland maturation. A few minor heterochronic shifts are detectable compared to aquatic indirect and terrestrial direct developing anurans. ConclusionSkin development and metamorphic rearrangement in anurans with different reproductive modes is very similar and correlates with thyroid gland maturation indicating that skin development in anurans might be constrained by thyroid hormone activity. Neuromasts are the major exception being present in aquatic and terrestrial indirect developing species but not in terrestrial direct developing anurans. Heterochronic shifts detected during skin development indicate that at least the differentiation of multicellular gland complexes might represent a developmental module similar to neuromasts.

zoology↗

bioRxiv2025

Developmental stages of Arthroleptella villiersi (Pyxicephalidae)

Terrestrialization in anurans is associated with the evolution of endotrophy. It is hypothesized that heterochrony, or changes in the time or rate of developmental events, is associated with the development in endotrophic species. To analyse the developmental heterochrony, we investigated and revised the description of the development in Arthroleptella villierisi, a small frog species of the family Pyxicephalidae, found in the Cape fold mountain region of the Western Cape, South Africa. We also compared the developmental stages of A. villiersi to the heterochronic patterns of taxa with endotrophic terrestrial indirect and direct development using heterochrony plots to identify heterochronic shifts during development. As a result, we found that the terrestrial endotrophic larva of A. villiersi shares external similarities with exotrophic, aquatic larvae in having a long muscularized tail with a fin, a lateral line system and an opercular fold that completely covers the forelimbs. However, other developmental events like the reduction of larval mouthparts and the pre-displaced fore- and hindlimb development is comparatively similar to direct developing taxa. The results of our study show that the timing of early developmental events can be shifted profoundly, while the timing of later events seem to be more conserved in anuran development. We interpret that some of these heterochronic shifts might be consequences of functional and developmental constraints underlying the establishment of the adult body plan.

developmental biology↗

bioRxiv2024

Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage

Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 [A] resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-particle variation in the images than we had previously thought to exist. Similarly, we found that images of ribulose bisphosphate carboxylase/oxygenase (rubisco) also exhibited a much greater amount of heterogeneity than expected. By comparison to simulations of images, we verified that the heterogeneity is not explained by the known features of the LPP, shot noise, or differences in particle orientation. We also demonstrate that our specimens are comparable to those previously used in the literature, based on using the final-reconstruction resolution as the metric for evaluation. All of this leads us to the hypothesis that the heterogeneity is due to damage that has occurred either during purification of the specimen or during preparation of the grids. It is not, however, our goal to explain the causes of heterogeneity; rather, we report that using the LPP has made the apparent damage too obvious to be ignored. In hindsight, similar heterogeneity can be seen in images of apoF and the 20S proteasome which others had recorded with a Volta phase plate. We therefore conclude that the increased contrast of phase-plate images (at low spatial frequencies) should also make it possible to visualize, on a single-particle basis, various forms of biologically functional heterogeneity in structure that had previously gone unnoticed. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/606536v1_ufig1.gif" ALT="Figure 1"> View larger version (101K): org.highwire.dtl.DTLVardef@1c85263org.highwire.dtl.DTLVardef@990352org.highwire.dtl.DTLVardef@1a920b3org.highwire.dtl.DTLVardef@a1fcf0_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIPhase plates recover low-frequency information with significantly improved SNR C_LIO_LILaser phase-plate images reveal unexpected amounts of structural heterogeneity C_LIO_LIIn retrospect, similar heterogeneity can also be seen in Volta phase-plate images C_LIO_LIParticle heterogeneity produces "structural noise", which may diminish map quality C_LI

biophysics↗

bioRxiv2023

Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

microRNAs are particularly important during brain development, however, the composition and temporal dynamics of miRNA regulatory networks are not sufficiently characterized. Here, we performed small RNA sequencing of mouse embryonic cortical samples at E14, E17, and P0 as well as in neural progenitor cells differentiated in vitro into neurons. Using co-expression network analysis, we detected clusters of miRNAs that were co-regulated at distinct developmental stages. miRNAs such as miR-92a/b acted as hubs during early, and miR-124 and miR-137 during late neurogenesis. Notably, validated targets of P0 hub miRNAs were enriched for down-regulated genes related to stem cell proliferation, negative regulation of neuronal differentiation and RNA splicing, among others, suggesting that miRNAs are particularly important for modulating transcriptional programs of crucial factors that guide the switch to neuronal differentiation. As most genes contain binding sites for more than one miRNA, we furthermore constructed a co-targeting network where numerous miRNAs shared more targets than expected by chance. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced transcriptional silencing effect compared to single miRNAs. Taken together, our study provides a comprehensive resource of miRNA longitudinal expression changes during corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can shape embryonic brain development.

developmental biology↗

bioRxiv2023

Analysis of DNA transposition by DNA transposases in human cells

This manuscript discusses the recent report "Cognate restriction of transposition by piggyBac-like proteins" in Nucleic Acids Research by Beckermann et al and related recent publications about the inability to detect DNA transposition activity of human domesticated DNA transposase PGBD5. Measuring DNA transposition activity of transposases in human cells, where these enzymes can act on endogenous genomic substrates and induce DNA damage, is complicated by these and other cellular responses. Possible reasons for the discordant findings of Beckermann et al with prior independent reports of PGBD5 DNA transposition by Helou et al and Henssen et al and specific details of experimental methods in human cells are presented. In particular, by using independent experiments that reproduce PGBD5-mediated genomic integration, we demonstrate how supraphysiologic and ectopic overexpression of PGBD5 can cause DNA damage and cell death, and artifactual loss of apparent activity in clonogenic transposition reporter assays. While PGBD5 can support apparent DNA transposition, its cellular activity predominantly involves double-strand DNA breaks, deletions and other DNA rearrangements. We discuss the implications of this phenomenon for the interpretation of experimental assays and activities of domesticated DNA transposases.

molecular biology↗

bioRxiv2023

Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy

We identify thermal magnetic field fluctuations, caused by thermal electron motion ("Johnson noise") in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.

molecular biology↗

bioRxiv2021

Can Stephen Curry really know? - Conscious access to outcome prediction of motor actions

The NBA player Stephen Curry has a habit of turning away from the basket right after taking three-point shots, presumably because he can predict the success of his shot. For such a consciously accessible prediction to be possible, Stephen Curry needs access to internal processes of outcome prediction and valuation. Computational simulations and empirical data suggest that the quality of internal prediction processes is related to motor expertise. Whether the results of internal predictions can reliably be consciously accessed is less clear. In the current study, 30 participants each practiced a virtual goal-oriented throwing task for 1000 trials. Every second trial, they were required to verbally predict the success of the current throw. Results showed that on average, conscious prediction accuracy was above an individually computed chance level, taking into account individual success rates and response strategies. Furthermore, prediction accuracy was related to throwing performance. Participants with better performance predicted the success of their throws more accurately than participants with poorer performance. Moreover, for the poorer performing individuals, movement execution was negatively affected by the verbalized predictions required, and they did not show variation in speech characteristics (response latency) between correct and incorrect predictions. This indicates reduced quality of conscious access to internal processes of outcome prediction.

neuroscience↗

bioRxiv2020

Parallel evolution of direct development in frogs - Skin and thyroid gland development in African Squeaker Frogs (Anura: Arthroleptidae: Arthroleptis)

Cases of parallel evolution offer the possibility to identify adaptive traits and to uncover developmental constraints on the evolutionary trajectories of these traits. The independent evolution of direct development, from the ancestral biphasic life history in frogs is such a case of parallel evolution. In frogs, aquatic larvae (tadpoles) differ profoundly from their adult forms and exhibit a stunning diversity regarding their habitats, morphology and feeding behaviors. The transition from the tadpole to the adult is a climactic, thyroid hormone (TH)-dependent process of profound and fast morphological rearrangement called metamorphosis. One of the organ systems that experiences the most comprehensive metamorphic rearrangements is the skin. Direct-developing frogs lack a free-swimming tadpole and hatch from terrestrial eggs as fully formed froglets. In the few species examined, development is characterized by the condensed and transient formation of some tadpole-specific features and the early formation of adult-specific features during a "cryptic" metamorphosis. In this study we show that skin in direct-developing African squeaker frogs (Arthroleptis) is also repatterned from a tadpole-like to an adult-like histology during a cryptic metamorphosis. This repatterning correlates with an increase of thyroid gland activity. A comparison with data from the Puerto Rican coqui (Eleutherodactylus coqui) reveals that direct development might have evolved in parallel in these frogs by a comparable heterochronic shift of thyroid gland activity. This suggests that the development of many adult-features is still constrained by the ancestral dependency on thyroid hormone signaling.

developmental biology↗

bioRxiv2020

Measuring Metacognition of Direct and Indirect Parameters of Voluntary Movement

We can make exquisitely precise movements without the apparent need for conscious monitoring. But can we monitor the low-level movement parameters when prompted? And what are the mechanisms that allow us to monitor our movements? To answer these questions, we designed a semi-virtual ball throwing task. On each trial, participants first threw a virtual ball by moving their arm (with or without visual feedback, or replayed from a previous trial) and then made a two-alternative forced choice on the resulting ball trajectory. They then rated their confidence in their decision. We measured metacognitive efficiency using meta-d/d and compared it between different informational domains of the first-order task (motor, visuomotor or visual information alone), as well as between two different versions of the task based on different parameters of the movement: proximal (position of the arm) or distal (resulting trajectory of the ball thrown). We found that participants were able to monitor their performance based on distal motor information as well as when proximal information was available. Their metacognitive efficiency was also equally high in conditions with different sources of information available. The analysis of correlations across participants revealed an unexpected result: while metacognitive efficiency correlated between informational domains (which would indicate domain-generality of metacognition), it did not correlate across the different parameters of movement. We discuss possible sources of this discrepancy and argue that specific first-order task demands may play a crucial role in our metacognitive ability and should be considered when making inferences about domain-generality based on correlations.

neuroscience↗