Biology subjects

Wilhelm, S.

Publications and source records attributed to Wilhelm, S..

13 recordsLinked to original sources

bioRxiv2026

Structural mechanism of Gasdermin E-mediated mtDNA release from apoptotic mitochondria

During apoptosis, the permeabilization of the mitochondrial inner membrane (MIM) through still-unclear mechanisms releases mtDNA into the cytosol, triggering the inflammatory cGAS/STING pathway under low caspase activity. Here, we report that, in apoptosis, the active form of the pore-forming protein Gasdermin E (GSDME-N) damages mitochondria before plasma membrane disruption. We visualize GSDME-N pore-like nano-assemblies in the MIM of apoptotic cells and of isolated mitochondria, which we bridge with the cryo-EM structure of the GSDME-N pore in mitochondria-like membranes. Deep membrane insertion of the anchor domain, which acts as a determinant of GSDME-N cardiolipin binding preferences, supports a role in pore formation. Notably, GSDME depletion results in a reduction in cristae swelling, MIM extrusion and mtDNA release during apoptosis. Subsequently, this decreases STING activation and inflammatory responses under caspase inhibition. Our findings reveal that GSDME mediates MIM permeabilization and mtDNA release during apoptosis and define the mechanism of GSDME-mediated membrane damage.

molecular biology↗

bioRxiv2026

Three catalase-peroxidases promote extended stationary phase survival of Vibrio natriegens during ecologically relevant exposures to exogenous hydrogen peroxide

Vibrio natriegens is an emerging model organism in laboratory and biotechnology research that is known for its fast growth rate and diverse metabolic capabilities. However, little is known about its response to oxidative stress. Reactive oxygen species (ROS) are ubiquitous stressors for most aerobic life and without mitigation can lead to cellular damage and sometimes death. V. natriegens is unusual amongst the Vibrio genus and Proteobacterial phylum in having three copies of katG encoding the bifunctional ROS defense enzyme catalase-peroxidase. The biological significance of having three copies of this protective gene was investigated with phylogenetics and gene inactivation studies. We determined that two of the katG copies arose recently via duplication and subsequent divergence. Analysis of single, double, and triple {Delta}katG constructs revealed each katG gene product contributes to survival during exposure to ecologically relevant concentrations of exogenous hydrogen peroxide (HOOH) under stationary phase conditions but found the genes were dispensable for HOOH resistance during exponential growth. We also demonstrated the involvement of the RpoS regulon in V. natriegens oxidative stress response in stationary phase. As an outcome of this investigation, we identified and repaired several spontaneous loss-of-function mutations of rpoS in laboratory cultures of the V. natriegens type strain ATCC 14048. Together, these results provide physiological and evolutionary insights into V. natriegens ROS response.

microbiology↗

bioRxiv2026

Nyx: a flexible framework for sleep scoring across species, lifespan and modalities

Sleep is a key factor in almost every physiological process, yet scoring tools lag behind innovations in basic to clinical research. New automated algorithms are trained on narrow datasets, typically healthy adult mouse or human, and fail to generalise, leaving labs to fall back on slow, laborious, and often poorly reproducible manual scoring. Here we introduce Nyx, an unsupervised framework built on principal component analysis that flexibly clusters epochs into sleep states, akin to how spike-sorting algorithms cluster single-neuron activity. Validated on about 8,000 hours spanning 19 independent datasets, it generalises across species, lifespan, recording modalities, and altered sleep architectures, matching human inter-scorer agreement. Beyond this, Nyx opens new ground for modern sleep research: classifying NREM subtypes in rodents, revealing states that cut across canonical boundaries in non-mammalian species, and enabling real-time, closed-loop manipulation. Distributed as an open-source package with a graphical user interface, Nyx offers an accessible, explainable framework built to scale with the pace of innovation itself.

neuroscience↗

bioRxiv2026

Prospective pan-cancer phosphoproteomics at clinical scale extends therapeutic options in precision oncology

Genomics-guided precision oncology has improved survival in cancer entities with actionable mutations but cannot capture oncogenic signaling that manifests at the protein level. Here, we report a prospective, real-world pan-cancer study profiling proteomes and phosphoproteomes of 1,998 tumor samples from adults and children with rare or advanced cancers enrolled in the German precision oncology programs DKFZ/NCT/DKTK MASTER, CATCH and INFORM and their molecular tumor boards (MTBs). We developed tumor proteome activity status (TOPAS) scores for 46 clinically relevant kinases, an immune activity score capturing antigen presentation and T-cell activation and identified therapeutically targetable cell-surface proteins for 94% of patients. These readouts enhance MTB recommendations by exposing actionable non-genomic kinase activity, refining interpretation of oncogenic genome alterations, and highlighting cell-surface treatment options. Three proof-of-concept analyses indicate clinical utility including kinase activity-stratified pazopanib response in sarcoma, immune activity score-tracked checkpoint-inhibitor outcomes pan-cancer, and a phosphoproteomic biomarker distinguishing EGFR-inhibitor response in chordoma.

cancer biology↗

bioRxiv2026

Sleep spindles enhance latent working memory representations

Working memory (WM) allows recently encountered information to be maintained over short periods, yet neural mechanisms supporting this short-term accessibility remain debated. Recent work suggests that WM representations can be maintained without persistent neural firing, in latent synaptic states often termed "activity-silent" memory. Such states can be reactivated by brief perturbations of cortical networks ("pinging"), providing a way to probe otherwise hidden representations. If such latent states rely on synaptic plasticity, they may be sensitive to sleep-dependent recalibration of cortical circuits. Here, we test whether sleep spindles, transient thalamo-cortical oscillations linked to synaptic plasticity, shape post-sleep accessibility of WM representations. Thirty participants performed a visual WM task before and after a daytime nap while high-density EEG was recorded. During the post-nap task, brief visual impulses were used to probe latent WM states, enabling multivariate decoding of memorised content. We show that longer spindle duration during prior NREM sleep predicts both improved post-sleep WM performance and higher-fidelity impulse-evoked decoding of item-specific representations, even when controlling for pre-sleep WM ability. These relationships were selective to spindles; slow-oscillation duration and other oscillatory metrics showed no corresponding effects. Together, our findings link sleep spindle dynamics to the neural readout of activity-silent WM and suggest that sleep-dependent synaptic recalibration optimises cortical circuits for subsequent, short-term information processing.

neuroscience↗

bioRxiv2026

The phosphodiesterase-5 inhibitor vardenafil reverses sleep deprivation-induced amnesia in mice

Sleep deprivation (SD) disrupts memory processes, particularly those dependent on the hippocampus. Six hours of SD after training in a hippocampus-dependent task typically induces amnesia in mice and impairs performance upon memory testing later. However, we previously demonstrated that object-location memories (OLMs) encoded under SD conditions can be recovered several days later, suggesting that these memories were not lost but suboptimally stored. Given that engrams of a specific memory are distributed across multiple functionally connected brain regions, we hypothesized that SD-induced amnesia arises from disrupted network alterations extending beyond the hippocampus. Consistent with this, brain-wide cFos mapping revealed a widespread reduction in cFos in memory associated regions during recall in SD mice and connectivity analysis identified the hippocampus as a central hub in this network. Since cGMP signaling modulates memory processes, we next tested whether the cGMP-specific PDE5 inhibitor vardenafil could restore access to these latent memories. One day after training, vardenafil reversed SD-induced OLM impairment when administered 30 minutes before testing, but this effect was lost when testing occurred several days later. To achieve persistent access to OLMs formed under SD conditions, we combined vardenafil treatment with optogenetic engram stimulation. This combined approach successfully maintained OLM retrievability for several days post-manipulation. Crucially, successful retrieval in these mice was associated with a significant increase in engram cell reactivation within the dorsal dentate gyrus compared to mice that failed to recall. Collectively, these findings provide novel insight into the molecular and network mechanisms underlying SD-induced amnesia and offer a strong rationale for developing targeted PDE5-mediated therapies to reverse SD-related memory deficits. HighlightsO_LISD-induced amnesia is associated with reduced cFos expression within memory-associative circuitry C_LIO_LIThe phosphodiestarase-5-inhibitor vardenafil can be used to restore memory access C_LIO_LICombining optogenetics with vardenafil treatment sustains memory retrieval over several days C_LIO_LISuccessful retrieval reflects increased reactivation of engram cells in the dentate gyrus C_LI

neuroscience↗

bioRxiv2025

The tumor suppressor CYLD acts as a deubiquitinase for mTOR to constrain its activity

Proper control of mTOR (mechanistic/mammalian target of rapamycin) signaling is relevant for health, disease and ageing. Information from intra- and extra-cellular signaling cues is transmitted to mTOR through an intricate signaling network that impinges on the Rag and Rheb GTPases to regulate its localization and activity. Interestingly, although mTOR is a heavily ubiquitinated protein, the role of this post- translational modification (PTM) in regulating its activation status remains poorly understood. Here, through an unbiased RNAi screen, we identified the tumor suppressor CYLD deubiquitinase (DUB) as a direct negative regulator of both mTORC1 and mTORC2 activities. Mechanistically, CYLD interacts with mTOR and removes non-degradative, K63-linked ubiquitin (Ub) chains from multiple of its residues. Consequently, CYLD loss-of-function cells are characterized by mTORC1/2 hyperactivation, elevated rates of protein synthesis, increased cell size, and resistance to serum-starvation-induced activation of cell death pathways. Moreover, silencing of cyld-1, the C. elegans CYLD ortholog, fully reverses the extended lifespan of low- TORC1-activity mutant worms. Finally, we find that inactivation of CYLD is associated with hyperactivation of mTORC1 also in skin biopsies from CYLD cutaneous syndrome (CCS) patients. In sum, our findings highlight CYLD as a sentinel of mTOR hyperactivation via direct control of its ubiquitination, and suggest that dysregulated mTOR activity may contribute to the development and progression of CCS tumors.

cell biology↗

bioRxiv2024

Time of day of infection shapes development of a eukaryotic algal-Nucleocytoviricota virocell

Aureococcus anophagefferens represents one component of a model host-virus system (with the "giant virus" Kratosvirus quantuckense). Studies to define its ribocell (uninfected cells) and virocell (virus-infected cells) forms are needed, as both are abundant during algal blooms. A linkage between light-derived energy, virus particle production and virocell formation has been noted. We explored how the time of day (morning, afternoon, late day) of virus-host contact shaped virocell ontogeny. In parallel, we explored the need for light derived energy in this mixotrophic plankter by inhibiting photosystem II (PSII). Using flow cytometry and photochemical assessments, we examined the physiology of infected cells and controls, and estimated virus particle production by virocells. We observed distinct differences between ribocell and virocell response to treatments, including reductions in virus particle production during reduced light (i.e., duration) and PSII inhibition. Collectively this work demonstrates the importance of light in shaping the fate of infected cells and provides insight into the factors that constrain in situ blooms. Most significantly, we show that time of day when a virus and host come into contact influences viral particle production, and therefore bloom dynamics; a factor that needs to be considered in future bloom modeling work.

microbiology↗

bioRxiv2024

Metatranscriptomics reveals declines in ice cover influence winter viral community activity

Freshwater lakes are sentinels of environmental change, and climate change-driven declines in ice cover have been shown to disrupt aquatic communities and jeopardize ecosystem services. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet there is relatively little known about how declining ice cover will influence viral community activity. Lake Erie is a critical freshwater ecosystem and serves as a model system to assess how ice cover extent will affect winter limnology. We surveyed size selected surface water metatranscriptomes for conserved viral hallmark genes as a proxy for active virus populations and compared activity profiles between ice-covered and ice-free conditions from two contrasting winters. Active virus communities were present in both conditions, spanning diverse phylogenetic clades of bacteriophage (Caudovirales), giant viruses (Nucleocytoviricota), and RNA viruses (Orthornavirae). However, viral activity was significantly shaped by the extent of ice cover. Notably, viral richness and relative transcript abundance in the surface waters were reduced under ice relative to the ice-free conditions. Correlations with microbial community metrics suggest the differences in viral communities are at least in part driven by the decreased winter diatom bloom associated with declines in ice cover. Overall, our data suggest viral community activity is influenced by ice cover extent, and viruses may serve as sentinels of environmental disturbance and ecosystem response(s) to climate change. IMPORTANCEAs ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities during winter months might respond to these changing ice-cover conditions. Despite the documented controls viruses have on microbial communities, little is known regarding the relationship between virus activity and ice cover extent. By using metatranscriptomics to investigate virus communities, we show that viral community activity is sensitive to ice cover extent, likely due in part to ice cover-driven shifts in host community structure. This work serves to build our understanding of how viral communities will function in a future, potentially ice-free, climate.

microbiology↗

bioRxiv2024

Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea

The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. According to temporal niche partitioning theory, competition for scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism structuring uptake of limiting nutrients and facilitating coexistence of diverse microbes in open ocean ecosystems.

ecology↗

bioRxiv2024

Featural and spatial interference with functionally active and passive items in working memory

Functionally active and passive states in working memory have been related to different neural mechanisms. Memoranda in active states might be maintained by persistent neural firing, whereas memoranda in passive states might be maintained through short-term synaptic plasticity. We reasoned that this might make these items differentially susceptible to interference during maintenance, in particular that passively maintained items might be more robust. To test this hypothesis, we gave our participants a working memory task in which one item was prioritised (active) by always probing it first, while the other item was deprioritised (passive) by always probing it second. In two experiments, on half the trials, we presented an interfering task during memory maintenance, in which the stimuli matched either the feature dimension of the memory items (colour or orientation), or their spatial location. Whether the interfering task appeared on a given trial was unpredictable. In a third experiment where participants were given prior knowledge of the interference condition, and finally in a fourth experiment we used a reward-based prioritisation cue. Across experiments, we found that both active and passive memory items were affected by interference to a similar extent, with overall performance being closely matched in all experiments. We further investigated precision and probability of target response parameters from the standard mixture model, which also showed no differences between states. We conclude that active and passive items, although potentially stored in different neuronal states, do not show differential susceptibility to interference. Public significance statementThe ability to briefly remember information is critical to human cognition. Our so-called working memory is nevertheless rather limited, able to hold only a few items at any one time, and prone to forgetting when we are briefly distracted. Yet, there is reason to believe that not all information in working memory is equally vulnerable. Items that are more passively stored, because they will only be required after some time, might be more resilient to interference. Items that are stored actively, for more immediate recall, might be more easily disrupted. Here, we investigated the effect of an interference task on the retention of both active and passive items in working memory. Our results showed that active and passive items are equally affected by interference, suggesting that resilience in working memory does not depend on the functional state of the items therein.

neuroscience↗

bioRxiv2023

Spatially and Functionally Distinct mTORC1 Entities Orchestrate the Cellular Response to Amino Acid Availability

Amino acid (AA) availability is a robust determinant of cell growth, through controlling mTORC1 activity 1. According to the predominant model in the field, AA sufficiency drives the recruitment and activation of mTORC1 on the lysosomal surface by the heterodimeric Rag GTPases, from where it coordinates the majority of cellular processes (reviewed in 2,3). Importantly, however, 15 years after its initial discovery, the teleonomy of the proposed lysosomal regulation of mTORC1, and where mTORC1 acts on its effector proteins remain enigmatic 4. Here, by using multiple pharmacological and genetic means to perturb the lysosomal AA sensing and protein recycling machineries, we describe the spatial separation of mTORC1 regulation and downstream functions in mammalian cells, with lysosomal and non-lysosomal mTORC1 phosphorylating distinct substrates in response to different AA sources. Moreover, we reveal that a fraction of mTOR localizes at lysosomes due to basal lysosomal proteolysis that locally supplies new AAs, even in cells grown in the presence of extracellular nutrients, whereas cytoplasmic mTORC1 is regulated by exogenous AAs. Overall, our study substantially expands our knowledge about the topology of mTORC1 regulation by AAs, and hints at the existence of distinct, Rag- and lysosome-independent mechanisms that control its activity at other subcellular locations. Given the importance of mTORC1 signalling and AA sensing for human ageing and disease 2, our findings will likely open new directions toward the identification of function-specific mTORC1 regulators, and suggest new targets for drug discovery against conditions with dysregulated mTORC1 activity in the future.

cell biology↗

bioRxiv2023

Maintenance of colour memoranda in activity-quiescent working memory states: Evidence from impulse perturbation

The neural mechanisms underlying working memory maintenance pose a challenge for investigation, as sustained neural activity may not always be observable. To address this, the method of impulse perturbation has been employed to examine memorized information during activity-quiescent periods. However, this approach has mainly focused on spatially localized or referenced stimuli, leaving it unclear whether non-spatial memoranda share similar neural maintenance mechanisms. This study aimed to fill this gap by applying the impulse perturbation method to working memory for colours, which are inherently non-spatial stimuli. EEG data from 30 participants performing a delayed match-to-sample task were analysed, with one of the presented items being retro-cued as task-relevant. Our findings indicate that both cued and uncued colours could be decoded from impulse-evoked activity, in contrast to previous reports on working memory for orientation gratings. Additionally, we explored colour decoding from ongoing oscillations in the alpha band and discovered that cued items could be decoded, potentially influenced by attention, whereas uncued items could not. These results suggest subtle differences between the representation of colours and stimuli with spatial properties. However, they also demonstrate that both types of information can be accessed through visual impulse perturbation, regardless of their specific neural states.

neuroscience↗