Biology subjects

Schmid, F.

Publications and source records attributed to Schmid, F..

14 recordsLinked to original sources

bioRxiv2026

Kinase-phosphatase cycles drive self-sustained oscillations of protein condensates

Phase-separated protein condensates organize biochemical processes in cells. ATP-driven enzymatic reactions can change the physical properties and even trigger the dissolution of such condensates. Here we use molecular simulations to show how ATP-driven kinase and phosphatase reactions modulate the organization of TDP-43 low complexity domain (LCD) condensates. TDP-43 phosphorylation is enhanced by condensation, as CK1{delta} preferentially binds to and acts in TDP-43 LCD condensates, whereas dephosphorylation by the phosphatase calcineurin occurs predominantly in the dilute phase. This differential recruitment of kinases and phosphatases, together with the slow redistribution of kinases into newly formed condensates, triggers oscillatory appearance and disappearance of TDP-43 LCD condensates. The oscillations are self-sustained, persisting at constant chemical driving, showing that an antagonistic kinase-phosphatase pair can endow a condensate with autonomous dynamics rather than only setting its structure.

biophysics↗

bioRxiv2026

Graph-Based Classification of Penetrating Arteries and Veins in Whole-Mouse Vasculature Datasets

Advances in whole-brain imaging have produced large-scale vascular datasets, yet most lack artery-vein annotations. However, this is essential for quantitative analysis of whole brain vascular structure, blood flow simulation and translational cerebrovascular research. For unlabelled datasets, manual labelling is infeasible at network scale, and surface-vessel tracing is hampered by reconstruction artefacts, limiting the insights that can be gained from these datasets. Here, we focus on penetrating vessel trees, i.e. descending arteries (A) and ascending veins (V). A supervised Random Forest classifier is trained on graph-derived morphological and topological tree features, including persistent homology. Training uses datasets from two imaging modalities: Light sheet (LS) microscopy with arterial staining and two-photon (TP) micrscopy with manual labelling in smaller samples. Classification reached 96% balanced accuracy on independent TP dataset and 93% on LS datasets. Topological features alone achieved competitive accuracy without relying on diameter measurements, demonstrating cross-modality portability. Arteries exhibit larger diameters and longer inter-bifurcation segments, likely facilitating their functional task of directed blood delivery. The veins show greater branching complexity, allowing low-pressure drainage. These signatures are stable across modalities, supporting their physological relevance. The framework enables A-V label transfer to unlabelled whole-brain TP graph datasets, validated through the V:A ratio as a function of middle cerebral artery (MCA) distance. Operating on graph representations derived from any volumetric imaging modality and requiring no retraining, the approach is applicable to LS, TP, and likely other imaging platforms, providing a scalable foundation for A-V quantification, vascular topological analysis, and haemodynamic modelling.

neuroscience↗

bioRxiv2026

A Phosphorylation-Induced Micellization switch in the low complexity domain of TDP-43

Abstract textPhase separation (PS) of the low-complexity domain (LCD) of TDP-43 is linked to pathogenic aggregates in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). Here, we show that extensive phosphorylation of the LCD C-terminus redirects its self-assembly. Coarse-grained Monte Carlo simulations predicted that 12 Ser phosphorylations partition the 148-residue LCD into a hydrophobic N-terminal and highly charged C-terminal block, favoring finite-sized micellization over macroscopic PS. In vitro, LCD phosphorylated by casein kinase 1 delta (CK1{delta}; mean of 12 phosphorylations by native mass spectrometry) and phosphomimetic 12D/12DD mutants formed spherical nanoparticles ({approx} 20-50 nm) above a low-micromolar critical micelle concentration, whereas the unphosphorylated LCD underwent reversible PS that matured into fibrils. Increasing ionic strength shifted the mutants toward anisotropic morphologies (worm-like 12D micelles and rigid 12DD nanocylinders). Turbidity assays and confocal imaging directly visualized the absence of PS in the phosphorylated form. Negative-stain and cryo-EM confirmed the spherical micellar architecture for the phosphorylated LCD and 12D/12DD mimics. Our data identify phosphorylation as a molecular switch tuning macrophase separation and fibril formation of TDP-43 LCD, providing a framework for an aggregation-protective role through microphase separation into size-limited micelles. Whether these assemblies are stable or kinetically trapped on pathological timescales remains unclear.

biophysics↗

bioRxiv2026

Multi-Domain Interplay Controls Full-Length TDP-43 Phase Separation and Condensate Dynamics

TDP-43 (TAR DNA-binding protein 43) is a 414-amino acid protein with a structured N-terminal domain (NTD), two RNA recognition motifs (RRM1 and RRM2), and a long disordered C-terminal low complexity domain (LCD). TDP-43 forms phase-separated condensates as part of its physiological function in RNA processing. However, aberrant TDP-43 condensation, changes in condensate material properties, and subsequent aggregation are linked to the development of neurodegenerative diseases. Using explicit-solvent, near-atomic resolution coarse-grained simulations we demonstrate how the interplay among different domains drives phase separation of the full-length protein.We directly capture how the secondary structure of a conserved helix in the LCD modulates phase separation, and follow the effect of phosphomimicking mutations on the condensation of full-length TDP-43. C-terminal phosphomimicking mutations rewire the interactions of the LCD by increasing solvation locally and enhancing Na+ binding to the LCD. Our simulations and in vitro experiments emphasize the importance of the aromatic residues in the LCD but also of N-terminal residues 1-101 including the NTD for full-length TDP-43 condensation. With a G[o]-type approach we capture not just conformational flexibility but also specific dimer formation through NTD-NTD interactions and how they modulate the phase behavior as well as the dynamic and interfacial properties of full-length TDP-43 condensates.

biophysics↗

bioRxiv2026

Blood Pressure Regulates Functional Coupling of L-Type Ca2+ Channels: Reimaging the Foundation of Cerebral Blood Flow Control.

The myogenic response is the key autoregulatory mechanism setting cerebral blood flow and its mechanistic foundation is intimately tied to depolarization and the voltage gating of L-type Ca2+ channels (CaV1.2). While critical, this study argues for an additional mechanism, that of pressure itself enhancing CaV1.2 activity via cooperative gating and perimembrane trafficking of channels subunits. These novel insights were pursued at the cell level using patch-clamp electrophysiology and advanced microscopy, and then functionally in pressurized arteries through measures of tone and intracellular [Ca2+]i. Key findings were confirmed in mutant mice with disrupted functional coupling and translated into arteries procured from human brain tissue. From cerebral blood flow simulations of semi-realistic microvascular networks, we predict that loss of this alternative mechanism leads to maldistribution of brain blood flow and potentially a diminishment of cognitive function. This study reveals previously unrecognized pressure-sensitive CaV1.2 regulatory mechanism that advances understanding of cerebral blood flow. SignificanceBlood pressure sets base arterial constriction - a response critical for blood flow control in brain. This response is tied to CaV1.2 channels and their presumptive and exclusive activation by voltage, reasoning now under great scrutiny. We establish herein with advance methods, a second mode of CaV1.2 pressure regulation, that of enhanced functional cooperativity among neighboring channels. This novel mechano-response is tied to PKC and its ability to set channel phosphorylation and CaV1.2 trafficking. CaV1.2 pressure regulation was observed in human tissues and its disruption (mutant mice) impaired myogenic tone in the presence of preserved voltage control. Cerebral microvascular modeling highlights that losing this mechanism destabilizes blood flow distribution in brain, the knock-on effect being comprised cognitive function.

physiology↗

bioRxiv2026

RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation

Alternative splicing, regulated by RNA-binding proteins (RBPs), enables the generation of diverse transcript isoforms critical for cellular function. However, how RNA secondary structure impacts RBP binding and function remains poorly understood. Here, we unravel how RNA G-quadruplexes (rG4s) facilitate cooperativity in splicing regulation by the RBP heterogeneous nuclear ribonucleoprotein H (HNRNPH). Through high-throughput in vivo and in vitro studies combined with theoretical modeling, we dissect how rG4s mediate cooperative HNRNPH binding to RNA, ultimately modulating the splicing of hundreds of exons. rG4 unfolding by HNRNPH exposes multiple G-rich binding sites, thereby establishing indirect cooperativity, which is further amplified to achieve switch-like splicing regulation. HNRNPH-mediated regulation is evident in breast cancer patients, with tumors showing rG4-disrupting variants and global HNRNPH alterations, driving distinct splicing patterns that distinguish tumor subtypes. Overall, our findings offer valuable insights into the mechanistic role of RNA secondary structures in cooperative RBP binding and splicing regulation and highlight the clinical relevance of HNRNPH-dependent splicing in cancer. HighlightsO_LIHundreds of cassette exons are cooperatively regulated by HNRNPH. C_LIO_LIUnfolding of RNA G-quadruplexes (rG4s) at HNRNPH binding sites facilitates indirect cooperativity in RNA binding. C_LIO_LIMulti-step splicing amplifies the response into highly switch-like regulation. C_LIO_LIrG4-disrupting variants and changing HNRNPH expression are associated with breast cancer phenotypes. C_LI

molecular biology↗

bioRxiv2025

Loss of Cerebral Autoregulation After Stroke Drives Abnormal Perfusion Patterns

Cerebral autoregulation stabilizes cerebral blood flow (CBF) in response to variations in blood pressure, primarily through dynamic adjustments in arterial caliber. However, the impact of autoregulation mechanisms on local vascular responses and microcirculatory perfusion remains poorly understood. Given that impaired autoregulation is common in pathologies such as ischemic stroke, quantifying vessel-level responses can help to inform clinical strategies. Here, we present a novel in silico model that incorporates static myogenic and endothelial regulatory mechanisms to simulate CBF in large microvascular networks derived from realistic surface vasculatures of mice with and without leptomeningeal collaterals (LMCs). We assessed the role of autoregulation mechanisms under three conditions: i) healthy autoregulation, ii) ischaemic stroke and reperfusion with altered vascular reactivity, and iii) chronic autoregulation dysfunction after stroke. For healthy autoregulation, our model reproduced the classic static autoregulation curve and identified the dominant contribution of surface arteries in buffering pressure changes. Networks with lower descending arteriole density exhibited more extensive arterial dilations, reflecting the topological influence on vessel diameter changes. During reperfusion after stroke, we investigated the interplay between LMCs and parameters governing the vasoreactive response. While LMCs play a crucial role in maintaining residual perfusion in adjacent regions during MCA occlusion, our results suggest that their extent alone does not substantially influence perfusion after recanalization. Instead, alterations in myogenic reactivity emerged as the key contributor to hyperperfusion, underscoring the importance of regulatory mechanisms in determining reperfusion outcomes. To mimic chronic autoregulatory dysfunction, we progressively impaired regulatory capacity in arteries on the middle cerebral artery (MCA) side, reflecting the territory previously affected by stroke. The loss of autoregulation in proximal vessels significantly disrupts capillary perfusion and alters the autoregulation curve. To our knowledge, this is the first in silico study to explore cerebral autoregulation at the microvascular level under both physiological and pathological conditions. Our findings provide mechanistic insight into how individual vessel behavior shapes global flow regulation and highlight myogenic tone as a potential therapeutic target to reduce reperfusion-related complications in stroke.

physiology↗

bioRxiv2025

Genetic correlation-guided mega-analysis of DO mice provides mechanistic insight and candidate genes for age-related pathologies

Diversity Outbred (DO) mice are a powerful model system for mapping complex traits due to their high genetic diversity and mapping resolution. However, while there are extensive tools available for standard genetic analysis in DO mice, fewer techniques have been implemented to facilitate integrated, cross-study analysis. Here, we implement Haseman-Elston regression to estimate genetic correlations among 7,233 phenotypes measured across eleven independent DO mouse studies. We used this network of genetic correlations to cluster phenotypes according to shared genetics, which enhanced the power to detect quantitative trait loci (QTL). This approach empowered the detection of 884 QTL for 383 meta-phenotypes, explaining an average of 40.36% of the total genetic variance per mega-analysis. We leveraged this network for insights into specific areas of biology, including lifespan, frailty, immune composition, histological and functional lung phenotypes, and histological phenotypes of the aorta. We found the genetics of lifespan to share limited correlation with the genetics of frailty but stronger correlation with the genetics of immune cell composition. Additionally, mega-analyses driven by genetic correlations identified candidate genes (e.g. Cdkn2b) associated with degraded extracellular matrix in the aorta. Finally, an ensemble of genetic analyses implicated pulmonary neuroendocrine cell signaling and/or differentiation as a key driver of multiple lung pathophenotypes.

genetics↗

bioRxiv2024

Assessing the helical stability of polyXYs at the boundaries of Intrinsically Disordered Regions with MD simulations

Intrinsically disordered regions (IDRs) in proteins lack stable structure. By carrying many hydrophilic and charged residues, it prevents them from forming globular domains and contributes to their flexibility and accessibility. Naturally, regions with reduced amino acid composition (low complexity regions; LCRs) occur within IDRs. Disorder and low complexity in protein sequences are linked to various biological functions including phase separation, regulation, and molecular interactions, and mutations in these regions can contribute to several diseases including cancer. Understanding these biological properties requires examination of the structural properties of IDRs and the LCRs within, but their inherently dynamic nature requires specific approaches combining sequence analyses, structure predictions and molecular dynamics (MD) simulations. Here, we leverage our previous work where we identified that some types of LCRs combining two residues (polyXY) are frequent within IDRs and confer them with propensity to form helical conformation. We identify a significant accumulation of such polyXYs at the ends of IDRs following alpha-helices that start outside the IDR and may extend through the polyXY into the IDR, particularly from the N-terminal end of the IDR. MD simulations support the dynamic nature of such helical conformations. Our results suggest a mechanism by which evolutionary emergence of LCRs at IDR ends could provide proteins with flexible regions for fold-upon-binding.

bioinformatics↗

bioRxiv2024

Conditions for the co-existence of promoter and gene-body condensates

In cells, transcription is tightly regulated on multiple layers. The condensation of the transcription machinery into distinct phases is hypothesised to spatio-temporally fine tune RNA polymerase II behaviour during two key stages, transcription initiation and the elongation of the nascent RNA transcripts. However, it has remained unclear whether these phases would mix when present at the same time or remain distinct chemical environments; either as multi-phase condensates or by forming entirely separate condensates. Here we combine particle-based multi-scale simulations and experiments in the model organism C. elegans to characterise the biophysical properties of RNA polymerase II condensates. Both simulations and the in vivo work describe a lower critical solution temperature (LCST) behaviour of RNA Polymerase II, with condensates dissolving at lower temperatures whereas higher temperatures promote condensate stability. Importantly this gradual change in temperature correlates with an incremental transcriptional response to temperature, but is largely uncoupled from the classical stress response. The LCST behaviour of CTD also highlights that these condensates are physio-chemically distinct from heterochromatin condensates. Expanding the simulations we model how the degree of phosphorylation of the disordered C-terminal domain of RNA polymerase II (CTD), which is characteristic for each step of transcription, controls demixing of CTD and pCTD in line with phase separation experiments. We show that the two phases putatively underpinning the initiation of transcription and transcription elongation constitute distinct chemical environments and are in agreement with RNA polymerase II condensates observed in C. elegans embryos by super resolution microscopy. Our analysis reveals how depending on its post-translational modifications and its interaction partners a single protein can adopt multiple morphologies and how partially engulfed condensates promote the selective recruitment of additional factors to the different phases.

biophysics↗

bioRxiv2024

Impaired drainage through capillary-venous networks contributes to age-related white matter loss

The progressive loss of cerebral white matter during aging contributes to cognitive decline, but whether reduced blood flow is a cause or consequence remains debated. Using deep multi-photon imaging in mice, we examined microvascular networks perfusing myelinated tissues in cortical layer 6 and corpus callosum. We identified sparse, wide-reaching venules, termed principal cortical venules, that exclusively drain deep tissues and resemble vasculature at the human cortex and U-fiber interface. Aging involved selective constriction and rarefaction of capillaries in deep branches of principal cortical venules. This resulted in mild hypoperfusion that was associated with microgliosis, astrogliosis and demyelination in deep tissues, but not upper cortex. Inducing a comparable hypoperfusion in adult mice using carotid artery stenosis triggered a similar tissue pathology specific to layer 6 and corpus callosum. Thus, impaired capillary-venous drainage is a contributor to hypoperfusion and a potential therapeutic target for preserving blood flow to white matter during aging.

neuroscience↗

bioRxiv2022

Deficiency in pericyte remodeling as a basis for impaired capillary flow and structure during brain aging

Deterioration of brain capillary flow and architecture is a hallmark of aging and dementia. It remains unclear how loss of brain pericytes in these conditions contributes to capillary dysfunction. Here, we conduct cause-and-effect studies by optically ablating pericytes in adult and aged mice in vivo. Focal pericyte loss induces capillary dilation without blood-brain barrier disruption. These abnormal dilations are exacerbated in the aged brain, and result in increased flow heterogeneity in capillary networks. A subset of affected capillaries experience reduced perfusion due to flow steal. Some capillaries stall in flow and regress, leading to loss of capillary connectivity. Remodeling of neighboring pericytes restores endothelial coverage and vascular tone within days. Pericyte remodeling is slower in the aged brain, resulting in regions of persistent capillary dilation. These findings link pericyte loss to disruption of capillary flow and structure. They also identify pericyte remodeling as a therapeutic target to preserve capillary flow dynamics.

neuroscience↗

bioRxiv2020

The severity of microstrokes depends on local vascular topology and baseline perfusion

1Cortical microinfarcts are caused by blood flow disturbances and are linked to pathologies like cerebral amyloid angiopathy and dementia. Despite their relevance for disease progression, microinfarcts often remain undetected and the smallest scale of disturbance has not yet been identified. We employ blood flow simulations in realistic microvascular networks from the mouse cortex to quantify the impact of single capillary occlusions. We reveal that the severity of a microstroke is strongly affected by the local vascular topology and the baseline flow rate in the occluded capillary. The largest changes in flow rate are observed in capillaries with two in- and two outflows. Interestingly, this specific topological configuration only occurs with a frequency of 8%, while the majority of capillaries are likely designed to efficiently supply oxygen and nutrients. Taken together, microstrokes likely induce a cascade of local disturbances in the surrounding tissue, which might accumulate and impair energy supply locally.

neuroscience↗

bioRxiv2018

Identification of biological mechanisms by semantic classifier systems

The interpretability of a classification model is one of its most essential characteristics. It allows for the generation of new hypotheses on the molecular background of a disease. However, it is questionable if more complex molecular regulations can be reconstructed from such limited sets of data. To bridge the gap between complexity and interpretability, we replace the de novo reconstruction of these processes by a hybrid classification approach partially based on existing domain knowledge. Using semantic building blocks that reflect real biological processes these models were able to construct hypotheses on the underlying genetic configuration of the analysed phenotypes. As in the building process, also these hypotheses are composed of high-level biology-based terms. The semantic information we utilise from gene ontology is a vocabulary which comprises the essential processes or components of a biological system. The constructed semantic multi-classifier system consists of expert base classifiers which each select the most suitable term for characterising their assigned problems. Our experiments conducted on datasets of three distinct research fields revealed terms with well-known associations to the analysed context. Furthermore, some of the chosen terms do not seem to be obviously related to the issue and thus lead to new, hypotheses to pursue.\n\nAuthor summaryData mining strategies are designed for an unbiased de novo analysis of large sample collections and aim at the detection of frequent patterns or relationships. Later on, the gained information can be used to characterise diagnostically relevant classes and for providing hints to the underlying mechanisms which may cause a specific phenotype or disease. However, the practical use of data mining techniques can be restricted by the available resources and might not correctly reconstruct complex relationships such as signalling pathways.\n\nTo counteract this, we devised a semantic approach to the issue: a multi-classifier system which incorporates existing biological knowledge and returns interpretable models based on these high-level semantic terms. As a novel feature, these models also allow for qualitative analysis and hypothesis generation on the molecular processes and their relationships leading to different phenotypes or diseases.

systems biology↗