Biology subjects

Schwarz, A.

Publications and source records attributed to Schwarz, A..

17 recordsLinked to original sources

bioRxiv2026

H3K4me3 recruits the chromatin remodeling DILL-PICKLE-PEPPERCORN complexes to promoters in plants

The plant CHD chromatin remodeler PICKLE (PKL) is a master regulator of cellular identity and differentiation, controlling developmental, hormonal and stress-response processes. Yet the molecular mechanisms underlying its function remain unclear. Here, we show that PKL forms three complexes, each composed of a protein of previously unknown function and one of three mutually exclusive novel DNAJ proteins that recruit HSP70-1. Simultaneous loss of all three DNAJs phenocopies the pkl mutant, indicating functional redundancy among PKL complexes. In vitro activity assays and cryo-electron microscopy reveal that PKL clamps nucleosomal DNA via its ATPase motor domain and recognizes H3K4me3 through its double chromodomain. Genome-wide profiling shows that H3K4me3 recognition positions PKL complexes at genic promoters to bidirectionally fine-tune gene expression. Together, these results provide structure-function insight into PKL recruitment and its control of developmental gene expression, and reveal a chaperone-coupled complex assembly that offers a broader perspective on how chaperone networks may support chromatin remodeling complexes across eukaryotes.

plant biology↗

bioRxiv2026

Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

Lysosomal membrane integrity is essential for cellular homeostasis, and its failure drives lysosomal storage disorders (LSD) and neurodegeneration. The dipeptide L-leucyl-L-leucine methyl ester (LLOMe) is widely used to model lysosomal damage, yet its mechanism remains poorly understood. The prevailing view holds that LLOMe polymerizes into membrane-permeabilizing peptide chains within the lysosomal lumen. Using cryo-electron tomography in cultured cells and primary neurons, we visualized the structural basis of LLOMe-induced lysosomal damage. We reveal that LLOMe forms amyloid structures within lysosomes that directly interact with and rupture the limiting membrane through mechanical stress. In vitro reconstitution confirms this amyloid-mediated mechanism. These findings establish a structural paradigm for lysosomal membrane disruption and provide insights into how disease-relevant protein aggregates, implicated in neurodegeneration and LSD, may compromise lysosomal integrity.

cell biology↗

bioRxiv2025

MEP-independent silent periods in hand muscles elicited by Transcranial Magnetic Stimulation of the ventral premotor cortex: a non-invasive tool to explore premotor negative motor areas

ObjectiveWe investigate the possibility to disrupt motor activity via premotor and parietal cortex stimulation, by inducing cortical silent periods (cSPs) in the voluntarily activated upper limb. MethodsWe analyzed data from 17 subjects with normal brain function, using navigated TMS (nTMS) on individual MR anatomies. We applied single-pulse biphasic stimulation at 120% of resting motor threshold (rMT) in blocks of 30 stimulations on each spot of a 10-16 point grid covering the inferior parietal and frontal lobes in the dominant hemisphere while participants performed voluntary submaximal contraction. Electromyography (EMG) was recorded bilaterally from intrinsic hand muscles. ResultsWe observed cSPs not preceded by a MEP in the contralateral hand in 16/17 participants. The maximum overlap, of individual areas where such MEP-independent cSPs could be evoked, corresponded to the ventral precentral gyrus (MNI coordinates: [x=-57, y=7, z=33]). In a subset of stimulus sites, MEP-independent cSPs were bilateral, with contralateral predominance. Canonical short-latency MEPs were observed in all patients, with maximum overlap over the primary motor cortex. We also observed rare contralateral long-latency (> 23 ms) MEP-like responses from peri-Rolandic TMS. ConclusionsMEP-independent cSPs are systematically elicitable in healthy participants They likely reflect interference with premotor representations of ongoing movements. They offer a novel possibility to investigate higher-order motor functions in the experimental and clinical neurosciences.

neuroscience↗

bioRxiv2025

Correlative MS Imaging for cellular identification and analysis of in situ cryo-ET

In situ cryo-electron tomography (cryo-ET) offers direct access to protein structures in their native state and environment. A central challenge for this technique is the identification and classification of imaged cells, as sample heterogeneity with respect to cell type and functional state can significantly impact the data. Currently, cells can be classified using subtomogram averaging or fluorescent labeling, which require sufficiently distinguishable macromolecules, genetic modifications, or the availability of suitable labels. In MALDI-MS Imaging (MSI) individual cells can be identified and classified reliably, making use of the distributions of phospholipid species, metabolites and small proteins with characteristic profiles for specific cell types. Here we present an integrated pipeline combining MSI and in situ cryo-ET for single-cell identification and classification. Our approach enables MSI data acquisition directly from EM grids and can be used on any eukaryotic single-cell cryo-ET sample without prior modification in less than 36 h. We apply this workflow to describe cell-to-cell heterogeneity in cultured HeLa cells, to distinguish between distantly related HeLa and Polytomella cells, and between primary cultured rat neurons and glial cells. Finally we present a data integration workflow combining cryo-ET, light microscopy and MSI aligned in the same coordinate system to facilitate efficient data visualization and interpretation. We anticipate that this approach will change the way that structural biologists can approach cellular heterogeneity in cryo-ET, as cells can be identified and classified reliably post acquisition.

biophysics↗

bioRxiv2025

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 73,082 samples from humans (including 58,506 of the gut microbiome), 10,703 animal samples, 5,146 ocean water samples, and 21,802 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status and medication for humans, host species and captivity status for animals, and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.

microbiology↗

bioRxiv2025

A Lipid Prodrug Strategy Enhances Targeted Protein Degrader CNS Pharmacokinetics

Targeted protein degraders that recruit the von-hippel Lindau E3-ligase complex often have poor physicochemical properties, requiring extensive medicinal chemistry optimization prior to use in hypothesis-testing experiments in vivo, and with few blood-brain-barrier permeable examples disclosed. In this study, we systematically examine a panel of fatty acid promoieties as agents to enhance degrader pharmacokinetics and BBB-exposure. We characterize effects on cellular E3-ligase engagement, cellular BRD4 degradation kinetics, murine plasma stability, and murine blood plasma and brain pharmacokinetics and pharmacodynamics. We identify degrader prodrugs with significantly improved CNS exposure relative to the parent degrader. This led to successful BRD4. degradation in perfused brain samples, demonstrating that fatty acid promoieties can accelerate progress towards proof of principle in vivo experiments for CNS degrader projects.

pharmacology and toxicology↗

bioRxiv2024

Synaptic accumulation of GluN2B-containing NMDA receptors mediates the effects of BDNF-TrkB signalling on synaptic plasticity and in epileptogenesis

Brain-derived neurotrophic factor (BDNF) is a key mediator of synaptic plasticity and memory formation in the hippocampus. However, the BDNF-induced alterations in the glutamate receptors coupled to the plasticity of glutamatergic synapses in the hippocampus have not been elucidated. In this work we investigated the putative role of GluN2B-containing NMDA receptors in the plasticity of glutamatergic synapses induced by BDNF. Stimulation of hippocampal synaptoneurosomes with BDNF led to a significant time-dependent increase in the synaptic surface expression of GluN2B-containing NMDA receptors as determined by immunocytochemistry with colocalization with pre- (vesicular glutamate transporter) and post-synaptic markers (PSD95). Similarly, BDNF induced the synaptic accumulation of GluN2B-containing NMDA receptors at the synapse in cultured hippocampal neurons, by a mechanism sensitive to the PKC inhibitor G[O]6983. The effects of PKC may be mediated by phosphorylation of Pyk2, as suggested by western blot experiments analyzing the phosphorylation of the kinase on Tyrosine 402. GluN2B-containing NMDA receptors mediated the effects of BDNF in the facilitation of the early phase of long-term potentiation (LTP) of hippocampal CA1 synapses induced by {theta}-burst stimulation, since the effect of the neurotrophin was abrogated in the presence of the GluN2B inhibitor Co 101244. In the absence of BDNF, the GluN2B inhibitor did not effect LTP. Surface accumulation of GluN2B-containing NMDA receptors was also observed in hippocampal synaptoneurosomes isolated from rats subjected to the pilocarpine model of temporal lobe epilepsy, after reaching Status epilepticus, an effect that was inhibited by administration of the TrkB receptor inhibitor ANA-12. Together, these results show that the synaptic accumulation of GluN2B-containing NMDA receptors mediate the effects of BDNF in the plasticity of glutamatergic synapses in the hippocampus.

neuroscience↗

bioRxiv2024

In situ structure and rotary states of mitochondrial ATP synthase in whole cells

Cells depend on a continuous supply of ATP, the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical gradient is established across the inner mitochondrial membrane. The ATP synthase harnesses the energy of the gradient to generate ATP from ADP and inorganic phosphate. We determined the structure of ATP synthase within mitochondria of the unicellular alga Polytomella by electron cryo-tomography. Sub-tomogram averaging revealed six rotary positions of the central stalk, subclassified into 21 substates of the F1 head. The Polytomella ATP synthase forms helical arrays with multiple adjacent rows defining the cristae ridges. The structure of ATP synthase under native operating conditions in the presence of a membrane potential represents a pivotal step toward the analysis of membrane protein complexes in situ.

molecular biology↗

bioRxiv2023

Terpenes from Cannabis sativa Induce Antinociception in Mouse Chronic Neuropathic Pain via Activation of Spinal Cord Adenosine A2A Receptors

Terpenes are small hydrocarbon compounds that impart aroma and taste to many plants, including Cannabis sativa. A number of studies have shown that terpenes can produce pain relief in various pain states in both humans and animals. However, these studies were methodologically limited and few established mechanisms of action. In our previous work, we showed that the terpenes geraniol, linalool, {beta}-pinene, - humulene, and {beta}-caryophyllene produced cannabimimetic behavioral effects via multiple receptor targets. We thus expanded this work to explore the efficacy and mechanism of these Cannabis terpenes in relieving chronic pain. We first tested for antinociceptive efficacy by injecting terpenes (200 mg/kg, IP) into male and female CD- 1 mice with chemotherapy-induced peripheral neuropathy (CIPN) or lipopolysaccharide-induced inflammatory pain, finding that the terpenes produced roughly equal efficacy to 10 mg/kg morphine or 3.2 mg/kg WIN55,212. We further found that none of the terpenes produced reward as measured by conditioned place preference, while low doses of terpene (100 mg/kg) combined with morphine (3.2 mg/kg) produced enhanced antinociception vs. either alone. We then used the adenosine A2A receptor (A2AR) selective antagonist istradefylline (3.2 mg/kg, IP) and spinal cord-specific CRISPR knockdown of the A2AR to identify this receptor as the mechanism for terpene antinociception in CIPN. In vitro cAMP and binding studies and in silico modeling studies further suggested that the terpenes act as A2AR agonists. Together these studies identify Cannabis terpenes as potential therapeutics for chronic neuropathic pain, and identify a receptor mechanism in the spinal cord for this activity.

neuroscience↗

bioRxiv2022

Intermediate Gray Matter Interneurons in the Lumbar Spinal Cord Play a Critical and Necessary Role in Coordinated Locomotion

Locomotion is a complex task involving excitatory and inhibitory circuitry in spinal gray matter. While genetic knockouts examine the function of unique spinal interneuron (SpIN) subtypes, the phenotype of combined premotor interneuron loss remains to be explored. We modified a kainic acid lesion to damage intermediate gray matter (laminae V-VII) in the lumbar spinal enlargement (spinal L2-L4) in female rats. A thorough, tailored behavioral evaluation revealed deficits in gross hindlimb function, skilled walking, coordination, balance and gait two-weeks post-injury. Using a Random Forest algorithm, we combined these behavioral assessments into a highly predictive binary classification system which strongly correlated with structural deficits in the rostro-caudal axis. Machine-learning quantification confirmed interneuronal damage to laminae V-VII in spinal L2-L4 correlates with hindlimb dysfunction. White matter damage and lower motoneuron loss did not correlate with behavioral deficits. Animals do not regain lost sensorimotor function three months after injury, indicating that natural recovery of the spinal cord cannot compensate for loss of laminae V-VII neurons. As spinal cord injuries are often located at spinal enlargements, this research lays the groundwork for new neuroregenerative therapies to replace these lost neuronal pools vital to sensorimotor function. HighlightsO_LIFunctional deficits in coordination, balance, rhythmic walking and gait follow two weeks after a lumbar (L2-L4) intermediate (V-VII) gray matter spinal cord injury in rats C_LIO_LIDeficits correlate with neuronal loss in laminae V-VII in spinal levels L2-L4 but do not correlate with lower motoneuron loss or white matter damage nor do animals show signs of sensory dysfunction due to spinal cord injury C_LIO_LICoordination deficits remain after three months, indicating that natural recovery cannot compensate for this interneuronal loss C_LIO_LINewly developed machine-learning models non-invasively fully classify injured animals by functional readouts equivalent to time-intensive endpoint histological analysis C_LI

neuroscience↗

bioRxiv2022

C. difficile is overdiagnosed in adults and a commensal in infants

Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. To investigate the gut microbiome composition in CDI patients, we analysed 534 metagenomes from 10 publicly available CDI study populations. We then tracked C. difficile on a global scale, screening 42,900 metagenomes from 253 public studies. Among the CDI cohorts, we detected C. difficile in only 30% of the stool samples from CDI patients. However, we found that multiple other toxigenic species capable of inducing CDI-like symptomatology were prevalent. In addition, the majority of the investigated studies did not adhere to the recommended guidelines for a correct CDI diagnosis. In the global survey, we found that C. difficile prevalence, abundance and biotic context were age-dependent. C. difficile is a rare taxon associated with reduced diversity in healthy adults, but common and associated with increased diversity in infants. We identified a group of species co-occurring with C. difficile exclusively in healthy infants, enriched in obligate anaerobes and in species typical of the healthy adult gut microbiome. C. difficile in healthy infants was therefore associated with multiple indicators of healthy gut microbiome maturation. Our analysis raises concerns about potential CDI overdiagnosis and suggests that C. difficile is an important commensal in infants and that its asymptomatic carriage in adults depends on microbial context.

microbiology↗

bioRxiv2021

The European Prevention of Alzheimer's Dementia (EPAD) MRI Dataset and Processing Workflow

The European Prevention of Alzheimer Dementia (EPAD) is a multi-center study that aims to characterize the preclinical and prodromal stages of Alzheimers Disease. The EPAD imaging dataset includes core (3D T1w, 3D FLAIR) and advanced (ASL, diffusion MRI, and resting-state fMRI) MRI sequences. Here, we give an overview of the semi-automatic multimodal and multisite pipeline that we developed to curate, preprocess, quality control (QC), and compute image-derived phenotypes (IDPs) from the EPAD MRI dataset. This pipeline harmonizes DICOM data structure across sites and performs standardized MRI preprocessing steps. A semi-automated MRI QC procedure was implemented to visualize and flag MRI images next to site-specific distributions of QC features -- i.e. metrics that represent image quality. The value of each of these QC features was evaluated through comparison with visual assessment and step-wise parameter selection based on logistic regression. IDPs were computed from 5 different MRI modalities and their sanity and potential clinical relevance were ascertained by assessing their relationship with biological markers of aging and dementia. The EPAD v1500.0 data release encompassed core structural scans from 1356 participants 842 fMRI, 831 dMRI, and 858 ASL scans. From 1356 3D T1w images, we identified 17 images with poor quality and 61 with moderate quality. Five QC features -- Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Coefficient of Joint Variation (CJV), Foreground-Background energy Ratio (FBER), and Image Quality Rate (IQR) -- were selected as the most informative on image quality by comparison with visual assessment. The multimodal IDPs showed greater impairment in associations with age and dementia biomarkers, demonstrating the potential of the dataset for future clinical analyses.

neuroscience↗

bioRxiv2021

Ligands binding to the cellular prion protein induce its protective proteolytic release with therapeutic potential in neurodegenerative proteinopathies

The cellular prion protein (PrPC) is a central player in neurodegenerative diseases caused by protein misfolding, such as prion diseases or Alzheimers disease (AD). Expression levels of this GPI-anchored glycoprotein, especially at the neuronal cell surface, critically correlate with various pathomechanistic aspects underlying these diseases, such as templated misfolding (in prion diseases) and neurotoxicity and, hence, with disease progression and severity. In stark contrast to cell-associated PrPC, soluble extracellular forms or fragments of PrP are linked with neuroprotective effects, which is likely due to their ability to interfere with neurotoxic disease-associated protein conformers in the interstitial fluid. Fittingly, the endogenous proteolytic release of PrPC by the metalloprotease ADAM10 ( shedding) was characterized as a protective mechanism. Here, using a recently generated cleavage-site specific antibody, we shed new light on earlier studies by demonstrating that shed PrP (sPrP) negatively correlates with conformational conversion (in prion disease) and is markedly redistributed in murine brain in the presence of prion deposits or AD-associated amyloid plaques indicating a blocking and sequestrating activity. Importantly, we reveal that administration of certain PrP-directed antibodies and other ligands results in increased PrP shedding in cells and organotypic brain slice cultures. We also provide mechanistic and structural insight into this shedding-stimulating effect. In addition, we identified a striking exception to this, as one particular neuroprotective antibody, due to its special binding characteristics, did not cause increased shedding but rather strong surface clustering followed by fast endocytosis and degradation of PrPC. Both mechanisms may contribute to the beneficial action described for some PrP-directed antibodies/ligands and pave the way for new therapeutic strategies against devastating and currently incurable neurodegenerative diseases.

neuroscience↗

bioRxiv2020

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and the development of safe vaccines. The large scale tomography data set of SARS-CoV-2 used for this study is therefore sufficient to resolve structural features to below 5 [A]ngstrom, and is publicly available at EMPIAR-10453.

molecular biology↗

bioRxiv2020

Technology-aided assessment of functionally relevant sensorimotor impairments in arm and hand of post-stroke individuals

BackgroundAssessing arm and hand sensorimotor impairments that are functionally relevant is essential to optimize the impact of neurorehabilitation interventions. Technology-aided assessments should provide a sensitive and objective characterization of upper limb impairments, but often provide arm weight support and neglect the importance of the hand, thereby questioning their functional relevance. The Virtual Peg Insertion Test (VPIT) addresses these limitations by quantifying arm movements and grip forces during a goal-directed manipulation task without arm weight support. The aim of this work was to evaluate the potential and robustness of the VPIT metrics to inform on sensorimotor impairments in arm and hand, and especially identify the functional relevance of the detected impairments. MethodsArm and hand sensorimotor impairments were systematically characterized in 30 chronic stroke patients using conventional clinical scales and the VPIT. For the latter, ten previously established kinematic and kinetic core metrics were extracted and compared to conventional clinical scales of impairment and activity limitations. Additionally, the robustness of the VPIT metrics was investigated by analyzing their clinimetric properties (test-retest reliability, measurement error, and learning effects). ResultsTwenty-three of the participants, the ones with mild to moderate sensorimotor impairments and without strong cognitive deficits, were able to successfully complete the VPIT protocol (duration 16.6 min). The VPIT metrics detected impairments in arm and hand in 90.0% of the participants, and were sensitive to increased muscle tone and pathological joint coupling. Most importantly, moderate to high significant correlations between conventional scales of activity limitations and the VPIT metrics were found, thereby indicating their functional relevance when grasping and transporting lightweight objects as well as dexterous finger manipulations. Lastly, the robustness of three out of the ten VPIT core metrics in post-stroke individuals was confirmed. ConclusionsThis work provides evidence that technology-aided assessments requiring goal-directed manipulations without arm weight support can provide an objective, robust, and clinically feasible way to assess functionally relevant sensorimotor impairments in arm and hand in chronic post-stroke individuals with mild to moderate deficits. This allows better identifying impairments with high functional relevance and can contribute to optimizing the functional benefits of neurorehabilitation interventions. Retrospectively registered: clinicaltrials.gov/ct2/show/NCT03135093

neuroscience↗

bioRxiv2019

An Objective Technology-based Assessment of Arm and Hand Sensorimotor Disability in Neurological Disorders

BackgroundDetailed assessments of upper limb disability are essential to understand and monitor sensorimotor recovery. Usually, multiple timeconsuming assessments are required to define a holistic sensorimotor profile of proximal (shoulder-elbow) and distal (wrist-hand) impairments and their impact on the capacity to perform activities. We propose and evaluate a novel physiologically-motivated computational framework for objectively assessing sensorimotor profiles in neurological patients using a single, rapid technology-based assessment involving goal-directed arm and hand movements. MethodsThe Virtual Peg Insertion Test (VPIT) was administered to 121 healthy and 80 neurological subjects. The framework provides 25 kinematic and kinetic metrics expected to describe 12 sensorimotor components representative of ataxia and paresis and their influence on task performance, as well as one overall disability measure. The feasibility (protocol duration), structural validity (factor analysis and correlations{rho} between sensorimotor components), concurrent validity (correlation with Action Research Arm Test; ARAT), and discriminant validity (comparing healthy controls and patients, and patients with different disability levels) were evaluated. ResultsThe median VPIT protocol duration was 16.5min in neurological patients. The sensor-based metrics could unambiguously be grouped into 12 mostly independent (median |{rho}|=0.14) components. Ten components showed significant differences between healthy and impaired subjects and nine components indicated clear trends across disability levels, without any ceiling effects. The VPIT overall disability measure and ARAT were moderately correlated ({rho}=-0.53, p<0.001). ConclusionsThis work demonstrates the possibility to rapidly, holistically, and objectively assess proximal and distal sensorimotor impairments and their influence on the capacity to perform activities with a single assessment.

neuroscience↗

bioRxiv2018

Growth differentiation factor-15 regulates oxLDL-induced lipid homeostasis and autophagy in human macrophages

Growth differentiation factor-15 (GDF-15), a divergent and distant member of the transforming growth factor-{beta} superfamily, is suggested as a risk factor for cardiovascular diseases. Thus, we are interested to investigate the influence of GDF-15 in lipid homeostasis and autophagy in macrophages (M{Phi}) during foam cell formation. Our investigations represent the impairment of GDF-15 on modulators of autophagy and lipid homeostasis in PMA-differentiated human THP-1 M{Phi}. In this context, in vitro resulted GDF-15 silencing in a reduction of lipid accumulation, whereas the addition of recombinant (r)GDF-15 increased the lipid accumulation in human M{Phi} independent of oxidized (ox)LDL. Additionally, GDF-15 affected the expression of autophagy-relevant proteins (p62, Atg5 and Atg12/Atg5 protein complex) and the p62 accumulation in THP-1 M{Phi}. Hence, our data suggest that GDF-15 is involved in the regulation of the lipid homoeostasis of human M{Phi} by regulating autophagic processes.

cell biology↗