Biology subjects

Strauss, M.

Publications and source records attributed to Strauss, M..

17 recordsLinked to original sources

bioRxiv2026

The Structural Basis of Genome Silencing: The Inactive X Chromosome Resolved by Electron Spectroscopic Imaging

The eukaryotic nucleus has a hierarchical organization that permits genomic regulation. The genome is packaged as chromatin, which is silenced conditionally as facultative heterochromatin, or more stably silenced as constitutive heterochromatin. The smaller fractions of the genome that contain gene-rich sequences are organized into open chromatin conformations known as euchromatin. The inactive X (Xi) chromosome territory presents a uniquely powerful model system to investigate chromosome-scale gene silencing, as the entire chromosome undergoes coordinated epigenetic repression. The unique chromosome-wide silencing event provides a tractable system for investigating how molecular mechanisms of gene repression are translated into mesoscale structural features. This work builds on previous structural studies of the Xi that have leveraged conventional electron microscopy (EM) and cryo-EM, which have led to remarkable insights into the structural underpinnings of genome silencing. These approaches, however, are unable to directly distinguish chromatin from RNA and protein features. To resolve the molecular composition of the Xi chromosome territory and to provide a model of the structural organization of the chromatin, RNA and protein we analyzed the Xi using Electron Spectroscopic Imaging (ESI). We are able to resolve structural features without the use of contrast enhancing stains, using the distinct elemental signatures of chromatin, RNA and protein and combining them into composite images. By coupling ESI and electron tomography, we can circumvent the projection limitation of EM and provide an unprecedented view of the spatial organization of chromatin fibres in relation to structural features including RNA and proteins in 3D. Additionally, we employed correlative light-microscopy with ESI in physical serial sections and computationally assembled a structural model of the entire Xi chromosome territory revealing an intricate spatial network with distinct chromatin domains, distributed RNA-protein clusters, and identified a large, and previously uncharacterized mesoscale non-chromatin structure. Together, these observations provide new insights into the architecture of the Xi chromosome territory and shed electrons on the structural basis of chromosome-scale genome organization.

cell biology↗

bioRxiv2026

Multi-parametric spectral modeling disentangles synaptic kinetics and neural excitability from non-invasive electrophysiological recordings

Spectral modeling of electrophysiological recordings enables non-invasive characterization of neural excitability. However, current approaches rely on a single spectral index, limiting insight into the multiple biophysical processes underlying excitation-inhibition balance. Here, we introduce a biologically informed, multi-parametric spectral analysis that disentangles neural excitability and synaptic kinetics from recordings. As a proof of concept, we demonstrate that this approach captures signatures of hyperexcitability and glutamate reuptake dysfunction characteristic of Alzheimer's disease.

neuroscience↗

bioRxiv2026

SELECT-seq allows Pre-Sequencing Enrichment of SNP Edits in One-Pot Single-Cell Whole-Transcriptome Sequencing

Advances in high-throughput sequencing have associated millions of putative genetic variants with disease. However, scalable experimental methods to establish causal relationships between genetic variants and downstream transcriptional outcomes remain a major challenge. Single-cell methods that integrate genotyping with transcriptomic profiling provide a way to address this, but do not enable pre-sequencing enrichment of correctly edited cells, limiting scale. We present SELECT-seq (SNP Enrichment Leveraging Cas12a Targeting), a rapid method that allows SNP-specific PCR amplification and Cas12a-mediated fluorescence detection simultaneously with whole-transcriptome amplification. This one-pot workflow enables identification and enrichment of SNP-bearing single cells, making a rapid and scalable methodology for analysis of genotype-phenotype linkage avoiding laborious single cell cloning steps. As a proof of principle we show that SELECT-seq distinguishes U-2 OS and T-47D cell lines based on a PIK3CA (NM_006218.4:c.3463A>G) mutation while preserving transcriptome integrity. It physically enriches a rare NRF2 T80K (NM_006164.5:c.390C>A) mutant cells (6.7%) from a prime-edited pool, achieving 86% genotype accuracy, and shows 87.5% directional concordance in the transcriptomic effects compared with a clonal NRF2 T80K cell line. SELECT-seq thus provides a rapid, scalable and widely accessible approach for mapping genotype-phenotype relationships at single-cell resolution.

molecular biology↗

bioRxiv2024

Cardiac responses to auditory irregularities reveal hierarchical information processing during sleep

Our ability to process environmental stimuli varies during sleep. Although much research focused on neural processing, emerging evidence shows that bodily signals may play a key role in understanding high-level sensory processing during sleep. Here, we tested how cardiac responses to the local-global paradigm, a typical oddball task probing the processing of simple (local) and complex (global) sensory irregularities. To do so, we analyzed electrocardiography (ECG) signals in a total of 56 participants from two existing datasets which contained cerebral responses to local auditory irregularities, but which did not analyze the ECG data before. We found that cardiac activity slowed down after global, but not local, auditory irregularities, revealing the presence of global deviance effect in Rapid Eye Movement (REM) sleep. In contrast, cardiac activity was faster after local, but not global, deviants in Non-Rapid Eye Movement (NREM) sleep. Overall, our results demonstrate that cardiac responses to auditory irregularities inform about hierarchical information processing and its variations during sleep beyond cerebral activity. They highlight the embodiment of cognitive function and the value of cardiac signals to understand the variations of sensory processing during sleep.

neuroscience↗

bioRxiv2024

IFNγ initiates TLR9-dependent autoimmune hepatitis in DNase II deficient mice

Patients with biallelic hypomorphic mutation in DNASE2 develop systemic autoinflammation and early-onset liver fibrosis. Prior studies showed that Dnase2-/- Ifnar-/- double knockout (DKO) mice develop Type I IFN-independent liver inflammation, but immune mechanisms were unclear. We now show that DKO mice recapitulate many features of human autoimmune hepatitis (AIH), including periportal and interstitial inflammation and fibrosis and elevated ALT. Infiltrating cells include CD8+ tissue resident memory T cells, type I innate lymphoid cells, and inflammatory monocyte/macrophage cells that replace the Kupffer cell pool. Importantly, TLR9 expression by bone marrow-derived cells is required for the the development of AIH. TLR9 is highly expressed by inflammatory myeloid cells but not long-lived Kupffer cells. Furthermore, the initial recruitment of TLR9 expressing monocytes and subsequent activation of lymphocytes requires IFN{gamma} signaling. These findings highlight a critical role of feed forward loop between TLR9 expressing monocyte-lineage cells and IFNg producing lymphocytes in autoimmune hepatitis.

immunology↗

bioRxiv2023

Mutations in Fibronectin Dysregulate Chondrogenesis in Corner Fracture Type Spondylometaphyseal Dysplasia

Fibronectin (FN) is an extracellular matrix glycoprotein essential for the development and function of major vertebrate organ systems. Mutations in FN result in an autosomal dominant skeletal dysplasia termed corner fracture-type spondylometaphyseal dysplasia (SMDCF). The precise pathomechanisms through which mutant FN induces impaired skeletal development remain elusive. Here, we have generated patient-derived induced pluripotent stem cells as a cell culture model for SMDCF to investigate the consequences of FN mutations on mesenchymal stem cells (MSCs) and their differentiation into cartilage-producing chondrocytes. In line with our previous data, FN mutations disrupted protein secretion from MSCs, causing a notable increase in intracellular FN and a significant decrease in extracellular FN levels. Analyses of plasma samples from SMDCF patients also showed reduced FN in circulation. FN and endoplasmic reticulum (ER) protein folding chaperones (BIP, HSP47) accumulated in MSCs within ribosome-covered cytosolic vesicles that emerged from the ER and transitioned into lysosomes. Massive amounts of these vesicles were not cleared from the cytosol. The accumulation of intracellular FN and ER proteins elevated cellular stress markers and altered mitochondrial structure. Bulk RNA sequencing revealed a specific transcriptomic dysregulation of the patient-derived cells relative to controls. Analysis of MSC differentiation into chondrocytes showed impaired mesenchymal condensation, reduced chondrogenic markers, and compromised cell proliferation in mutant cells. FN mutant cells also displayed altered FN splice variants under chondrogenic stimuli. Moreover, FN mutant cells exhibited significantly lower transforming growth factor beta-1 (TGF{beta}1) expression, crucial for mesenchymal condensation. Exogenous FN or TGF{beta}1 supplementation effectively improved the MSC condensation and promoted chondrogenesis in FN mutant cells. These findings demonstrate the cellular consequences of FN mutations in SMDCF and explain the molecular pathways involved in the associated altered chondrogenesis. Significance /Highlights* SMDCF-causing mutations in fibronectin impair protein secretion in iPSC-derived mesenchymal stem cells. * Mutant fibronectin and ER protein folding chaperones are directly exported from the rough endoplasmic reticulum into vesicles covered with ribosomes, which transition into lysosomes. * The cells cannot clear the massive accumulation of cytosolic vesicles. * Mutations in fibronectin impair stem cell proliferation, mesenchymal condensation, and the differentiation of MSCs into chondrocytes. * Exogenous addition of purified fibronectin or TGF{beta}-1 improves mesenchymal condensation and chondrogenesis of the FN mutant stem cells.

cell biology↗

bioRxiv2023

Microfibril-associated glycoprotein 4 forms octamers that mediate interactions with elastogenic proteins and cells

Microfibrillar-associated protein 4 (MFAP4) is a 36-kDa extracellular glycoprotein with critical roles in human pathologies, including fibrosis in several organ systems, chronic obstructive pulmonary disease, and cardiovascular disorders. In elastic tissues such as arteries, lungs, and skin, MFAP4 associates with microfibrils and elastic fibres, which are the central extracellular fibres affected in thoracic aneurysms. MFAP4 directly interacts with elastogenic proteins, including fibrillin-1 and tropoelastin, and with cells via integrins. MFAP4 multimerisation represents a critical hallmark required for its physiological and pathological properties. However, molecular details and functional consequences of MFAP4 multimerisation are lacking. Here we present a cryo-electron microscopy structure of human MFAP4. In the presence of calcium, MFAP4 assembles as an octamer with D2 point group symmetry, where two sets of homodimers constitute the top and bottom halves of each octamer. Each of the homodimers is linked together by an inter-molecular disulfide bond. An engineered C34S missense mutation in MFAP4 prevented disulfide-bond formation between monomers, but the mutant formed octamers similar to wild type MFAP4. The atomic model, built into the 3.55 [A] cryo-EM map, suggests that several salt-bridges are important for interactions within and between homodimers, while non-polar interactions are important for octamer halves to assemble. In the absence of calcium, MFAP4 dissociates into tetramers, representing the top/bottom halves of the octamers. Binding studies with elastogenic proteins, including fibrillin-1, tropoelastin, LTBP4, and small fibulins showed that MFAP4 has multiple surfaces for protein-protein interactions, which depend upon the higher-order assembly of MFAP4. While the disulfide-bond mediated by C34S contributes little to those protein interactions, it modulated cell interaction. When MFAP4 forms assemblies with fibrillin-1, it abrogates MFAP4 interactions with cells. Overall, the study provides detailed molecular structure-function relationships of MFAP4 interactions with elastogenic proteins and cells.

cell biology↗

bioRxiv2023

Structure and function of a hexameric cyanophycin synthetase 2

Cyanophycin is a natural polymer composed of a poly-aspartate backbone with arginine attached to each of the aspartate sidechains. Produced by a wide range of bacteria, which mainly use it as a store of fixed nitrogen, it has many promising industrial applications. Cyanophycin can be synthesized from the amino acids Asp and Arg by the widespread cyanophycin synthetase 1 (CphA1), or from the dipeptide {beta}-Asp-Arg by the cyanobacterial enzyme cyanophycin synthetase 2 (CphA2). CphA2 enzymes display a range of oligomeric states, from dimers to dodecamers. Recently, the crystal structure of a CphA2 dimer was solved but could not be obtained in complex with substrate. Here, we report cryo-EM structures of the hexameric CphA2 from Stanieria sp. at ~2.8 [A] resolution, both with and without ATP and cyanophycin. The structures show a trimer-of-dimers hexameric architecture, and substrate-binding interactions that are similar to those of CphA1. Mutagenesis experiments demonstrate the importance of several conserved substrate-binding residues. We also find that a Q416A/R528G double mutation prevents hexamer formation and use this double mutant to show that hexamerization augments the rate of cyanophycin synthesis. Together, these results increase our mechanistic understanding of how an interesting green polymer is biosynthesized.

biochemistry↗

bioRxiv2020

A paired liver biopsy and plasma proteomics study reveals circulating biomarkers for alcohol-related liver disease

Existing tests for detecting liver fibrosis, inflammation and steatosis, three stages of liver disease that are still reversible are severely hampered by limited accuracy or invasive nature. Here, we present a paired liver-plasma proteomics approach to infer molecular pathophysiology and to identify biomarkers in a cross-sectional alcohol-related liver disease cohort of nearly 600 individuals. Metabolic functions were downregulated whereas fibrosis-associated signaling and novel immune responses were upregulated, but only half of tissue proteome changes were transmitted to the circulation. Machine learning models based on our biomarker panels outperformed existing tests, laying the foundation for a generic proteomic liver health assessment.

biochemistry↗

bioRxiv2020

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

Vesicle-inducing protein in plastids (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-shaping function. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket that is required for VIPP1 oligomerization. Inside the rings lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In vivo point mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Our study provides a structural basis for understanding how the oligomerization of VIPP1 drives the biogenesis of thylakoid membranes and protects these life-giving membranes from environmental stress.

plant biology↗

bioRxiv2020

Structural basis for decoding active histone methylation marks by Polycomb Repressive Complex 2

Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and trimethylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro. Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.

biochemistry↗

bioRxiv2020

Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate.

The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and opening of holes at the two and quasi-three-fold symmetry axes of the capsid. The resultant particle is called a 135S particle or A-particle and is thought to be on the pathway to a productive infection. Previously published studies have concluded that the membrane interactive peptides, namely VP4 and the N-terminus of VP1, are irreversibly externalized in the 135S particle. However, using established protocols to produce the 135S particle, and single particle cryo-electron microscopy methods, we have identified at least two unique states that we call the early and late 135S particle. Surprisingly, only in the "late" 135S particles have detectable levels of the VP1 N-terminus trapped outside the capsid. Moreover, we observe a distinct density inside the capsid that can be accounted for by VP4 that remains associated with the genome. Taken together our results conclusively demonstrate that the 135S particle is not a unique conformation, but rather a family of conformations that could exist simultaneously. AUTHOR SUMMARYNonenveloped viruses need to provide mechanisms that allow their genomes to be delivered across membrane. This process remains poorly understood. For enterovirus such as poliovirus, genome delivery involves a program of conformational changes that include expansion of the particle and externalization of two normal internal peptides, VP4 and the VP1 N-terminus, which then insert into the cell membrane, triggering endocytosis and the creation of pores that facilitate the transfer of the viral RNA genome across the endosomal membrane. This manuscript describes five high-resolution cryo-EM structures of altered poliovirus particles that represent a number of intermediates along this pathway. The structures reveal several surprising findings, including the discovery of a new intermediate that is expanded but has not yet externalized the membrane interactive peptides, the clear identification of a unique exit site VP1 N-terminus, the demonstration that the externalized VP1 N-terminus partitions between two different sites in a temperature-dependent fashion, direct visualization of an amphipathic helix at the N-terminus of VP1 in an ideal position for interaction with cellular membranes, and the observation that a significant portion of VP4 remains inside the particle and accounts for a feature that had been previously ascribed to part of the viral RNA. These findings represent significant additions to our understanding of the cell entry process of an important class of human pathogens.

biophysics↗

bioRxiv2019

The novel shapeshifting bacterial phylum Saltatorellota

Our current understanding of a free-living bacterium - capable of withstanding a variety of environmental stresses-is represented by the image of a peptidoglycan-armored rigid casket. The making and breaking of peptidoglycan greatly determines cell shape. The cytoplasmic membrane follows this shape, pressed towards the cell wall by turgor pressure. Consequently, bacteria are morphologically static organisms, in contrast to eukaryotic cells that can facilitate shape changes. Here we report the discovery of the novel bacterial phylum Saltatorellota, that challenges this concept of a bacterial cell. Members of this phylum can change their shape, are capable of amoeba-like locomotion and trunk-formation through the creation of extensive pseudopodia-like structures. Two independent Saltatorellota cells can fuse, and they employ various forms of cell division from budding to canonical binary fission. Despite their polymorphisms, members of the Saltatorellota do possess a peptidoglycan cell wall. Their genomes encode flagella and type IV pili as well as a bacterial actin homolog, the saltatorellin. This protein is most similar to MamK, a dynamic filament-forming protein, that aligns and segregates magnetosome organelles via treadmilling. We found saltatorellin to form filaments in both, E. coli and Magnetospirillum gryphiswaldense, leading to the hypothesis that shapeshifting and pseudopodia formation might be driven by treadmilling of saltatorellin.

microbiology↗

bioRxiv2019

Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain

Glucose homeostasis and growth essentially depend on the peptide hormone insulin engaging its receptor. Despite biochemical and structural advances, a fundamental contradiction has persisted in the current understanding of insulin ligand-receptor interactions. While biochemistry predicts two distinct insulin binding sites, 1 and 2, recent structural analyses have only resolved site 1. Using a combined approach of cryo-EM and atomistic molecular dynamics simulation, we determined the structure of the entire dimeric insulin receptor ectodomain saturated with four insulin molecules. Complementing the previously described insulin-site 1 interaction, we present the first view of insulin bound to the discrete insulin receptor site 2. Insulin binding stabilizes the receptor ectodomain in a T-shaped conformation wherein the membrane-proximal domains converge and contact each other. These findings expand the current models of insulin binding to its receptor and of its regulation. In summary, we provide the structural basis enabling a comprehensive description of ligand-receptor interactions that ultimately will inform new approaches to structure-based drug design.\n\nIn briefA cryo-EM structure of the complete insulin receptor ectodomain saturated with four insulin ligands is reported. The structural model of the insulin-insulin receptor complex adopts a T-shaped conformation, reveals two additional insulin-binding sites potentially involved in the initial interaction of insulin with its receptor, and resolves the membrane proximal region.

biochemistry↗

bioRxiv2019

Giraffe Translocation Population Viability Analysis

Most populations of giraffes have declined in recent decades, leading to the recent decision to upgrade the species to vulnerable status, and some subspecies to endangered. Translocations have been used as a conservation tool to re-introduce giraffes to previously occupied areas or establish new populations, but guidelines for founding populations are lacking. To provide general guidelines for translocation projects regarding feasibility, we simulated various scenarios of translocated giraffe populations to identify viable age and sex distributions of founding populations using Population Viability Analysis (PVA) implemented in Vortex software. We explored the parameter space for demography (population growth rates: {lambda} = 1.001, 1.010, 1.024), and the genetic load (number of lethal equivalents: LE = 2.5, 6.29, 12.6), examining how variation in founding numbers (N = 5 to 80 females) and sex ratios (M:F = 0.1 to 0.5) affected 100-year probability of extinction and genetic diversity. We found that even very small numbers of founders (N [≤]10 females) can appear to be successful in the first decades due to transient positive population growth, but with moderate population growth rate and moderate genetic load, long-term population viability (probability of extinction <0.01) was only achieved with [≥]30 females and [≥]3 males released. To maintain >95% genetic diversity of the source population in an isolated population, 50 females and 5 males are recommended to comprise the founding population. Sensitivity analyses revealed first-year survival and reproductive rate were the simulation parameters with the greatest proportional influence on probability of extinction and genetic diversity. These simulations highlight important considerations for translocation success, and data gaps including true genetic load in wild giraffe populations.

ecology↗

bioRxiv2019

GPseudoClust: deconvolution of shared pseudo-trajectories at single-cell resolution

MotivationMany methods have been developed to cluster genes on the basis of their changes in mRNA expression over time, using bulk RNA-seq or microarray data. However, single-cell data may present a particular challenge for these algorithms, since the temporal ordering of cells is not directly observed. One way to address this is to first use pseudotime methods to order the cells, and then apply clustering techniques for time course data. However, pseudotime estimates are subject to high levels of uncertainty, and failing to account for this uncertainty is liable to lead to erroneous and/or over-confident gene clusters.\n\nResultsThe proposed method, GPseudoClust, is a novel approach that jointly infers pseudotem-poral ordering and gene clusters, and quantifies the uncertainty in both. GPseudoClust combines a recent method for pseudotime inference with nonparametric Bayesian clustering methods, efficient MCMC sampling, and novel subsampling strategies which aid computation. We consider a broad array of simulated and experimental datasets to demonstrate the effectiveness of GPseudoClust in a range of settings.\n\nAvailabilityAn implementation is available on GitHub: https://github.com/magStra/nonparametricSummaryPSM and https://github.com/magStra/GPseudoClust.\n\nContactms58@sanger.ac.uk\n\nSupplementary informationSupplementary materials are available.

bioinformatics↗

bioRxiv2018

Structure of a cytochrome-based bacterial nanowire

Electrically conductive pili from Geobacter species, termed bacterial \"nanowires\", are intensely studied for their biological significance and potential in the development of new materials. We have characterized a unique nanowire from conductive G. sulfurreducens pili preparations by cryo-electron microscopy composed solely of the c-type cytochrome OmcS. We present here, at 3.4 [A] resolution, a novel structure of a cytochrome-based filament and discuss its possible role in long-range biological electron transport.\n\nSummary sentenceCryo-electron microscopy reveals the remarkable assembly of a c-type cytochrome into filaments comprising a heme-based bacterial nanowire.

biophysics↗