bioRxiv : the preprint server for biology最新文献

Recent evidence indicates that the intraparietal sulcus (IPS) may play a causal role in action stopping, potentially representing a novel neuromodulation target for inhibitory control dysfunctions. Here, we leverage intracranial recordings in human subjects to establish the timing and directionality of information flow between IPS and prefrontal and cingulate regions during action stopping. Prior to successful inhibition, information flows primarily from the inferior frontal gyrus (IFG), a critical inhibitory control node, to IPS. In contrast, during stopping errors the communication between IPS and IFG is lacking, and IPS is engaged by posterior cingulate cortex, an area outside of the classical inhibition network and typically associated with default mode. Anterior cingulate and orbitofrontal cortex also display performance-dependent connectivity with IPS. Our functional connectivity results provide direct electrophysiological evidence that IPS is recruited by frontal and anterior cingulate areas to support action plan monitoring/updating, and by posterior cingulate during control failures.

Phagosome degradation is an evolutionally conserved and highly effective innate immune response against pathogen infections. The success of this process relies on the ability of phagocytes to regulate the maturation of phagosomes. However, the underlying molecular mechanisms and its roles in shaping downstream immune activation remain poorly understood. Here, we identify the proton-activated chloride (PAC) channel as a key negative regulator of phagosome maturation. PAC deletion enhanced phagosomal acidification and protease activities, leading to augmented bacterial killing in large peritoneal macrophages (LPMs) upon peritoneal Escherichia coli infection in mice. Surprisingly, phagosome bacterial degradation also stimulated STING-IRF3-interferon responses and inflammasome activation in LPMs, both of which are enhanced upon PAC deletion. The increased inflammasome activation and pyroptosis induced an unexpected release of cleaved gasdermin D, which localized to the surface of bacteria in the peritoneum and further contributed to their killing. Finally, enhanced bacterial clearance by PAC-deficient LPMs reduced proinflammatory immune cell infiltration and overall peritoneal inflammation, resulting in improved survival in mice. Our study thus provides new insights into the molecular mechanism of phagosome maturation and the dynamics of host defense response following phagosome-mediated bacterial degradation in peritoneal macrophages. It also highlights the potential of targeting the PAC channel as a therapeutic strategy for treating bacterial infections.

Evidence from human self-report and rodent models indicate cocaine can induce a negative affective state marked by panic and anxiety, which may reduce future cocaine use or promote co-use with opiates. Dynorphin-mediated signaling within the striatum is associated with negative affect following cocaine withdrawal and stress-induced cocaine seeking. Here, we used a trace conditioning procedure to first establish the optimum parameters to capture this transient cocaine negative affective state in wild type mice, then we investigated striatal opioid peptides as a substrate mediating cocaine conditioned place avoidance (CPA). Previous reports indicate that trace conditioning, where drug administration occurs after removal from the conditioning chamber, results in CPA to ethanol, nicotine, and amphetamine. We tested different cocaine doses, conditioning session lengths, and apparatus types, to determine which combination yields the best cocaine CPA. Cocaine CPA was moderately larger at the highest cocaine dose (25 mg/kg), but this did not generalize across apparatus types and the effect was transient, thus data were collapsed across all parameters. Cocaine conditioning scores were variable, but also became more polarized across conditioning, with approximately equal proportions developing preference and avoidance. We then correlated cocaine CPA with striatal gene expression levels of the opioid peptides enkephalin ( Penk ) and dynorphin ( Pdyn ) using qPCR. Cocaine CPA was correlated with low Pdyn levels and a low Pdyn : Penk ratio in the ventral, but not dorsal, striatum. Consistent with this, mice with higher striatal Pdyn relative to Penk were more resistant to developing cocaine CPA compared to littermate controls. This approach revealed a subset of subjects sensitive to the aversive state immediately following cocaine administration. Our findings suggest striatal dynorphin has opposing roles in mediating the aversion associated with acute cocaine intoxication versus cocaine withdrawal.

Myocardial Infarction (MI) is a major contributor to morbidity and mortality, wherein blood flow is blocked to a portion of the left ventricle and leads to myocardial necrosis and scar formation. Cardiac remodeling in response to MI is a major determinant of patient prognosis, so many therapies are under development to improve infarct healing. Part of this development involves in vitro therapy screening which can be accelerated by engineered heart tissues (EHTs). Unfortunately, EHTs often over-simplify the infarcted tissue microarchitecture by neglecting spatial variation found in infarcted ventricles. MI results in a spatially heterogeneous environment with an infarct zone composed mostly of extracellular matrix (ECM) and cardiac fibroblasts, contrasted with a remote (non-infarct) zone composed mostly of cardiomyocytes, and a border zone transitioning in between. The heterogeneous structure is accompanied by heterogeneous mechanics where the passive infarct zone is cyclically stretched under tension as the remote zone cyclically contracts with every heartbeat. We present an in vitro 3-dimensional tissue culture platform focused on mimicking the heterogeneous mechanical environment of post-infarct myocardium. Herein, EHTs were subjected to a cryowound injury to induce localized cell death in a central portion of beating tissues composed of neonatal rat cardiomyocytes and cardiac fibroblasts. After injury, the remote zone continued to contract (i.e., negative strains) while the wounded zone was cyclically stretched (i.e., positive tensile strains) with intermediate strains in the border zone. We also observed increased tissue stiffnesses in the wounded zone and border zone following injury, while the remote zone did not show the same stiffening. Collectively, this work establishes a novel in vitro platform for characterizing myocardial wound remodeling with both spatial and temporal resolution, contributing to a deeper understanding of MI and offering insights for potential therapeutic approaches.

Filoviruses pose a significant threat to human health with frequent outbreaks and high mortality. Although two vector-based vaccines are available for Ebola virus, a broadly protective filovirus vaccine remains elusive. In this study, we evaluate a general strategy for stabilizing glycoprotein (GP) structures of Ebola, Sudan, and Bundibugyo ebolaviruses and Ravn marburgvirus. A 3.2 Å-resolution crystal structure provides atomic details for the redesigned Ebola virus GP, and cryo-electron microscopy reveals how a pan-ebolavirus neutralizing antibody targets a conserved site on the Sudan virus GP (3.13 Å-resolution), in addition to a low-resolution model of antibody-bound Ravn virus GP. A self-assembling protein nanoparticle (SApNP), I3-01v9, is redesigned at the N-terminus to allow the optimal surface display of filovirus GP trimers. Following detailed in vitro characterization, the lymph node dynamics of Sudan virus GP and GP-presenting SApNPs are investigated in a mouse model. Compared with soluble GP trimer, SApNPs show ~112 times longer retention in lymph node follicles, up-to-28 times greater presentation on follicular dendritic cell dendrites, and up-to-3 times stronger germinal center reactions. Functional antibody responses induced by filovirus GP trimers and SApNPs bearing wildtype and modified glycans are assessed in mice. Our study provides a foundation for next-generation filovirus vaccine development.

Proteins phase-separate to form condensates that partition and concentrate biomolecules into membraneless compartments. These condensates can exhibit dichotomous behaviors in biology by supporting cellular physiology or instigating pathological protein aggregation ^1-3 . Tau and α- synuclein (αSyn) are neuronal proteins that form heterotypic (Tau:αSyn) condensates associated with both physiological and pathological processes. Tau and αSyn functionally regulate microtubules ^8-12 , but are also known to misfold and co-deposit in aggregates linked to various neurodegenerative diseases ^4,5,6,7 , which highlights the paradoxically ambivalent effect of Tau:αSyn condensation in health and disease. Here, we show that tubulin modulates Tau:αSyn condensates by promoting microtubule interactions, competitively inhibiting the formation of homotypic and heterotypic pathological oligomers. In the absence of tubulin, Tau-driven protein condensation accelerates the formation of toxic Tau:αSyn heterodimers and amyloid fibrils. However, tubulin partitioning into Tau:αSyn condensates modulates protein interactions, promotes microtubule polymerization, and prevents Tau and αSyn oligomerization and aggregation. We distinguished distinct Tau and αSyn structural states adopted in tubulin-absent (pathological) and tubulin-rich (physiological) condensates, correlating compact conformations with aggregation and extended conformations with function. Furthermore, using various neuronal cell models, we showed that loss of stable microtubules, which occurs in Alzheimer's disease and Parkinsons disease patients ^13,14 , results in pathological oligomer formation and loss of neurites, and that functional condensation using an inducible optogenetic Tau construct resulted in microtubule stablization. Our results identify that tubulin is a critical modulator in switching Tau:αSyn pathological condensates to physiological, mechanistically relating the loss of stable microtubules with disease progression. Tubulin restoration strategies and Tau-mediated microtubule stabilization can be potential therapies targeting both Tau-specific and Tau/αSyn mixed pathologies.

Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic environments involved in cellular functions. Proteins, nucleic acids, glycans and bio-compatible polymers are the machinery of cellular processes both in the cytosol and at the lipid membrane interface. Lipid species directly modulate membrane properties, and affect the interaction and function of other biomolecules. Natural molecular diffusion results in changes of local lipid distribution, affecting the membrane properties. Projecting biophysical and structural membrane and biopolymer properties to a two-dimensional plane can be beneficial to quantify molecular signatures in a reduced dimensional space to identify relevant interactions at the interface of interest, i.e. the membrane surface or biopolymer-surface interface. Here, we present a toolbox designed to project membrane and biopolymer properties to a two-dimensional plane to characterize patterns of interaction and spatial correlations between lipid-lipid and lipid-biopolymer interfaces. The toolbox contains two hubs implemented using MDAKits architecture, one for membranes and one for biopolymers, that can be used independently or together. Three case studies demonstrate the versatility of the toolbox with detailed tutorials in GitHub. The toolbox and tutorials will be periodically updated with other functionalities and resolutions to expand our understanding of the structure-function relationship of biomolecules in two-dimensions.

Finding correlations in spatial gene expression is fundamental in spatial transcriptomics, as co-expressed genes within a tissue are linked by regulation, function, pathway, or cell type. Yet, sparsity and noise in spatial transcriptomics data pose significant analytical challenges. Here, we introduce Smoothie, a method that denoises spatial transcriptomics data with Gaussian smoothing and constructs and integrates genome-wide co-expression networks. Utilizing implicit and explicit parallelization, Smoothie scales to datasets exceeding 100 million spatially resolved spots with fast run times and low memory usage. We demonstrate how co-expression networks measured by Smoothie enable precise gene module detection, functional annotation of uncharacterized genes, linkage of gene expression to genome architecture, and multi-sample comparisons to assess stable or dynamic gene expression patterns across tissues, conditions, and time points. Overall, Smoothie provides a scalable and versatile framework for extracting deep biological insights from high-resolution spatial transcriptomics data.

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA-protein crosslinking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, critical for regulating gene expression, may contribute to FA-induced pathogenesis as lysine and arginine residues serve as targets for FA-protein adduct formation. This study aimed to elucidate the effects of FA on histone methylation and acetylation patterns. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (100 μM) and high-dose (500 μM) FA for 1 hour, and their histone extracts were analyzed using high-resolution liquid chromatography-tandem mass spectrometry-based proteomics, followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79 and changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40, as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimer's disease. This study provides novel evidence of FA epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.

The interaction of mammals with a novel environment (NE) results in structural and functional changes in multiple brain areas, including the hippocampus. This experience-dependent circuit reorganization is driven in part by changes in gene expression however, the dynamic sensory experience-driven chromatin states and the diverse cell type specific gene expression programs that are regulated by novel experiences are not well described. We employed single- nucleus multiomics (snRNA- and ATAC-seq) and bulk RNA-seq of the hippocampal DG, CA3, and CA1 regions to characterize the temporal evolution of cell-type-specific chromatin accessibility and gene expression changes that occur in 14 different cell types of the hippocampus upon exposure of mice to a novel environment. We observe strong hippocampal regional specificity in excitatory neuron chromatin accessibility and gene expression as well as great diversity in the inhibitory neuron and non-neuronal transcriptional responses. The novel environment-regulated genes in each cell type were enriched for genes that encode secreted factors, and cell-type-specific expression of their cognate receptors identified promising candidates for the modulation of learning and memory processes. Our characterization of the effect of novel experience on chromatin revealed thousands of cell-type-specific changes in chromatin accessibility. Coordinated analysis of chromatin accessibility and gene expression changes within individual cell types identified Fos/AP-1 as a key driver of novel experience-induced changes in chromatin accessibility and cell-type-specific gene expression. Together, these data provide a rich resource of hippocampal chromatin accessibility and gene expression profiles across diverse cell types in response to novel experience, a physiological stimulus that affects learning and memory.