Biology subjects

Kumar, N.

Publications and source records attributed to Kumar, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Computational Design and Atomistic Validation of a High-Affinity VHH Nanobody Targeting the PI/RuvC Interface of Streptococcus pyogenes Cas9: A Bivalent Hub Strategy for CRISPR-Cas9 Enhancement

The CRISPR-Cas9 system has revolutionized genome engineering, yet its full therapeutic potential remains constrained by challenges in precisely modulating its activity and specificity. Here we report a fully computational end-to-end pipeline for the de novo design of a single-domain VHH nanobody (NbSpCas9-v1) targeting a structurally conserved, non-catalytic epitope at the PAM-interacting (PI) and RuvC-III interface of Streptococcus pyogenes Cas9 (SpCas9; PDB: 4UN3). Nanobody sequences were generated using BoltzGen, a generative diffusion binder design framework, and co-folded with SpCas9 using Boltz-2 to evaluate structural confidence and binding affinity. The top-ranked model (SpCas9_4UN3_Bivalent_Hub_v1) achieved a complex pLDDT of 0.8406, an aggregate score of 0.8016, and an ipTM of >0.8, indicating high confidence in the nanobody-antigen interface. The designed 1,616-residue quaternary complex (SpCas9 + sgRNA + DNA + nanobody) was subjected to 10 ns of all-atom molecular dynamics (MD) simulation using the AMBER14SB force field within the GROMACS/OpenMM framework. The complex stabilized at RMSD [~]6 [A] with a radius of gyration of 39-44 [A], confirming thermodynamic stability under physiological conditions (310 K, 0.15 M NaCl). A conserved 96.3 [A] inter-molecular distance between the nanobody centroid and the HNH catalytic residue H840 establishes NbSpCas9-v1 as a distal, non-inhibitory binder -- ideally suited for a Bivalent Hub architecture recruiting secondary effectors to the Cas9 ribonucleoprotein (RNP). The nanobody-Cas9 interface is stabilized by 8 hydrogen bonds, 4 salt bridges, and [~]1,850 [A]2 of buried solvent-accessible surface area. These results provide a rigorous structural and dynamic foundation for experimental validation of VHH-based CRISPR-Cas9 enhancers and modulators. GRAPHICAL ABSTRACTThe computational workflow proceeds from SpCas9 crystal structure acquisition (PDB: 4UN3) through BoltzGen nanobody design, Boltz-2 structural co-folding, 10 ns explicit-solvent MD validation, and Bivalent Hub functional characterization. The PyMOL rendering below shows the full quaternary complex at atomistic resolution.

bioinformatics↗

bioRxiv2026

Watkins wheat landraces: a treasure of stripe rust resistance alleles identified using multi-model association analyses

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains a major global constraint to wheat production. Rapid pathogen evolution, exemplified by the recent breakdown of Yr15 in Europe, underscores the need to identify diverse and durable resistance loci. The A.E. Watkins landrace collection represents a globally diverse pre-breeding resource with substantial untapped variation for stripe rust resistance. In this study, 297 Watkins landraces were evaluated against six diverse Pst isolates (representing six races and three North American lineages) and subjected to genome-wide association analysis using high-density whole-genome resequencing data. Continuous phenotypic variation was observed across isolates, with several accessions displaying stable resistance across all lineages. A total of 87 QTLs were identified across all 21 wheat chromosomes. Ten loci co-localized with designated or cloned Yr genes, including Yr84, Yr85, Yrq1, Yr71, Yr60, Yr62, Yr50, Yr68, Yr34, and Lr34/Yr18/Sr57. An additional 34 loci overlapped previously reported stripe rust QTL, whereas the majority did not coincide with known loci, suggesting potential novel resistance regions. Eighteen QTLs were supported by multiple isolates, and fourteen showed supports across statistical models, indicating robust genomic signals. Several Watkins accessions carried favorable alleles that co-localized with multiple Yr-aligned loci, identifying promising donor candidates for validation and pre-breeding. Key MessageGenome-wide association mapping of 297 Watkins wheat landraces across diverse stripe rust races & genetic lineages identified 87 QTL, including 10 formally designated Yr genes and 46 novel loci, highlighting Watkins landraces as valuable pre-breeding donors for novel all-stage stripe rust resistance.

plant biology↗

bioRxiv2026

Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity

Drought reshapes plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the [~]160 My monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven down regulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant cry for help and consequently contribute to alleviation of this abiotic stress.

plant biology↗

bioRxiv2026

HIV-1 gp120-induced lysosomal stress responses are controlled by TRPML1 redox sensors

Increased lysosomal stress responses (LSR) are commonly implicated in the pathogenesis of neurodegenerative disorders including HIV-1-associated neurocognitive disorders (HAND). The HIV-1 envelope glycoprotein gp120 causes LSR, increases levels of ferrous iron (Fe2+) in the cytosol and in mitochondria, disrupts the reactive species interactome (RSI), and increases neural cell death. Here, we report that TRPML1, an endolysosome redox-sensitive cation channel, is mechanistically involved in gp120-induced neurotoxicity. TRPML1 was activated by gp120-induced increases in cytosolic reactive oxygen species (ROS) and resulted in release of Fe2+ from endolysosomes in levels sufficient to increase cytosolic levels of Fe2+ and ROS as well as decrease levels of hydrogen sulfide (H2S). Reduced glutathione normally buffers intracellular Fe2+, but gp120 decreased endolysosome glutathione levels and disrupted this regulatory control mechanism thereby promoting TRPML1-mediated Fe2+ efflux from endolysosomes. TRPML1 redox activation led to changes to the RSI in endolysosomes including increased ROS, lipid peroxidation, nitric oxide, and sulfane sulfur as well as decreased H2S. These changes were accompanied by increased cysteine oxidation of luminal proteins and endolysosome deacidification. Pharmacological inhibition of TRPML1 or knocking down expression levels of TRPML prevented these effects. Thus, our findings suggest that TRPML1 redox activation controls gp120-induced endolysosome dysfunction and iron/redox imbalance, and further implicates TRPML1 in the pathogenesis of HAND.

cell biology↗

bioRxiv2026

Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants

Recognition of dsRNA triggers antiviral defense mediated by PKR and OAS3/RNase L pathways through translational arrest and RNA decay. This is accompanied by assembly of distinct cytoplasmic ribonucleoprotein (RNP) condensates termed stress granules (SGs) and RNase L-dependent bodies (RLBs). Here we show that adenovirus infection differentially modulates dsRNA sensors and RNP granule assembly. Infection with splicing-defective {Delta}E4 mutant leads to dsRNA accumulation and activation of both PKR and OAS3/RNase L, promoting formation of RLB-like granules. In contrast, mutants lacking virus-associated (VA) RNAs trigger PKR activation and assembly of SGs despite absence of detectable dsRNA. Proteomic analysis revealed distinct protein compositions of canonical SGs and RLBs, which were reflected in virus-induced granules. While {Delta}VA-induced granules were PKR-dependent, {Delta}E4 mutants induced RLB-like granules independently of PKR and RNase L. In these cells, granule assembly coincided with translational arrest independent of eIF2 phosphorylation, indicating additional pathways linking nuclear dsRNA sensing to translational control and RNP granule assembly during viral infection. These findings provide novel insights into how distinct dsRNA sensors modulate translation and RNP condensates in response to stress.

cell biology↗

bioRxiv2026

Fungal hydrophobins unleashed from food waste: production, rodlet assembly, and functional properties in Ganoderma adspersum

Ganoderma adspersum is a white-rot fungus (WRF) that produces amphipathic, surface-active proteins, known as hydrophobins. To explore sustainable routes for protein production and waste valorization, G. adspersum was cultivated under defined shaking conditions using different carbon and nitrogen sources, including apple skin food waste. From these cultures, we report for the first time the isolation and characterization of a novel class I hydrophobin, designated as Gad1. Atomic force microscopy revealed abundant rodlet-like nanostructures consistent with class I hydrophobin assemblies, and Raman spectroscopy confirmed {beta}-sheet enrichment typical of amyloid-like organization. MALDI-TOF mass spectrometry further identified Gad1 along with additional hydrophobin-like proteins in the foam. Hydrophobin-enriched foam extracts were used to form stable oil-in-water emulsions that could be converted into porous, freezedried composite aerogels. These findings expand the known diversity of hydrophobins in whiterot fungi and demonstrate that food-waste-derived substrates can support hydrophobin production and functional biomaterial formation.

biophysics↗

bioRxiv2025

De novo design of protein nanoparticles with integrated functional motifs

Computational design of self-assembling proteins has long relied on pre-existing structures and sequences, fundamentally limiting control over their structural and functional properties. Recent machine learning-based methods have transformed our ability to design functional small de novo proteins and oligomers, yet methods to design large de novo protein assemblies with structures tailored to specific applications are still underexplored. Here, we develop a generalizable method for designing de novo symmetric protein complexes that incorporate target functional motifs into their structures. We report 34 new protein nanoparticles that form on-target assemblies with cubic point group symmetries. The nanoparticles exhibit a wide variety of backbones that were designed with atom-level accuracy, as evidenced by several cryo-EM and crystal structures that reveal minimal deviations from the design models. We use the method to generate a de novo antigen-tailored nanoparticle vaccine that elicits robust immune responses in mice. These results establish a generalizable approach that can be used to design functional self-assembling protein complexes with structures tailored to specific applications.

biochemistry↗

bioRxiv2025

Counterconditioning Alcohol Cues: Neural and Behavioral Modulation of Automatic Tendencies and Pavlovian-to-Instrumental Transfer in Male Alcohol Users

ObjectiveRepeated alcohol-cue pairings with rewarding experiences establish automatic response tendencies that bias instrumental behavior through Pavlovian-to-instrumental transfer (PIT). How individual differences in approach and avoidance tendencies shape PIT and intervention responsiveness remains poorly understood. This study examined whether automatic tendencies differentially modulate PIT, and whether counterconditioning (CC) combined with retrieval cues can attenuate approach biases and cue-driven instrumental interference. MethodThirty-nine male alcohol users completed an Alcohol Approach-Avoidance Task and PIT task before and after CC, classified into approach or avoidance groups based on their baseline Alcohol Approach Index. Alcohol cues were paired with monetary loss during CC, with retrieval cues introduced to facilitate reactivation of newly formed aversive associations. Right frontal N2 and centroparietal P3 were examined as indices of early evaluative and attentional processing. ResultsDespite comparable behavioral PIT performance, approach-oriented individuals showed attenuated right frontal N2 during push actions at baseline, reflecting reduced frontal regulatory engagement during cue-incongruent responding. CC selectively reduced approach biases in the approach group, with retrieval cues producing additional reductions, accompanied by N2 and P3 restoration. CC recalibrated PIT interference by reducing push and increasing pull interference, particularly with retrieval cues. CC-induced changes in approach bias did not predict PIT interference, suggesting modulation through partially dissociable pathways. ConclusionsCC with retrieval cues selectively reduced approach biases and recalibrated cue-driven instrumental interference in approach-oriented individuals, providing proof-of-concept for retrieval cue-integrated CC as a targeted associative intervention and highlighting the importance of individual tendency profiles in intervention responsiveness.

neuroscience↗

bioRxiv2025

Oxidative stress-induced proteolytic activation of polyphenol oxidase triggers an oxidized flavonoids-mediated stress signaling in Camellia sinensis

Environmental perturbations often increase reactive oxygen species (ROS) production, inducing oxidative damage to various biomolecules. The cellular system utilizes ROS or ROS-generated metabolites to instigate signaling pathways, resulting in acclimation, growth inhibition, or programmed cell death (PCD) for sustaining stress. Various stress-generated or stress-activated signaling components and downstream pathways are identified in model plants; however, they are largely unexplored in non-model plants. Here, we report a stress-induced proteolytic activation of an evolutionarily conserved chloroplast-localized enzyme, polyphenol oxidase (PPO), that oxidizes catechins into theaflavins (TFs) and initiates a stress signaling under drought in Camellia sinensis (Tea). Germplasm-based analysis revealed a heightened proteolytic activation of PPO and consequent TFs accumulation in drought-susceptible genotypes. Transcriptome analysis revealed that PPO activation and TFs accumulation were linked to the activation of UPR(unfolded protein response)-like response, which was reinforced by virus-induced silencing and overexpression of PPO, and direct feeding of TFs in tea plants. Pharmacological treatments revealed that TFs interact with HSP90, activating a canonical IRE-bZIP60-dependent ER stress pathway resulting in PCD. Similar proteolytic activation of PPO and subsequent instigation of stress signaling in other plant species (tomato and wheat) demonstrated that PPO acts as an evolutionarily conserved stress sensor, instigating an inter-organelle communication in plants. Significance statementPPO, an evolutionarily conserved and chloroplast/plastid localized enzyme, senses stress and undergoes proteolytic activation to generate oxidized flavonoids/quinones that function as signaling molecules in Tea and likely in other plants. The oxidized flavonoids modulate protein folding machinery and augment folding stress, especially in the ER, inducing canonical IRE1-bZI60-dependent PCD. The finding shows that specific secondary metabolites likely have roles in instigating intra- and intercellular communication to sustain the adversities of stress in different plant species.

plant biology↗

bioRxiv2025

Anti-malarial contact dependent blocking of transmission of Plasmodium vivax by Anopheles darlingi mosquito vector

Malaria, caused by protozoa of the genus Plasmodium and transmitted to humans through the bite of mosquitoes of the genus Anopheles, remains a public health problem. Long-Lasting Insecticide -treated bed Nets (LLINS) and Indoor Residual Spraying (IRS) represent the main vector control measures for malaria prevention. However, to address the concerns of mosquito resistance to pyrethroids, other malaria control strategies are being explored for effectively blocking malaria transmission by eliminating or reducing the parasite in the vector. This study evaluated the use of antimalarials through tarsal contact of female Anopheles darlingi infected with Plasmodium vivax via a Direct Membrane Feeding Assay (DMFA). Female An. darlingi were exposed tarsally using Petri dishes impregnated with antimalarials at 1 mmol/m2 for exposure times of 6 or 60 minutes. Among the antimalarials evaluated were Atovaquone (ATQ), Tafenoquine (TQ), Chloroquine (CQ), Mefloquine (MQ), Primaquine (PQ), and the compound Nanchangmycin (NCG). Atovaquone was the only antimalarial evaluated before and after DMFA at exposure times of 60 min and 6 min. The results demonstrate complete elimination of P. vivax in female An. darlingi exposed to ATQ by tarsal contact 60 min before infection. ATQ was also effective 6 min before or after infection, reducing infection prevalence. In addition, MQ also significantly reduced infection intensity, but there was no difference in infection prevalence. No significant differences were observed for the other antimalarials. Author SummaryMalaria caused by Plasmodium vivax is the most prevalent in the Amazon region, with Anopheles darlingi as its main vector. Mosquito resistance to pyrethroid insecticides, already described in African countries, also raises an alarm for areas endemic for vivax malaria. Given this scenario, strategies that involve blocking parasite transmission have proven effective. Our study involved the transmission-blocking potential of antimalarials administered via tarsal contact to An. darlingi infected with P. vivax. Tarsal exposure involves the direct contact of the mosquitoes tarsi with surfaces impregnated with antimalarials. We speculate that in a real-world setting, this approach could be translated by treating surfaces like bed nets, eaves, or resting sites with the compounds, exploiting the natural resting and host-seeking behaviors of mosquitoes that bring their tarsi into contact with these treated substrates. If the drugs/compounds penetrate the cuticle, they could impact the parasites biological cycle within the vector. Our results confirmed this potential, Atovaquone was able to eliminate or reduce P. vivax from the midguts of An. darlingi at different exposure times, demonstrating successful uptake through the tarsi. Mefloquine was also reduced parasite intensity via tarsal contact. These findings reinforce the potential of this approach as a complementary tool in malaria control.

zoology↗

bioRxiv2025

Contextual Cues and Transition Statistics Drive Expression of Competing Motor Memories

Learning multiple motor skills without interference and expressing the correct one in a changing environment is a fundamental challenge. Contextual cues are known to help separate these memories, but how they interact during retrieval is not well understood. We investigated how the stability, recency, and transitional statistics of learning environments influence this process. Across six visuomotor adaptation experiments, participants learned opposing rotations (Tasks A and B) tagged with distinct contextual cues under different schedules (blocked or interleaved) and were tested in stable or dynamic environments. We found that while contextual cues can successfully separate memories, expression is systematically biased by learned transition statistics: towards more stable memories after imbalanced training, and towards more recent memories when stabilities are matched. Critically, when the stable statistics of training mismatched the volatile statistics of testing, cue-based retrieval collapsed, and behavior was dominated by these stability or recency biases. Conversely, learning in a high-entropy, interleaved environment enabled precise, cue-appropriate expression regardless of the testing schedule. These results demonstrate that memory retrieval is not cue-driven but arises from an arbitration process between cues and transition priors. Our findings reveal that memory retrieval involves weighting sensory information against latent priors derived from the history of context transitions. This work provides a unifying theoretical framework for understanding adaptive memory expression, positing that the brain leverages the learned statistical structure of the environment to infer which memory to recall, thereby balancing cue-driven selection with the stability and predictability of past experience. This principle offers a unifying explanation for interference, spontaneous recovery, and the benefits of variable practice, providing a more holistic model of adaptive motor behavior. Statement of SignificanceHow does a tennis player instantly switch between a forehand and a backhand? Our work reveals a fundamental principle of how the brain organizes and retrieves memories. We demonstrate that recalling a skill is not just about recognizing a contextual cue, but about an internal process of integrating that cue with the learned statistics of the environment, such as the stability and recency of past experiences. This finding provides a unifying framework for phenomena like interference and spontaneous recovery. It has significant implications for designing more effective training in sports and rehabilitation, where structuring practice around environmental statistics can optimize learning and promote flexible skill application.

neuroscience↗

bioRxiv2025

Cardioprotective effects of AMPK activation in H1N1 influenza virus infection

Cardiac complications are among the most common and severe extrapulmonary manifestations of influenza virus infection, yet they are rarely recapitulated in mouse models without immunodeficiency. We found that influenza virus A/California/04/2009 (H1N1) carrying a mouse-adaptive amino acid substitution in the PB2 protein (E158A) disseminates to the heart in WT C57BL/6 mice, where it induces inflammation, electrical dysfunction, and fibrotic remodeling. Influenza virus-infected heart tissue was significantly altered in mitochondrial metabolism, extracellular matrix, circadian rhythm, and immunity pathways. Particularly striking was activation of gene expression downstream of the mitochondrial biogenesis-promoting AMPK/PGC-1 axis, which occurred late in infection but failed to reverse the repression of mitochondria-associated genes, suggesting an insufficient or delayed compensatory response. Accordingly, we administered AMPK activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) early in infection and observed restoration of mitochondria-associated gene levels, amelioration of cardiac electrical dysfunction and fibrosis, and improvement in survival without overt effects on lung function. Overall, the advent of an immunocompetent model for severe influenza-associated cardiac dysfunction revealed activation of AMPK signaling as a host-targeted metabolic intervention for mitigating virus-induced heart pathologies

microbiology↗

bioRxiv2025

Multi Omics Driven Polypharmacology for Osteoarthritis Joint Regeneration

Osteoarthritis (OA) is a common degenerative condition of major joints with no effective cure. Yograj Guggulu (YG) is a well-established polyherbal formulation in Indian traditional medicine for the management of joint disorders. However, its mode of action remains unclear. We integrated multi omics network analysis with a rat model to investigate the effects of oral administration of YG on osteoarthritic joints. YG administration significantly alleviated pain and improved joint function. Imaging and histological analyses reveal that YG protects against structural degeneration in the joint with OA. Proteomic and metabolomic profiling, along with network analysis, uncovered that multiple components of YG alter protein expression in key pathways related to inflammation and cartilage degradation, thus validating the observed clinical effects. The efficacy of YG seems to be the result of the synergistic action of its diverse constituents. Our findings support the use of YG as a multitarget therapy for OA and encourage efforts for the potential repurposing of its active components.

systems biology↗

bioRxiv2025

Mechanistic insights and in vivo HIV suppression by the BRD4-targeting small molecule ZL0580

Epigenetic suppression and durable silencing of HIV represent a promising strategy to achieve ART-free remission, consistent with the "block and lock" HIV cure paradigm. BRD4 is a host epigenetic reader and plays a critical role in HIV transcriptional regulation. We previously identified ZL0580, a first-in-class BRD4-selective small molecule distinct from the pan-BET inhibitor JQ1, which induces HIV epigenetic suppression. However, detailed molecular mechanisms, pharmacokinetics (PK), and in vivo HIV-suppressive efficacy of ZL0580 remain undefined. Here, we show that ZL0580 selectively targets BRD4 bromodomain 1 (BD1) through interaction with a key glutamic acid residue (E151), as determined by structural modeling and mutagenesis. Transcriptomic profiling by RNA-seq reveals that ZL0580 and JQ1 induce opposing gene expression programs, consistent with their distinct effects on HIV proviral transcription and latency. In a humanized mouse model of HIV infection, ZL0580 monotherapy, or in combination with ART, potently suppressed active HIV replication, reducing the plasma viremia to nearly undetectable levels, and delayed viral rebound following treatment interruption. Collectively, these findings establish ZL0580 as an epigenetic suppressor of HIV in vivo and provide proof-of-concept for its potential as a "block and lock" HIV cure candidate, warranting further optimization and development.

microbiology↗

bioRxiv2025

Surveillance on California dairy farms reveals multiple sources of H5N1 transmission

Transmission routes of highly pathogenic H5N1 between cows or to humans remain unclear due to limited data from affected dairy farms. We performed air, farm wastewater, and milk sampling on 14 H5N1 positive dairy farms across two different California regions. Infectious virus was detected in the air in milking parlors and in wastewater streams, while viral RNA was found in exhaled breath of cows. Sequence analysis of infectious H5N1 virus from air and wastewater samples on one farm revealed viral variants relevant for potential human susceptibility. Longitudinal analysis of milk from the individual quarters of cows revealed a high prevalence of subclinical H5N1 positive cows. Additionally, a heterogeneous distribution of infected quarters that maintained a consistent pattern over time was observed, inconsistent with shared milking equipment serving as the sole transmission mode. The presence of subclinically infected cows was further supported by detection of antibodies in the milk of animals that exhibited no clinical signs during the H5N1 outbreak on one farm. Our data highlight additional sources and potential modes of H5N1 transmission on dairy farms.

microbiology↗

bioRxiv2025

Longitudinal Characterization of Compound Action Potentials in Chronic Vagus Nerve Recordings in Mice

The vagus nerve (VN) mediates bidirectional communication between the body and brain to maintain physiological homeostasis; likewise, alterations in ongoing vagal signaling may be indicators of disease and/or contribute to disease pathogenesis. Even though extensively documented in acute experiments, ongoing vagal activity has not been characterized longitudinally, over days or weeks, in mice, a preferred preclinical model. In addition, even though many VN recordings in mice occur during anesthesia, the effects of anesthesia on vagal signaling are unknown. This study uses a chronic implant mouse model to record vagal activity in anesthetized and awake, behaving animals for an average of 10 weeks and up to 6 months. Individual compound action potentials (CAPs) are tracked across multiple days by quantifying comparisons in features, including firing rates, waveform shape, inter-CAP interval histograms, and phase-locking to cardiac and respiratory signals while demonstrating long-term electrode-nerve interface viability and stable signal-to-noise ratios. Additionally, cytokine challenge experiments produced detectable CAP responses up to 3 months after electrode implantation. Lastly, awake recordings incorporated video analysis to identify and remove motion artifacts to preserve and extract neural and cardiac recordings during behavior. Results reveal diverse CAP populations with diverse physiological coupling and firing rates modulated by anesthesia. This work highlights the potential of chronic VN recordings to assess long-term changes in vagal activity in health and disease, with implications in discovery of autonomic markers of disease and closed-loop VNS stimulation strategies.

neuroscience↗

bioRxiv2025

Structural Validation of the Intermediate Leptomeningeal Layer in the Human Central Nervous System

Traditionally, the human central nervous system (CNS) is described as having three meningeal layers, from outer to inner: dura mater, arachnoid mater, and pia mater. The arachnoid and pia mater are called the leptomeninges, and the space between them is filled with cerebrospinal fluid (CSF). Using gross dissection, light microscopy, and ultrastructural analysis of fresh postmortem and cadaveric CNS specimens spanning fetal to adult ages (N=61), we demonstrate a fibrocellular intermediate leptomeningeal layer (ILL) from the cortex to the caudal end of the spinal cord. The ILL divides the subarachnoid space (SAS) into two distinct structural compartments, through which vessels and nerves pass. The ILL shows unique structural features, such as dips into the brains sulci and fissures, as a double-fold membrane that bears intra-layer trabeculae, carries vessels, and forms the perivascular sheath. Moreover, throughout the CNS, it appears to be a non-sieved barrier, characterized by the presence of tight and adherens junctions. ILL, predominantly in the spinal cord, contains macrophage-like cells, indicating its layer-specific immune properties. The ILL warrants recognition as a distinct human meningeal layer with potential barrier and immune functions. SignificanceO_ST_ABSAn Intermediate Leptomeningeal Layer encloses the Central Nervous System in HumansC_ST_ABSThe integrated analysis of our macroscopic, microscopic, and ultrastructural study provides robust support for an intermediate leptomeningeal layer (ILL) in the subarachnoid space (SAS) of the human central nervous system (CNS) along the entire neural axis. The ILL is a fibrocellular macroscopic structure, with restricted permeability, that divides the cerebrospinal fluid (CSF)-filled SAS into two distinct structural compartments. Uniquely, ILL revealed the presence of cells with macrophage-like properties, suggesting a possible role in immune surveillance. The ILL may redefine the established concept of protective coverings of CNS, CSF circulation dynamics, and the role of leptomeninges in health and disease, including drug delivery.

neuroscience↗

bioRxiv2025

12-Hydroxystearic acid induces epidermal keratinocytes to secrete antimicrobial peptides that are potent inhibitors of viral infection.

Epidermal keratinocytes produce antimicrobial peptides (AMPs) that serve as a crucial component of the skins innate immune barrier. These peptides effectively target a broad spectrum of pathogenic microorganisms while preserving commensal microbiota essential for skin barrier homeostasis and overall skin health. Regulating the release of these AMPs presents a promising approach to enhancing the skin barriers defense mechanisms with minimal side effects. We have identified 12-hydroxystearic acid (12-HSA) as a potent stimulator of AMP secretion from primary epidermal keratinocytes. Mechanistic investigations revealed that, akin to bacterial stimulation, 12-HSA induces AMP release through the downregulation of caspase-8, which subsequently activates the inflammasome. Notably, we discovered that 12-HSA mediates caspase-8 downregulation via the acute activation of DNA methyltransferase 3A (DNMT3A), leading to transcriptional silencing of the caspase-8 locus. Importantly, 12-HSA is widely utilized in the cosmetic industry for its several skin beneficial properties including hydration and emolliency. Our findings suggest that this compound can be leveraged to enhance innate immune defenses in the skin, effectively mobilizing stored AMPs from keratinocytes to counteract microbial threats. This discovery highlights the potential for 12-HSA as a novel agent in dermatological applications aimed at fortifying skin barrier immunity.

cell biology↗