Biology subjects

Leach, S.

Publications and source records attributed to Leach, S..

At least 19 recordsLinked to original sources

bioRxiv2026

REM Sleep Iota Oscillations Across the Lifespan

Iota oscillations are a newly discovered marker of wakefulness and rapid eye movement (REM) sleep. So far, iota in REM sleep has only been reported in the surface electroencephalography (EEG) of a small sample of young adults and in intracranial recordings of epileptic patients. Here, we investigated the presence of these oscillations in a large dataset (N=937) of high-density sleep EEG recordings from individuals 7 to 70 years old. We found that iota spectral peaks during REM sleep were between 25 and 40 Hz, slightly faster than in wake (25-35 Hz). Iota power was significantly associated with REM sleep architecture, increasing with both REM duration and across progressive sleep cycles. Iota peaks were observed in individuals of all ages, although the prevalence decreased gradually with age, from 88% in children to 44% in older adults. Most iota spectral peak properties (frequency, amplitude, timing, topography) likewise shifted with age. The most striking effect, however, was in bandwidth, such that children had narrow iota peaks, older adults had broad iota peaks, and 20-30 year olds could have either. It remains unclear whether narrowband and broadband iota are functionally equivalent. On shorter time scales (< 1 year), iota properties remained stable across measurements. Analyses of a separate dataset of monozygotic and dizygotic twins revealed high heritability of all iota peak properties except bandwidth. Overall, these results establish iota as a genetically determined trait-like marker of REM sleep with unique age-related changes. Iota oscillations open new avenues to investigate the interaction between sleep, genetics, development, and aging.

neuroscience↗

bioRxiv2026

Mucosal-associated invariant T cells support IL-15-dependent Treg response in skin injury and promote resolution of skin inflammation

Mucosal-associated invariant T (MAIT) cells are enriched at barrier sites, but their role in autoimmune skin inflammation remains unknown. Using cutaneous lupus as a model, we identify MAIT cells as protective regulators of skin inflammation and as critical upstream modulators of regulatory T cells (Treg). Topical MAIT cell activation with 5-OP-RU induced durable resolution of spontaneous skin lesions in MRL/lpr mice and suppressed TLR7-driven skin inflammation. MAIT cell activation selectively expanded and activated Treg populations in both healthy and lupus-like skin, while suppressing effector T cell cytokine production and cytotoxic programs. This MAIT-Treg axis was also activated in UV light-driven barrier injury in healthy murine and human skin, where MAIT cells were required for UV-elicited Treg expansion and function. In lupus-like skin, local MAIT cell activation restored the defective UVB-induced Treg response and limited CD8+ T cell expansion. Mechanistically, CCR2+ monocyte-derived antigen-presenting cells and IL-15 signaling were required for MAIT cell-driven Treg accumulation and therapeutic benefits of MAIT cells in inflamed skin. These studies identify a MAIT-IL-15-Treg axis that links barrier injury sensing to immune regulation, which is disrupted in cutaneous lupus, and nominate therapeutic MAIT cell activation as an unappreciated strategy for restoring immune homeostasis in inflamed skin.

immunology↗

bioRxiv2026

Structure informed xrRNA2 mutations in Zika virus provide a roadmap for vaccine development

Flaviviruses like Zika virus (ZIKV), contain RNA tertiary structures within the 3 untranslated region (UTR) that halt the 5-to-3 RNA exonuclease, Xrn1. Halting of Xrn1 at the two RNA structures, termed exonuclease-resistantRNA1 and 2 (xrRNA1 and xrRNA2), results in the formation of subgenomic flavivirus RNAs (sfRNA) that support viral pathogenesis. While the role of the flavivirus xrRNA1 in pathogenesis is well characterized, the role of the flavivirus xrRNA2 structure is not well studied. Using xrRNA crystal structure data, we inserted structure-informed mutations in ZIKV xrRNA2 to disrupt tertiary folding independent of significant sequence changes, evaluate sfRNA production, and define pathogenesis in a murine model of ZIKV infection. Compared to our prior work with ZIKV xrRNA1, we found that ZIKV xrRNA2 is under increased selection pressure to maintain sfRNA production resulting in multiple targeted mutations in xrRNA2 junctional region to induce a stable mutant. Using three targeted xrRNA junctional mutations termed ZIKV X2.L1, we found that the resulting ZIKV clone exhibits attenuated cell death in cultures and decreased viral growth in tissue cultures. In a murine model of ZIKV infection, mice inoculated with ZIKV X2.L1 exhibit significantly decreased symptomatic infection, improved survival, decreased end-organ infection in the brain, and continued robust neutralizing antibody responses to ZIKV. Despite attenuation, serum from ZIKV X2.L1-infected mice or mice vaccinated with ZIKV X2.L1, exhibited 100% protection from lethal ZIKV challenge. These studies show that RNA structure-informed mutations provide a robust model for flavivirus attenuation and vaccine design. Additional studies defining the mechanisms of robust neutralizing antibody responses and flavivirus-specific vaccine development are needed to continue the development of this novel vaccine platform approach for medically important flavivirus infections. Author summaryZika virus is a member of the Orthoflavivirus (referred to as flavivirus) genus that exhibit conserved RNA structures in the 3 untranslated region of the viral RNA genome. Two concerned RNA structures, termed exonuclease-resistant RNA 1 and 2, are important to support the ability of the virus to cause disease. While the first RNA structure is well studied, less is known about the role of exonuclease-resistant RNA 2 in the flavivirus infection. Using reverse genetics, we made mutations in the Zika virus exonuclease-resistant RNA 2 structure and studied how this mutant Zika virus was weakened or attenuated. We found that the mutant Zika virus clone exhibits reduced virus replication, reduced ability to kill cells, and decreased virulence in mouse models of Zika virus disease. Using this mutant virus as a potential vaccine candidate, we found that Zika virus with mutations in the exonuclease-resistant RNA 2 structure provide complete protection from lethal Zika virus challenge. These data suggest that targeting the second exonuclease resistant RNA structure in flaviviruses is a viable platform for the development of vaccine candidates for this important group of viruses.

microbiology↗

bioRxiv2026

Frontoparietal Hub Connectivity Integrates Information from Multiple Sources

Frontoparietal connector hubs are thought to support information integration across the brain, but this role has largely been inferred from static connectivity, leaving unclear how computational processes shape inter-regional connectivity during behavior. Here, we address this question using a model-based functional connectivity approach in human fMRI data. Thirty-Eight participants (males and females) performed a task requiring the integration of sensory evidence with an internally maintained state belief to guide behavior. We developed a computational model that combines these information sources into an integrated representation and generates distinct variables at successive stages of integration: uncertainty before choice (entropy), the inferred task representation guiding action (task belief), and feedback-driven updating (task inference error). We then tested how these variables modulate the connectivity of frontoparietal connector hubs. Entropy increased coupling between hubs and regions encoding task-relevant inputs and outputs during cue processing, suggesting enhanced communication under uncertainty. During task selection, task belief selectively modulated hub connectivity with motor regions according to the selected task. During feedback, task inference errors increased coupling with regions supporting task-relevant inputs and internal state, while reducing coupling with motor regions, consistent with updating internal representations. Together, our findings show that frontoparietal connector hubs implement integrative control by using an integrated representation to generate distinct computational signals that selectively and dynamically reconfigure inter-regional communication. SignificanceFlexible behavior depends on combining different kinds of information, but how the brain coordinates this integration remains unclear. The frontoparietal cortex is well positioned to support this process because it is broadly connected with many other systems. Here, we combined a computational model with functional MRI to test how integrating information changes patterns of functional connectivity. We find that a common set of signals is associated with dissociable changes in how frontoparietal regions couple with systems involved in perception, action, and internal updating. These findings reveal that integration generates multiple control signals that dynamically reconfigure brain-wide interactions to support goal-directed behavior.

neuroscience↗

bioRxiv2025

Fragile nucleosomes are essential for RNA Polymerase II to transcribe in eukaryotes

Nucleosomes are barriers to RNA Polymerase II (Pol II) transcribing along gene bodies in eukaryotes. We found that a fragile "tailless nucleosome" could be generated to resolve the Pol II pausing caused by the +1 nucleosome in metazoans. We hypothesized that "pan-acetylated nucleosomes" along gene bodies are fragile and are generated to resolve the resistance of nucleosomes to the elongation of Pol II. To confirm this hypothesis, we systematically analyzed pan-acetylation and pan-phosphorylation of the entire human genome in HEK293T cells. Herein, we show that both pan-acetylation and pan-phosphorylation of histones in nucleosomes along gene bodies are coupled with the activities of Pol II. Our results show that there are four major types of fragile nucleosomes required for Pol II to transcribe along gene bodies: nucleosomes without tails, nucleosomes with dominant acetylation, nucleosomes with dominant phosphorylation, and nucleosomes with both acetylation and phosphorylation.

genetics↗

bioRxiv2025

CDK11 activates CDK12 to trigger the elongation of RNA Polymerase II

CDK11 is an essential cyclin-dependent kinase in higher eukaryotes, yet its specific substrates and functional roles have remained elusive. Our findings reveal that CDK11 is functionally analogous to the yeast Bur1 kinase, phosphorylating the repeat region of hSpt5 and the linker domain of Rpb1 in RNA Polymerase II (Pol II). Inhibition of CDK11 results in a significant reduction of active Pol II not only at transcription start sites but also along gene bodies. Further investigation finds that CDK11 is crucial for the phosphorylation and activation of CDK12, which is essential for the elongation of Pol II. Moreover, we find that CDK10 can partially compensate for the function of CDK11. Combining with earlier functional elucidation of CDK9 from us, the consequent roles of CDK7/8, CDK9, CDK10/11, and CDK12/13 in transcription regulation in metazoans are established.

biochemistry↗

bioRxiv2025

The Infraslow Fluctuation of Sigma Power During Sleep in Young Individuals with Schizophrenia

A reduction in sleep spindles, a major electrophysiological characteristic of Non-Rapid Eye Movement sleep, has been suggested as a potential biomarker of schizophrenia. While research has primarily focused on the spindle quantity, recent studies have begun to explore their temporal dynamics throughout the night. In healthy individuals, sleep spindles fluctuate on an infraslow [~]50-second timescale, alternating between phases of high and low spindle activity. This fluctuation is referred to as the infraslow fluctuation of sigma power (ISFS), which is modulated by noradrenergic activity from the locus coeruleus and linked to the organization of arousal and memory reactivation processes during sleep. Given the known deficit in sleep spindles, dysregulation of noradrenergic activity, and impairments in sleep maintenance and memory in schizophrenia, this study investigates the ISFS in sleep electroencephalography data from individuals with either Childhood-Onset Schizophrenia (COS; N = 17) or Early-Onset Schizophrenia (EOS; N = 11), aged 9 to 21 years, alongside age- and sex-matched healthy controls (N = 56). The presence and strength of the ISFS were reduced in both COS and EOS groups compared to controls, particularly in central-parietal electrodes. No significant differences in these features of the ISFS were found between the two clinical groups, despite group differences in sleep spindle density and clinical characteristics. These findings suggest that the ISFS is observable but reduced in young patients with schizophrenia and support the notion that the timing of sleep spindles may inform pathomechanistic models of the disorder, as well as future diagnostic approaches and interventions.

neuroscience↗

bioRxiv2025

Local modulation of sleep slow waves depends on timing between auditory stimuli

Conflicting evidence exists regarding the role of the targeted slow-wave phase in determining the direction and spatial specificity of slow-wave activity (SWA) modulation via phase-targeted auditory stimulation (PTAS) during sleep. To reconcile these discrepancies, we re-analyzed high-density electroencephalography (hd-EEG) data from previous studies, focusing on SWA responses to auditory stimuli presented with varying inter-stimulus intervals (ISIs). Our analysis reveals that ISI is a primary determinant of PTAS-induced SWA modulation, exceeding the influence of targeted phase alone. Specifically, auditory stimulation with longer ISIs evoked a global increase in SWA, consistent with a stereotypical auditory-evoked K-complex (KC), independent of targeted phase. Conversely, longer stimulus trains with rapid successive stimulus presentation resulted in spatially localized, phase-dependent SWA modulation, with up-PTAS enhancing and down-PTAS reducing SWA locally around the targeted area. This distinction resolves inconsistencies in prior PTAS studies by demonstrating that phase alone in insufficient in predicting slow-wave responses. Rather, it was the ISI which determined whether PTAS resulted in a global, KC-mediated response or a local, phase-specific modulation of SWA. Consequently, our findings refine the mechanistic understanding of PTAS, suggesting that ISI regulates the engagement of distinct neural circuits and thereby potentially enables the targeted manipulation of specific slow-wave subtypes and their associated functions.

neuroscience↗

bioRxiv2024

Virus-free continuous directed evolution in human cells using somatic hypermutation

The B cells of the human immune system have evolved somatic hypermutation (SHM) mechanisms that introduce mutations at the immunoglobulin genomic loci at a significantly higher frequency than the rest of the genome thereby allowing them to evolve antibody sequences without compromising fitness due to genome-wide mutations. Inspired by these observations, here we developed a continuous directed evolution platform in human B cell lines (CODE-HB) that repurposes the SHM mechanisms to a stable, non-immunoglobulin genomic locus of the human B cell lines to continuously evolve cytosolic and surface displayed proteins with a broad mutational spectrum comprising of substitutions, deletions and insertions. We developed a human B cell surface display platform and used CODE-HB to evolve neutralizing antibodies targeting avian influenza and escape variants of influenza. Given the modularity and simplicity of CODE-HB, we anticipate that this platform can be used for rapidly evolving biotechnologically relevant biomolecules directly in human cells.

synthetic biology↗

bioRxiv2024

The Infraslow Fluctuation of Sigma Power During Sleep: Links to Markers of Arousal and Memory Reactivation Across Development

Sleep is both a state of disconnection from the environment and a critical period for restoration. But how does sleep balance responsiveness with the protection of key functions? The infraslow fluctuation of sigma power (ISFS)--the clustering of sleep spindles over 10-100 seconds--is thought to regulate this trade-off in rodents. However, the organization of arousal and memory reactivation markers within the human ISFS and its conservation in younger ages remain unclear. This study characterizes the ISFS from childhood to young adulthood (N = 154; ages 8-26), examining its relationship with functional markers. Results indicate that the ISFS is present across all ages, with frequency, variability, and strength increasing from early to late adolescence. Notably, markers of arousal and memory reactivation are organized within the spindle-rich ISFS peak. The consistent presence and organization of the ISFS suggest it is intrinsic to sleep, with adolescence marking a dynamic window. These insights may guide interventions to promote healthier sleep across development.

neuroscience↗

bioRxiv2024

Thalamocortical contributions to hierarchical cognitive control

Cognitive flexibility relies on hierarchically structured task representations that organize task contexts, relevant environmental features, and subordinate decisions. Despite ongoing interest in the human thalamus, its role in cognitive control has been understudied. This study explored thalamic representation and thalamocortical interactions that contribute to hierarchical cognitive control in humans. We found that several thalamic nuclei, including the anterior, mediodorsal, ventrolateral, and pulvinar nuclei, exhibited stronger evoked responses when subjects switch between task contexts. Decoding analysis revealed that thalamic activity encodes task contexts within the hierarchical task representations. To determine how thalamocortical interactions contribute to task representations, we developed a thalamocortical functional interaction model to predict task-related cortical representation. This data-driven model outperformed comparison models, particularly in predicting activity patterns in cortical regions that encode context representations. Collectively, our findings highlight the significant contribution of thalamic activity and thalamocortical interactions for contextually guided hierarchical cognitive control.

neuroscience↗

bioRxiv2023

Acoustically evoked K-complexes are sufficient to boost verbal memory consolidation during sleep

Over the past decade, phase-targeted auditory stimulation (PTAS), a neuromodulation approach which presents auditory stimuli locked to the ongoing phase of slow waves during sleep, has shown potential to enhance specific aspects of sleep functions. However, the complexity of PTAS responses complicates the establishment of causality between specific electroencephalographic events and observed benefits. Here, we used down-PTAS during sleep to specifically evoke the early, K-complex (KC)-like response following PTAS without leading to a sustained increase in slow-wave activity throughout the stimulation window. Over the course of two nights, one with down-PTAS, the other without, high-density electroencephalography (hd-EEG) was recorded from 14 young healthy adults. The early response exhibited striking similarities to evoked KCs and was associated with improved verbal memory consolidation via stimulus-evoked spindle events nested into the up-phase of ongoing 1 Hz waves in a central region. These findings suggest that the early, KC-like response is sufficient to boost memory, potentially by orchestrating aspects of the hippocampal-neocortical dialogue.

neuroscience↗

bioRxiv2023

Zika virus dumbbell-1 structure is critical for sfRNA presence and cytopathic effect during infection

Zika virus (ZIKV) contains multiple conserved RNA structures in the viral 3 untranslated region (UTR), including the structure known as dumbbell-1 (DB-1). Previous research has shown that the DB-1 structure is important for flavivirus genome replication and cytopathic effect (CPE). However, the role of the DB structure and the mechanism by which it contributes to viral pathogenesis is not known. Using recently solved flavivirus DB RNA structural data, we designed two DB-1 mutant ZIKV infectious clones termed ZIKV-TL.PK, which disrupts DB-1 tertiary folding and ZIKV-p.2.5, which alters DB-1 secondary structure formation. In cell culture, we found that viral genome replication of both mutant clones is not significantly affected compared to ZIKV-WT, but viral CPE is considerably decreased. We investigated sub-genomic flaviviral RNA (sfRNA) formation by both DB-1 mutants following A549 infection and found both mutant clones have decreased levels of all sfRNA species compared to ZIKV-WT during infection. To investigate the mechanism of decreased CPE in our DB-1 mutant clones, we assayed ZIKV DB mutant-infected A549 cells for cell viability and caspase activation. We found that cell viability is significantly increased in DB-1 mutant-infected cells compared to ZIKV-WT due to reduced caspase 3 activation. We also show that replication of the ZIKV-P.2.5 mutant was significantly restricted by type I interferon treatment without altering interferon stimulated gene expression. Using a murine model of ZIKV infection, we show that both ZIKV-DB-1 mutants exhibit reduced morbidity and mortality compared to ZIKV-WT virus due to tissue specific attenuation in ZIKV-DB viral replication in the brain tissue. Overall, our data show that the flavivirus DB-1 RNA structure is important for maintaining sfRNA levels during infection which supports caspase-3 dependent, viral cytopathic effect, type 1 interferon resistance, and viral pathogenesis in a mouse model.

microbiology↗

bioRxiv2022

'High-Density-SleepCleaner': An open-source, semi-automatic artifact removal routine tailored to high-density sleep EEG

BackgroundWith up to 256 channels, high-density electroencephalography (hd-EEG) has become essential to the sleep research field. The vast amount of data resulting from this magnitude of channels in overnight EEG recordings complicates the removal of artifacts. New MethodWe present a new, semi-automatic artifact removal routine specifically designed for sleep hd-EEG recordings. By employing a graphical user interface (GUI), the user assesses epochs in regard to four sleep quality markers (SQMs). Based on their topography and underlying EEG signal, the user eventually removes artifactual values. To identify artifacts, the user is required to have basic knowledge of the typical (patho-)physiological EEG they are interested in, as well as artifactual EEG. The final output consists of a binary matrix (channels x epochs). Channels affected by artifacts can be restored in afflicted epochs using epoch-wise interpolation, a function included in the online repository. ResultsThe routine was applied in 54 overnight sleep hd-EEG recordings. The proportion of bad epochs highly depends on the number of channels required to be artifact-free. Between 95% and 100% of bad epochs could be restored using epoch-wise interpolation. We furthermore present a detailed examination of two extreme cases (with few and many artifacts). For both nights, the topography and cyclic pattern of delta power look as expected after artifact removal. Comparison with Existing MethodsNumerous artifact removal methods exist, yet their scope of application usually targets short wake EEG recordings. The proposed routine provides a transparent, practical, and efficient approach to identify artifacts in overnight sleep hd-EEG recordings. ConclusionsThis method reliably identifies artifacts simultaneously in all channels and epochs.

neuroscience↗

bioRxiv2021

HAPPILEE: The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data

Low-density Electroencephalography (EEG) recordings (e.g. fewer than 32 electrodes) are widely-used in research and clinical practice and enable scalable brain function measurement across a variety of settings and populations. Though a number of automated pipelines have recently been proposed to standardize and optimize EEG preprocessing for high-density systems with state-of-the-art methods, few solutions have emerged that are compatible with low-density systems. However, low-density data often include long recording times and/or large sample sizes that would benefit from similar standardization and automation with contemporary methods. To address this need, we propose the HAPPE In Low Electrode Electroencephalography (HAPPILEE) pipeline as a standardized, automated pipeline optimized for EEG recordings with low density channel layouts of any size. HAPPILEE processes task-free (e.g. resting-state) and task-related EEG, and event-related potential (ERP) data, from raw files through a series of processing steps including filtering, line noise reduction, bad channel detection, artifact rejection from continuous data, segmentation, and bad segment rejection that have all been optimized for low density data. HAPPILEE also includes post-processing reports of data and pipeline quality metrics to facilitate the evaluation and reporting of data quality and processing-related changes to the data in a standardized manner. We describe multiple approaches with both recorded and simulated EEG data to optimize and validate pipeline performance. The HAPPILEE pipeline is freely available as part of HAPPE 2.0 software under the terms of the GNU General Public License at: https://github.com/PINE-Lab/HAPPE.

neuroscience↗

bioRxiv2021

Closed-loop auditory stimulation method to modulate sleep slow waves and motor learning performance in rats

Slow waves and cognitive output have been modulated in humans by phase-targeted auditory stimulation. However, to advance its technical development and further our understanding, implementation of the method in animal models is indispensable. Here, we report the successful employment of slow waves phase-targeted closed-loop auditory stimulation (CLAS) in rats. To validate this new tool both conceptually and functionally, we tested the effects of up- and down-phase CLAS on proportions and spectral characteristics of sleep, and on learning performance in the single pellet-reaching task, respectively. Without affecting 24-h sleep-wake behavior, CLAS specifically altered delta (slow waves) and sigma (sleep spindles) power persistently over chronic periods of stimulation. Down-phase CLAS exerted a detrimental effect on overall engagement and success rate in the behavioral test, and overall CLAS-dependent spectral changes were positively correlated with learning performance. Altogether, our results provide proof-of-principle evidence that phase-targeted CLAS of slow waves in rodents is efficient, safe and stable over chronic experimental periods, enabling the use of this high-specificity tool for basic and preclinical translational sleep research.

neuroscience↗

bioRxiv2020

GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers

Mast cells (MCs) are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the MC lineage-determining factors (LDTFs). However, it is unclear whether these LDTFs regulate chromatin accessibility at MC enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of MC identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We found that the number and densities of GATA2-but not MITF-bound sites at the super-enhancers were several folds higher than that at the typical enhancers. Our studies revealed that GATA2 promotes robust gene transcription to maintain MC identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key MC genes.

molecular biology↗

bioRxiv2020

Human and mouse transcriptome profiling identifies cross-species homology in pulmonary and lymph node mononuclear phagocytes

The mononuclear phagocyte (MP) system consists of macrophages, monocytes, and dendritic cells (DCs). MP subtypes play distinct functional roles in steady state and inflammatory conditions. Though murine MPs are well characterized, their pulmonary and lymph node (LN) human homologs remain poorly understood. To address this gap, we created a gene expression compendium across 15 distinct human and 9 distinct murine MPs from lung, LN, blood, and spleen. Human blood MPs and murine spleen MPs served as validation datasets, as the human-mouse MP homologs are relatively well-defined in these tissues. In-depth RNA sequencing identified corresponding human-mouse MP subtypes and determined marker genes shared and divergent across between species counterparts. Unexpectedly, at the gene expression level, only 13-23% of the top 1000 marker genes (i.e., genes not shared across species-specific MP subtypes) overlapped in corresponding human-mouse MP counterparts, indicating a need for caution when translating mouse studies to human gene targets and functions. Lastly, CD88 was useful in both species to distinguish macrophage and tissue monocytes from DCs. Our cross-species gene expression compendium serves as a resource for future translational studies to investigate beforehand whether pursuing specific MP subtypes, or genes will prove fruitful.

immunology↗