Biology subjects

Harris, R. E.

Publications and source records attributed to Harris, R. E..

15 recordsLinked to original sources

bioRxiv2026

Functional Connectivity Differences Underly Variable Centralized Symptom Relief After Hysterectomy

Approximately 1 in 4 women with chronic pelvic pain (CPP) report persistent pelvic pain after hysterectomy. Centralized symptoms-fatigue, multisite pain, and sleep disturbance, quantified using the Fibromyalgia Survey Score (FSS)-often co-occur with this risk, but the trajectory of centralized symptom burden after surgery, independent of pelvic pain outcome, is not well understood. Whether presurgical differences in central nervous system pain processing distinguish women whose centralized symptoms improve (improvers) from those whose do not (non-improvers) has not been tested. In this observational study, we assessed whether individuals who do and do not report improvement in FSS scores six months post-operatively differ in their baseline/pre-operative phenotypes and brain function. Sensory sensitivity scores were significantly higher in non-improvers than in improvers at baseline. We identified no significant, presurgical differences in age, average pelvic pain intensity, widespread pain, or pain interference between improvers and non-improvers. Functional connectivity was examined at rest and during the application of a distal, sustained pressure pain. We identified no significant group differences at rest. During sustained pressure pain, non-improvers showed greater connectivity than improvers between primary somatosensory cortex and posterior thalamic seeds with frontal, motor, cerebellar and limbic regions, but lower connectivity between the periaqueductal gray and subgenual cingulate cortex. Non-improvers also showed a greater pain-evoked increase in connectivity between the pelvic and leg representations of the primary sensory cortex and other sensorimotor regions in the pain-versus-rest contrast. Overall, non-improvers showed increased functional connectivity between regions associated with the multisensory integration of ascending pain, and decreased connectivity between regions associated with descending pain modulation. In exploratory analyses, some of these connections were additionally associated with symptom burden: sensory sensitivity, number of painful regions, and pain interference. This work may inform mechanisms of persistent symptom burden and guide surgical decision-making in patients with high central sensitization.

neuroscience↗

bioRxiv2026

A Beta-Binomial Model for Estimating Zero- or One-inflated Pain Trajectories

Chronic pain is a widespread public health issue that imposes substantial health, emotional, and economic burdens on individuals and communities. Because pain is subjective and lacks objective biomarkers, it is typically measured using patient-reported scores, often on a numerical scale from zero to ten. Increasingly, pain studies use ecological momentary assessment, with multiple daily assessments over days and across study phases (e.g., a series of baseline and post-intervention assessments). These data frequently show many ratings at the extremes (i.e., at minimum or maximum pain scores), commonly referred to as zero- and one-inflation in the statistical literature, along with considerable within-person variability both within and across days. These phenomena present challenges for statistical analyses, as they violate assumptions of most commonly used statistical techniques (e.g., the normality assumption of linear mixed models). We propose a Bayesian beta-binomial mixed-effects model for modeling potential zero- or one-inflated pain scores while accounting for variability using random effects on the mean and variance parameters across subjects. A simulation study demonstrates that the method accurately estimates model parameters across realistic sample sizes, time points, and zero- and one-inflation levels. An application to data from two longitudinal pain studies demonstrates that the model fits the data better and, when correctly specified, yields accurate uncertainty intervals for longitudinal changes in pain compared to existing models, especially for zero- and one-inflated outcomes. Additionally, the model directly estimates the probability of clinically meaningful pain events. The proposed method provides a powerful statistical framework for studying the patient-reported pain trajectories.

bioinformatics↗

bioRxiv2026

Discovery of a small peptide that activates both APCCdc20 and APCCdh1 in yeast, driving increased lifespan

Aging is accompanied by molecular hallmarks conserved from yeast to humans. One such hallmark, senescence, is an irreversible nondividing state that promotes aging. We previously reported that mutants of the yeast Anaphase Promoting Complex (APC) shorten the lifespan of both dividing and nondividing cells. Here, we propose that activation of the APC will promote the maintenance of quiescent yeast cells, thereby delaying senescence and aging. We observed that APC activity in aging quiescent cells becomes increasingly impaired, as the APC substrates Clb1 and Mps1 accumulated within aging cells reintroduced back into the cell cycle. To identify peptide activators of the APC, we used a yeast 2-hybrid screen to recover peptides that interacted with the APC subunit Apc10. Recovered peptides were tested for their effects on the replicative lifespan (RLS) of dividing cells, and the chronological lifespan (CLS) of nondividing cells. Several peptides increased the RLS of wild type cells, but only one peptide (C43-4) increased CLS, which requires the APC Cdh1 co-activator, but not the Cdc20 co-activator. In cells expressing C43-4, Clb1 and Mps1 levels remained low when aging quiescent cells were reintroduced back into the cell cycle. The addition of a synthetic C43-4 to aging quiescent cells increased CLS even when added at late stages of aging. Mutations to APC subunits and co-activators blocked the ability of C43-4 to extend CLS. Htz1, which shares sequence homology with C43-4, was found to suppress APC mutant phenotypes and stabilize Apc10. We individually mutated the 6 amino acids in C43-4 that were shared with Htz1; one of the mutants disrupted the C43-4-Apc10 2-hybrid interaction and abolished the C43-4-dependent increase in CLS. C43-4 action is evolutionarily conserved, as C43-4 increased C. elegans lifespan in a daf-16- and aak-2-dependent manner. Our results describe the discovery of an evolutionarily conserved translational peptide that is the first of its kind to specifically activate the anti-aging APCCdh1 complex.

genetics↗

bioRxiv2025

Zinc-induced folding and solution structure of the eponymous novel zinc finger from the ZC4H2 protein

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil, and a single novel zinc finger with four cysteines and two histidines from which the protein gets its name. Alpha Fold 3 confidently predicts a structure for the zinc finger but also for similarly sized random sequences, providing equivocal information on its folding status. We show using a synthetic peptide fragment that the zinc finger of ZC4H2 is genuine, and folds around zinc ion with picomolar affinity. NMR pH titration of histidines and UV-Vis of a cobalt complex of the peptide indicate its four cysteines coordinate zinc while two histidines do not participate in binding. The experimental NMR structure of the zinc finger has a novel structural motif similar to RANBP2 zinc fingers, in which two orthogonal hairpins each contribute two cysteines to coordinate zinc. Most of the nine ZARD mutations that occur in the ZC4H2 zinc finger likely perturb this structure. While the ZC4H2 zinc finger shares the folding motif and cysteine-ligand spacing of the RANBP2 family, it is missing key substrate-binding residues. Unlike the NZF branch of the RANBP2 family, the ZC4H2 zinc finger does not bind ubiquitin. Since the ZC4H2 zinc finger occurs in a single copy it is also unlikely to bind DNA. Based on sequence homology to the VAB-23 protein, the ZC4H2 zinc finger may bind RNA of a currently undetermined sequence or have alternative unprecedented functions.

biophysics↗

bioRxiv2025

Asperous coordinates regenerative timing by regulating damage-induced WNT Signaling

Tissue regeneration requires precise control of signaling pathways to direct proliferation, differentiation, and patterning. While early responses to injury are well characterized, how differentiation is coordinated during later stages remains unclear. Here, we identify Asperous (Aspr), an EGF-repeat protein, as a regeneration-specific regulator in Drosophila wing discs. Aspr is dispensable for wing development but is strongly induced within 24 hours post-injury. Maintaining aspr expression inhibits differentiation and alters reparative growth, while loss impairs regeneration. Structural and expression analyses show Aspr is an extracellular protein secreted in extracellular vesicles (EVs), where it co-localizes with the WNT ligand Wingless (Wg). We find Aspr regulates post-injury but not developmental Wg signaling, potentially by influencing its secretion or availability via EVs. These findings suggest Aspr regulates WNT activity to ensure proper timing of cell fate specification during regeneration, revealing a mechanism by which signaling dynamics are temporally controlled during tissue repair.

developmental biology↗

bioRxiv2024

Image Processing in the Acute to Chronic Pain Signatures (A2CPS) Project

The Acute to Chronic Pain Signatures (A2CPS) project is a large-scale, multi-site initiative aimed at identifying biomarkers and biosignatures that predict the transition from acute to chronic pain. The project is collecting multimodal, longitudinal data from over 2,500 individuals at risk for developing chronic pain after surgery. Here we describe the neuroimaging component of A2CPS, including the acquisition protocols, processing pipelines, and contents of the initial data release. The imaging protocol includes structural, diffusion, resting-state and task-based functional magnetic resonance imaging (MRI) data. Data are collected across multiple clinical sites using different scanner manufacturers, with attention to protocol harmonization and quality control. The processing pipeline integrates several established neuroimaging tools to extract potential biomarkers, including measures of brain structure, connectivity, and pain-related neural signatures. The first data release includes pre-surgical imaging data for 595 participants, with high quality ratings across modalities (98.7% of sMRI, 99.8% of dMRI, and 94.6% of fMRI images were rated as acceptable or better). Initial analyses demonstrate expected relationships between brain-derived measures and clinical variables, such as associations between brain age and psychological factors. This dataset represents a valuable resource for both pain research and neuroimaging methods development, with future releases planned to include additional participants and expanded analysis pipelines and processed data derivatives.

neuroscience↗

bioRxiv2024

Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein-binding zinc-fingers

The transcription repressor BCL11A, which governs the switch from fetal to adult hemoglobin during development, is the target of the first FDA-approved CRISPR/Cas9 gene-editing therapy in humans. By targeting BCL11A, fetal hemoglobin expression is de-repressed to substitute for defective adult hemoglobin in inherited diseases including beta-thalassemia and sickle-cell anemia. BCL11A has six CCHH-type zinc-fingers of which domains 4-6 are necessary and sufficient for dsDNA binding. Here, we focus on the CCHC-type ZNF at the N-terminus of BCL11A (residues 46-72), Z0, thought to modulate oligomerization of the transcription repressor. Using NMR and CD spectroscopy, Z0 is shown to be a thermostable CCHC zinc-finger with a pM dissociation constant for zinc. The NMR structure of Z0 has a prototypical beta-beta-alpha fold, with a hydrophobic knob comprising about half the structure. The unusual proportion of hydrophobic residues in Z0 led us to investigate if this is more general in zinc-fingers that do not bind dsDNA. We used the ZF and WebLogo servers to examine sequences of zinc fingers with demonstrated DNA-binding function, non-binders, and the CCHC-type family of protein-binders. DNA-binders are distinguished by contiguous stretches of high-scoring zinc-fingers. Non-DNA-binders show a depletion of polar residues at the positions expected to contact nucleotides and increased divergence from sequence consensus making these domains more likely to be annotated as atypical, degenerate, or to be missed as zinc-fingers. We anticipate these sequence patterns will help distinguish DNA-binders from non-binders, an open problem in the functional understanding of zinc-finger motifs.

biophysics↗

bioRxiv2024

A threshold level of JNK activates damage-responsive enhancers via JAK/STAT to promote tissue regeneration

Tissue regeneration requires precise activation and coordination of genes, many of which are reused from development. While key factors have been identified, how their expression is initiated and spatially regulated after injury remains unclear. The stress-activated MAP kinase JNK is a conserved driver of regeneration and promotes expression of genes involved in proliferation, growth, and cell fate changes in Drosophila. However, how JNK selectively activates its targets in damaged tissue is not well understood. We previously identified Damage-Responsive, Maturity-Silenced (DRMS) enhancers as JNK-activated elements critical for regeneration. Here, we show that cell death is dispensable for the activation of these enhancers, which only depends on JNK and its immediate downstream effectors. One of these is JAK/STAT, which acts as a direct, additional input necessary to expand enhancer activity into the wound periphery where JNK alone is insufficient. Furthermore, we demonstrate that a threshold level of JNK is required to initiate enhancer activation. Together, our findings reveal how JNK and JAK/STAT signaling cooperate to drive spatially and temporally regulated gene expression through damage-responsive enhancers, ensuring proper regenerative outcomes.

genetics↗

bioRxiv2024

Regeneration following tissue necrosis is mediated by non-apoptotic caspase activity

Tissue necrosis is a devastating complication for many human diseases and injuries. Unfortunately, our understanding of necrosis and how it impacts surrounding healthy tissue - an essential consideration when developing effective methods to treat such injuries - has been limited by a lack of robust genetically tractable models. Our lab previously established a method to study necrosis-induced regeneration in the Drosophila wing imaginal disc, which revealed a unique phenomenon whereby cells at a distance from the injury upregulate caspase activity in a process called Necrosis-induced Apoptosis (NiA) that is vital for regeneration. Here we have further investigated this phenomenon, showing that NiA is predominantly associated with the highly regenerative pouch region of the disc, shaped by genetic factors present in the presumptive hinge. Furthermore, we find that a proportion of NiA fail to undergo apoptosis, instead surviving effector caspase activation to persist within the tissue and stimulate reparative proliferation late in regeneration. This proliferation relies on the initiator caspase Dronc, and occurs independent of JNK, ROS or mitogens associated with the previously characterized Apoptosis-induced Proliferation (AiP) mechanism. These data reveal a new means by which non-apoptotic Dronc signaling promotes regenerative proliferation in response to necrotic damage.

genetics↗

bioRxiv2023

Psychedelic Concentrations of Nitrous Oxide Reduce Functional Differentiation in Frontoparietal and Somatomotor Cortical Networks

AO_SCPLOWBSTRACTC_SCPLOWDespite the longstanding use of nitrous oxide and descriptions of its psychological effects more than a century ago, there is a paucity of neurobiological investigation of associated psychedelic experiences. Identifying the impact of nitrous oxide on functional brain networks would advance understanding and contribute to the growing body of research in psychedelic neuroscience. Based on human resting-state fMRI data acquired before and during the administration of 35% nitrous oxide, we measured the brains functional geometry (through analysis of cortical gradients) and temporal dynamics (through analysis of co-activation patterns). Both analyses show that nitrous oxide reduces functional differentiation in frontoparietal and somatomotor networks. Importantly, the subjective psychedelic experience induced by nitrous oxide is inversely correlated with the degree of functional differentiation. Thus, like classical psychedelics acting on 5-HT2 receptors, nitrous oxide flattens the functional geometry of the cortex and disrupts temporal dynamics in association with psychoactive effects.

neuroscience↗

bioRxiv2022

Canonical and Non-Canonical Psychedelic Drugs Induce Common Network Changes in Human Cortex

AO_SCPLOWBSTRACTC_SCPLOWThe neurobiology of the psychedelic experience is not fully elucidated. Identifying common brain network changes induced by both canonical (i.e., acting at the 5-HT2 receptor) and non-canonical psychedelics would provide mechanistic insight into state-specific characteristics. We analyzed whole-brain functional connectivity based on resting-state fMRI data in humans, acquired before and during the administration of nitrous oxide, ketamine, and lysergic acid diethylamide. We report that, despite distinct molecular mechanisms and modes of delivery, all three psychedelics reduced within-network functional connectivity and enhanced between-network functional connectivity. More specifically, all drugs tested increased connectivity between right temporoparietal junction and bilateral intraparietal sulcus as well as between precuneus and left intraparietal sulcus. These regions fall within the posterior cortical "hot zone," posited to mediate the content of consciousness. Thus, both canonical and non-canonical psychedelics modulate networks within an area of known relevance for conscious experience, identifying a biologically plausible candidate for their subjective effects.

neuroscience↗

bioRxiv2021

Explosive Synchronization-Based Brain Modulation Reduces Hypersensitivity in The Brain Network: A Computational Model Study

Fibromyalgia (FM) is a chronic pain condition that is characterized by hypersensitivity to multi-modal sensory stimuli, widespread pain, and fatigue. We have previously proposed explosive synchronization (ES), a phenomenon wherein a small perturbation to a network can lead to an abrupt state transition, as a potential mechanism of the hypersensitive FM brain. Therefore, we hypothesized that converting a brain network from ES to general synchronization (GS) may reduce the hypersensitivity of FM brain. To find an effective brain network modulation to convert ES into GS, we constructed a large-scale brain network model near criticality (i.e., an optimally balanced state between order and disorders), which reflects brain dynamics in conscious wakefulness, and adjusted two parameters: local structural connectivity and signal randomness of target brain regions. The network sensitivity to global stimuli was compared between the brain networks before and after the modulation. We found that only increasing the local connectivity of hubs (nodes with intense connections) changes ES to GS, reducing the sensitivity, whereas other types of modulation such as decreasing local connectivity, increasing and decreasing signal randomness are not effective. This study would help to develop a network mechanism-based brain modulation method to reduce the hypersensitivity in FM. Author summaryPhase transitions, the physical processes of transition between system states in nature, are divided into two broad categories: first and second-order phase transitions. For example, boiling water presents abrupt transition (a first-order) along with high sensitivity to temperature change, distinct from gradual magnetization near Curie temperature (a second-order). Recently, we found that chronic pain shows specific brain network configurations that can induce the first-order transition, so-called explosive synchronization. In this modeling study, we tried to identify a modulation method that can convert a first-order transition into a second-order transition in the brain network, expecting that it may inhibit the hypersensitivity in chronic pain. We found that increasing structural connectivity of hubs changes the type of phase transition in the brain network, significantly reducing network sensitivity.

neuroscience↗

bioRxiv2021

Necrosis-induced apoptosis promotes regeneration in Drosophila wing imaginal discs

Regeneration is a complex process that requires a coordinated genetic response to tissue loss. Signals from dying cells are crucial to this process and are best understood in the context of regeneration following programmed cell death, like apoptosis. Conversely, regeneration following unregulated forms of death such as necrosis have yet to be fully explored. Here we have developed a method to investigate regeneration following necrosis using the Drosophila wing imaginal disc. We show that necrosis stimulates regeneration at an equivalent level to that of apoptosis-mediated cell death and activates a similar response at the wound edge involving localized JNK signaling. Unexpectedly however, necrosis also results in significant apoptosis far from the site of ablation, which we have termed necrosis-induced apoptosis (NiA). This apoptosis occurs independent of changes at the wound edge and importantly does not rely on JNK signaling. Furthermore, we find that blocking NiA limits proliferation and subsequently inhibits regeneration, suggesting that tissues damaged by necrosis can activate programmed cell death at a distance from the injury to promote regeneration.

genetics↗

bioRxiv2020

Neural correlates of the shamanic state of consciousness

Despite the use of shamanism as a healing practice for several millennia, few empirical studies of the shamanic state of consciousness exist. We investigated the neural correlates of shamanic trance using high-density electroencephalography (EEG) in 24 shamanic practitioners and 24 healthy controls during rest, shamanic drumming, and classical music listening, followed by a validated assessment of altered states of consciousness. EEG data were used to assess changes in absolute power, connectivity, signal diversity, and criticality, which were correlated with assessment measures. We also compared assessment scores to those of individuals in a previous study under the influence of psychedelics. Shamanic practitioners were significantly different from controls in several domains of altered states of consciousness, with scores comparable to or exceeding that of healthy volunteers under the influence of psychedelics. Practitioners also displayed increased gamma power during drumming that positively correlated with elementary visual alterations. Furthermore, shamanic practitioners had decreased low alpha and increased low beta connectivity during drumming and classical music, and decreased neural signal diversity in the gamma band during drumming that inversely correlated with insightfulness. Finally, criticality in practitioners was increased during drumming in the low and high beta and gamma bands, with increases in the low beta band correlating with complex imagery and elementary visual alterations. These findings suggest that psychedelic drug-induced and non-pharmacologic alterations in consciousness have overlapping phenomenal traits but are distinct states of consciousness, as reflected by the unique brain-related changes during shamanic trance compared to previous literature investigating the psychedelic state.

neuroscience↗

bioRxiv2019

Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers

Like tissues of many organisms, Drosophila imaginal discs lose the ability to regenerate as they mature. This loss of regenerative capacity coincides with reduced damage-responsive expression of multiple genes needed for regeneration. Our previous work showed that two such genes, wg and Wnt6, are regulated by a single damage-responsive enhancer, which becomes progressively inactivated via Polycomb-mediated silencing as discs mature. Here we explore the generality of this mechanism, and identify numerous damage-responsive, maturity-silenced (DRMS) enhancers, some near genes known to be required for regeneration such as Mmp1, as well as near genes that we now show function in regeneration. Using a novel GAL4-independent tissue ablation system we characterize two DRMS-associated genes, apontic (apt), which curtails regeneration and CG9752/asperous (aspr), which promotes it. This mechanism of suppressing regeneration by silencing damage-responsive enhancers at multiple loci can be partially overcome by reducing activity of the chromatin regulator extra sex combs (esc).

developmental biology↗