Biology subjects

Moore, M. J.

Publications and source records attributed to Moore, M. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Exploring the role of prior exposure and image quality in neural and behavioural prediction effects

According to predictive processing theories, the brain achieves efficiency in perception by comparing current sensory inputs with stored representations of the external world. Previous research has shown that manipulations of expectation can alter neural processing of low-level visual features as well as more complex, naturalistic objects. It remains unclear, however, precisely how the effects of expectancy are altered through learning and changes in stimulus fidelity. Here, we characterised behaviour and neural activity patterns while systematically varying individuals prior exposure to object sequences and the quality of the stimuli therein. Participants viewed rapid image sequences while we recorded their brain activity using electroencephalography (EEG). The stimulus sequences were probabilistically structured such that the appearance of each object was either expected, unexpected, or random. Participants were faster and more accurate in detecting cued target stimuli when these were expected relative to unexpected or random. Multivariate analysis of EEG activity patterns time-locked to the appearance of object images revealed reliably reduced decoding accuracy for both expected and unexpected stimuli relative to random stimuli. These patterns were consistent across exposure and image quality conditions, though exploratory analyses suggested that subtle changes in neural prediction effects may be linked to exposure. The findings do not provide strong support that the brain differentially represents expected versus unexpected object information and suggest that exposure and image quality do not reliably interact with predictive processes in object recognition.

neuroscience↗

bioRxiv2026

Semantic category and presentation frequency-based expectations are associated with distinct neural prediction effects.

Past work has indicated that expectation can modulate neural responses to visual stimuli, but it is unclear whether these effects remain consistent across different types of unexpected stimuli. Here, we measured and compared neural prediction effects associated with semantic category and presentation frequency-based expectations in real-world object stimuli. Participants (n = 35) viewed real-world object images in rapid serial visual presentation (RSVP) streams. Semantically unexpected stimuli occurred when a stimulus was presented in a semantically incongruent stream. Low-frequency violations occurred when a rarely presented stimulus was displayed in a semantically congruent stream. Multivariate pattern analysis of electroencephalography (EEG) was used to quantify and compare the degree of information represented in neural activity for stimuli in different prediction conditions. Semantically expected stimuli yielded lower decoding accuracy relative to random (unpredictable) stimuli (125-313 ms post-onset) while semantically unexpected stimuli exhibited increased decoding accuracy (199-238 ms & 523-559 ms). Low-frequency violations yielded decoding accuracy which was not significantly different from semantically expected stimuli. Exploratory analyses indicated that dissimilarity between expected and presented stimuli quantified in terms of higher-level stimulus features, but not low-level visual features, modulated the observed neural prediction effects. These results demonstrate that different types of prediction violations have distinct modulatory effects on neural responses, providing novel insight into the neural implementation of predictive processing.

neuroscience↗

bioRxiv2026

Isoform-specific cofactor recruitment through the intrinsically disordered N-terminus of p63 underlies differential transcriptional activities

The transcription factor p63 is critical for epithelial development and implicated in tumorigenesis. However, our understanding of the role of p63 in development and disease has been complicated by its diverse isoforms. As a member of the p53 family member of genes, TP63 encodes for numerous isoforms, including the N-terminal variants TAp63 and {Delta}Np63, which are generated through alternative promoter usage. TAp63 and {Delta}Np63 share various structural domains, including the DNA-binding domain, and primarily differ in their N-terminus which consists of intrinsically disordered regions (IDRs). The isoforms are known to have different functions, including tumor suppression in the case of TAp63 and pro-tumor formation for {Delta}Np63, but how the N-terminus contributes to isoform-specific gene regulatory effects has yet to be elucidated. Using both genomic and TurboID proximity-labeling proteomic approaches, we show that the N-terminus mediates differential interactions with cofactors that have direct effects on isoform function, specifically the regulation of apoptosis. We find that the N-terminus of TAp63 interacts with more transcriptional machinery, leading to stronger transcriptional activity by TAp63 than {Delta}Np63. However, {Delta}Np63 maintains interactions with coactivators, suggesting it can retain some transactivation capabilities. Strikingly, the N-terminus of TAp63 displays enriched interactions with chromatin modifiers, including the histone acetyltransferase KAT2A, that result in TAp63-specific binding at inaccessible sites. We find that an IDR-mediated interaction with KAT2A is involved in regulation of apoptosis by TAp63. Collectively, our results suggest a model in which TAp63 and {Delta}Np63 broadly share genomic occupancy, but differential interactions with cofactors contribute to isoform-specific regulation by TAp63 and {Delta}Np63.

molecular biology↗

bioRxiv2025

Sleep-like slow waves in wakefulness index post-stroke behavioural alterations

Increases in high-amplitude, low-frequency EEG oscillations during non-rapid eye movement (NREM) sleep serve as markers of neuronal silencing, which disrupts functional connectivity and is associated with a loss of awareness and responsiveness. Cortical slowing likewise occurs during wakefulness, upon sleep deprivation, and accompanies performance deterioration. Recent work has revealed similar oscillations (termed sleep-like slow waves) following stroke in brain regions close or connected to a brain lesion, offering a plausible but untested mechanism for stroke-related behavioural impairment. Here, we simultaneously recorded EEG and behavioural performance while 30 unilateral stroke patients (12 left hemisphere, 18 right hemisphere) and 27 age-matched healthy adults completed a computerised perceptual decision-making task. Sleep-like slow waves occurred more frequently in stroke patients relative to healthy controls. Furthermore, there was a significant correlation between slow wave occurrence and the accuracy and speed of perceptual reports in stroke patients, suggesting that variations in the occurrence of slow waves may contribute to cognitive heterogeneity post-stroke. Evidence that sleep-like slow waves predict deficits in perceptual decision-making following stroke indicates that stroke-induced lesions can destabilize cortical networks extending beyond the damaged regions, thereby contributing to broader cognitive impairments.

neuroscience↗

bioRxiv2025

Methodological choices strongly modulate the sensitivity and specificity of lesion-symptom mapping analyses

Lesion mapping results can vary substantially as a function of specific analysis parameters, but the extent to which individual methodological choices interact to modulate the sensitivity and specificity of results is not clear. Here, we employed a large-scale simulation approach to inform practical recommendations for lesion symptom mapping studies. Routine clinical imaging from 959 stroke survivors (mean age = 72.5, 49.3% female) was used to conduct 384,780 lesion mapping analyses based on simulated behavioural data. Each simulated analysis used different combinations of plausible sample inclusion criteria, analysis parameters (e.g., correction factors), analysis types (e.g., univariate vs. multivariate), and underlying target correlates. Simulated analysis accuracy (Dice similarity coefficient and percent coverage of target correlates) was compared across designs. Overall, analysis accuracy varied widely and was substantially modulated by the specific design used. Analyses that maximised lesion coverage by including large and diverse samples reliably outperformed analyses using more restricted samples. Analyses using direct total lesion volume controls outperformed analyses using other (or no) volume corrections across all accuracy measures. False discovery rate corrections yielded the best performance in terms of target coverage, while permutation corrections yielded the best Dice coefficients. While multivariate approaches were more accurate than univariate analyses in terms of Dice coefficient, univariate analyses generated higher target hit rates and percent target coverage. These results identify specific analysis designs suitable for studies aiming to maximise their sensitivity and/or specificity to underlying critical correlates, while highlighting the inferential strengths and weaknesses of these complementary approaches.

neuroscience↗

bioRxiv2025

Human microphysiological model of dorsal root ganglion-spinal cord dorsal horn circuitry recapitulates opioid induced effects

Microphysiological systems (MPSs) are engineered, in vitro platforms which have been established as viable alternatives to animal models for pre-clinical research with unique advantages over conventional model systems. Many MPSs utilize 3-dimensional (3D) tissue constructs that enable biomimetic cell-cell interactions, allow for extended culture periods, and provide the time necessary for the emergence of physical and physiological characteristics of more mature tissues. Here, we present a novel MPS using human induced pluripotent stem cell (hiPSC)-derived spinal cord dorsal horn (SCDH) spheroids co-cultured with hiPSC-derived dorsal root ganglion (DRG) sensory spheroids in a microengineered hydrogel system to create a "connectoid" model of afferent pain circuitry. SCDH spheroids were functionally innervated by peripheral sensory neurons, and prolonged maturation of hiPSC-derived SCDH neurons within the connectoid system enabled derivation of crucial late-born cell types unattainable using 2D differentiations. Furthermore, hiPSC-derived SCDH spheroids spontaneously generate rhythmic, complex, synaptically-driven electrophysiological waveforms that are disinhibited by morphine exposure, consistent with spinal mechanisms of opioid-induced pruritus and hypersensitivity. One Sentence SummaryhiPSC-derived afferent sensory circuitry model, with NK1R+ spinal cord dorsal horn neurons, yields electrophysiologically mimetic response to opioids.

bioengineering↗

bioRxiv2025

Long-Term Potentiation and Closed-Loop Learning in Paired Brain Organoids for CNS Drug Discovery

Learning and memory, central to cognitive function and critical targets for drug discovery in neurological disorders, fundamentally rely on synaptic plasticity, such as long-term potentiation (LTP). We developed an embedded electrode array (EEA) capable of supporting paired CNS-3D brain organoids, derived from human, induced pluripotent stem cells (iPSCs), that were interconnected via guided axonal growth, as a novel functional biomarker model for probing learning-related plasticity in vitro. Using open-loop stimulation protocols, a robust, network-level LTP in trained organoids was demonstrated that was not observed in untrained organoids. Importantly, LTP was enhanced in the presence of elevated levels of brain-derived neurotrophic factor (BDNF), and it was prevented by the NMDA receptor antagonist AP5. Furthermore, a closed-loop "maze-game", inspired by Pac-Man(R), demonstrated that paired brain organoids could learn to perform better in the game when given reinforcement feedback, and that this effect depended on BDNF. This integrated platform provides a human-relevant in vitro model of synaptic plasticity and cognitive function, establishing a functional biomarker platform for central nervous system (CNS) drug discovery and linking game performance as a measurable readout of learning-related plasticity to the emerging field of organoid intelligence.

bioengineering↗

bioRxiv2025

Human Peripheral Nerve-on-a-Chip on a Multiwell Microelectrode Array as a Scalable Preclinical Neurotoxicity Assay

Reliable human-relevant models of peripheral nerve function remain a critical unmet need in preclinical drug development, particularly for predicting neurotoxicity and bridging the gap to clinical translation. Here, we introduce a next generation Nerve-on-a-Chip, PNS-3D organoids, as a novel human-cell-based 3D peripheral nerve microphysiological system (MPS) that recapitulates key functional and structural features of native nerves, including long-distance axonal outgrowth, physiological myelination, and clinically translational population level electrophysiology. The platform integrates iPSC-derived human sensory neurons and primary human Schwann cells within a spatially organized 3D environment, coupled to a custom embedded electrode array that enables high-content, longitudinal, and clinically translatable functional assessments. As a proof of concept, we evaluated the platforms predictive power using vincristine, a chemotherapeutic agent known to cause chemotherapy-induced peripheral neuropathy (CIPN). PNS-3D organoids captured dose- and time-dependent deficits in nerve conduction velocity, compound action potential amplitude, and axonal degeneration, with IC values in line with human clinical exposures-- outperforming traditional 2D cultures and in vivo benchmarks. Transcriptomic and morphological analyses further revealed neuron-specific degeneration consistent with axonopathy. These results validate the platform as a human-relevant, clinically translation, and scalable solution, enabling mechanistic safety assessment and drug discovery for neurotoxic and neuroprotective therapeutics.

pharmacology and toxicology↗

bioRxiv2024

Structural insights into CXCR4 modulation and oligomerization

Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. CXCR4 also serves as a key target for diseases such as cancer and HIV. Previously reported crystal structures of CXCR4 bound to antagonists revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood, including its activation by CXCL12, as well as its assembly into higher-order oligomers. Here, we use cryoelectron microscopy (cryoEM) to investigate various modes of CXCR4 regulation in the presence and absence of Gi protein. CXCL12 activates CXCR4 by inserting its N-terminus deep into the CXCR4 orthosteric pocket. The binding of FDA-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the 7 transmembrane helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its CDR-H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal, to our knowledge, previously undescribed modes of GPCR oligomerization. Remarkably, CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function.

biochemistry↗

bioRxiv2023

Neurophysiological mechanisms underlying post-stroke deficits in contralesional perceptual processing

Slowed responding to sensory inputs presented in contralesional space is pervasive following unilateral cerebral stroke, but the causal neurophysiological pathway by which this occurs remains unclear. To this end, here we leverage a perceptual decision-making framework to disambiguate information processing stages between sensation and action in 30 unilateral stroke patients (18 right hemisphere, 12 left hemisphere) and 27 neurologically healthy adults. By recording neural activity using electroencephalography (EEG) during task performance, we show that the relationship between strokes in either hemisphere and slowed contralesional response times is sequentially mediated by weaker target selection signals in the contralateral hemisphere (the N2c ERP), and subsequently delayed evidence accumulation signals (the centroparietal positivity). Notably, asymmetries in CPP and response times across hemispheres are associated with everyday functioning. Together, these data suggest a plausible neurophysiological pathway by which post-stroke contralesional slowing arises and highlight the utility of neurophysiological assessments for tracking clinically relevant behaviour.

neuroscience↗

bioRxiv2022

Functional mRNA delivery to hematopoietic stem and progenitor cells in vivo.

Gene correction of hematopoietic stem cells (HSC) is a promising therapeutic approach for multiple disorders. Current methods, however, require HSC collection from patients, gene correction during ex vivo culture, and re-infusion of corrected HSC into patients conditioned with chemotherapeutic agents. These approaches are complex, and the conditioning creates toxicities. We show that a lipid nanoparticle (LNP) can deliver mRNA encoding a reporter or a gene editing protein to HSC, with one injection transfecting [~]25% of mouse HSC, and repeated doses resulting in higher editing efficiencies. We also demonstrate LNP-driven in vivo mRNA delivery to HSC in non-human primates and humanized mice. These results demonstrate a translatable approach to deliver mRNA encoding therapeutic proteins, or gene correcting tools, to HSC that do not require cell culture or toxic conditioning. One-Sentence SummaryLNP can deliver functional mRNA to mouse, non-human primate, and human HSC.

immunology↗

bioRxiv2022

Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM

The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length /{beta} TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.

biochemistry↗

bioRxiv2021

Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus

Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking non-coding regions, summary coalescent methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic and morphological diversity in the group. We found that the combination of exons and flanking non-coding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple origins of the evolution of bee pollination from ancestral hawkmoth pollination, the evolution of edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively address a relatively common but recalcitrant problem in evolutionary biology.

evolutionary biology↗

bioRxiv2020

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data, species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we herein recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and chloroplast genomes to reconstruct deep and shallow phylogenies of plants.

evolutionary biology↗

bioRxiv2020

Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation.

mRNA translation and degradation are strongly interconnected processes that participate in the fine tuning of gene expression. Particularly, targeting mRNAs to translation-dependent degradation (TDD) could attenuate protein expression by making any increase in mRNA translation self-limiting. However, the extent to which TDD is a general mechanism for limiting protein expression is currently unknown. Here we describe a comprehensive analysis of basal and signal-induced TDD in mouse primary CD4 T cells. Our data indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner, both in resting and activated cells. Our analysis further identifies the length of untranslated regions, the density of ribosomes and the GC content of the coding region as major determinants of TDD magnitude. Consistent with this, all transcripts that undergo changes in ribosome density upon T cell activation display a corresponding change in their TDD level. Surprisingly, the amplitude of translation-independent mRNA decay (TID) appears as a mirror image of TDD. Moreover, TID also responds to changes in ribosome density upon T cell activation but in the opposite direction from the one observed for TDD. Our data demonstrate a strong interconnection between mRNA translation and decay in mammalian cells. Furthermore, they indicate that ribosome density is a major determinant of the pathway by which transcripts are degraded within cells.

genomics↗

bioRxiv2020

The draft genome of the endangered, relictual plant Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms and perils of evolutionary specialization

Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionary long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) and investigated the evolutionary history of K. uniflora, along with mechanisms related to its endangered status. Phylogenomic analyses based on 497 single copy genes confirmed the sister relationship between K. uniflora and Circaeaster agrestis, which were estimated to have diverged around 52 Mya. Proliferation of LTR retrotransposons in K. uniflora is estimated to occur around 2.7 Mya, coinciding with one recent uplift of the Hengduan Mountains between the late Miocene and late Pliocene. Across 12 species of monocots, early-diverging eudicots and core eudicots, K. uniflora showed significant overrepresentation in gene families associated with DNA repair and underrepresentation in gene families associated with stress response. Most of the plastid ndh genes were found to be lost not only in the plastome but also in the nuclear genome of K. uniflora. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while at the same time, reducing genetic diversity which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.

genomics↗

bioRxiv2019

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways

BackgroundAlternative splicing (AS), which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing AS pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses. ResultsRNA immunoprecipitation in tandem (RIPiT) of exon junction complex (EJC) components allows for purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and, therefore, translation-dependent mRNA decay. Here we compared EJC RIPiT-Seq to whole cell RNA-Seq data from HEK293 cells. Consistent with expectation, the flux through known AS-NMD pathways is substantially higher than that captured by RNA-Seq. Our EJC RIPiT-Seq also definitively demonstrates that the splicing machinery itself has no ability to detect reading frame. We identified thousands of previously unannotated splicing events; while many can be attributed to "splicing noise", others are evolutionarily-conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis. ConclusionsDeep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the NMD-linked AS pathway predominates. EJC RIPiT-Seq also enabled identification of numerous conserved but previously unannotated AS-NMD events.

bioinformatics↗

bioRxiv2019

Free circular introns with an unusual branchpoint in neuronal projections

The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.

cell biology↗