Biology subjects

Moore, Z.

Publications and source records attributed to Moore, Z..

7 recordsLinked to original sources

bioRxiv2026

Amplitude without phase: interpersonal movement coordination grades inter-brain coupling

Interpersonal movement coordination is a foundational feature of human sociality, scaffolding communication, affiliation, and joint action from infancy onward. Whether this behavioral coupling is accompanied by genuine coupling between brains, rather than one manufactured by shared sensory input or motion artifact, has proven difficult to establish. We recorded dual-brain EEG with synchronized head-mounted accelerometry from participant-partner dyads (16 dyads, 155 dyad-condition recordings) across six conditions grading interpersonal coordination from stillness to fully reciprocal joint movement, using improvisational dance to elicit sustained, naturalistic, gradable coordination. Windowed cross-correlation confirmed graded, partner-specific movement coordination, including a lead-lag signature that reversed with who led. Against a pseudo-dyad surrogate, inter-brain synchrony took one specific form: amplitude-envelope coupling in the high-beta and gamma bands, robust to a leakage-corrected measure, with no phase-based or slow-band coupling. Within dyads, movement synchrony predicted the strength of this amplitude coupling (standardized beta = 0.54 in gamma), an association that strengthened monotonically with frequency, held under a dyad fixed-effects estimator, and was undiminished when the amount of movement was entered into the model. Movement synchrony and inter-brain coupling also co-fluctuated within interactions, above surrogate. Two control analyses excluded the leading alternatives: the coupling was not sensorimotor rhythm-tracking, since corticokinematic coherence was present but non-localized and not movement-selective, and not a shared movement-frequency rhythm linking the brains. These results identify interpersonal movement coordination as an organizing variable for inter-brain coupling and specify that coupling as fast-band amplitude co-modulation, not phase synchrony. Brains couple when bodies coordinate, not when they merely move together.

neuroscience↗

bioRxiv2026

The Choreography of Coupled Brains: Coordinated Movement and Multi-Scale Neural Synchrony in Musical Theater for Individuals with Developmental Disabilities

Performing together, which demands moving, singing, and coordinating in real time, is among the most social things people do, yet whether such coordination synchronizes not only behavior but brain activity, within and between performers, has rarely been examined during genuine performance. In this pilot study, we used mobile electroencephalography, including dual-brain hyperscanning of co-performing partners, to resolve neural change over a 16-week musical-theater program in adolescents and adults with developmental disabilities, the majority autistic. We examined four levels: behavior, spectral power, within-brain (source-space) connectivity, and between-brain synchrony, framing all estimates as effect sizes. Anxiety decreased from pre- to post-intervention, consistently across participant and parent reports. During performance, high-beta and gamma power and within-brain amplitude connectivity rose broadly across the cortex, with maximal effects seen in parieto-occipital regions. Between-brain coupling was similarly carried by amplitude co-fluctuation rather than phase; however, it was graded by the degree of interpersonal movement coordination (strongest when partners mirrored one another) and scaled with movement vigor. Local and within-brain changes were thus broad and state-like, whereas coupling between brains was specific to interpersonal coordination. Coordinated movement may organize neural synchrony across scales, positioning musical theater as a tractable model for studying the social brain in motion.

neuroscience↗

bioRxiv2025

Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

The intra- and inter-tumoral heterogeneity of glioblastoma represents a significant therapeutic challenge, as well as difficulty in generating reliable models for in vitro studies. Historical 2D adherent cell lines do not recapitulate this complexity, whereas both patient-derived neurospheres (PDN) and organoids (PDO) demonstrate intra-tumoral heterogeneity. Here, we quantify the tumor cell composition from matched models established from the same primary tumor using a series of multi-omic interrogations. We find that both patient-derived models recapitulate the genomic, epigenomic and tumor cell heterogeneity of the primary tissue. Furthermore, single-nuclei RNA sequencing revealed a subset of organoids containing small numbers of non-malignant cells from neuron and immune cell lineages. Harnessing the intra-tumoral heterogeneity of PDN models, we reveal the impact of temozolomide chemotherapy on individual cell states, altering composition of tumors over time in response to treatment. Our data confirms that both patient-derived models recapitulate patient intra-tumoral heterogeneity providing a platform for tumor cell state refined therapeutic studies. Key PointsO_LIGeneration of matched patient-derived neurosphere and organoid models from resected GBM tissue C_LIO_LINeurosphere models exhibit greater proliferative signatures C_LIO_LIBoth patient-derived models recapitulate genomic and epigenomic features of the primary tissue C_LIO_LISingle-nuclei RNA sequencing reveals both models recapitulate intra-tumoral heterogeneity of the primary tissue C_LIO_LINeurosphere models enable interrogation of therapeutic responses in the context of heterogeneity C_LI Importance of studyPatient derived models can be powerful tools when they faithfully recapitulate the tumor tissue from which they are derived. In glioblastoma, patient derived neurospheres (PDN) and organoids (PDO) have both been used in studies, however the differences between these models and the recapitulation of patient heterogeneity remain to be fully characterized. To address this, we performed multi-omic profiling of PDN and PDO models generated from the same tumor tissue. We find that that across a range of data modalities, both model systems exhibit a high level of resemblance to tissue, and critically, maintain heterogeneity and tumor cell composition. The importance of modeling heterogeneity was demonstrated in PDN models, where temozolomide treatment specifically alters the abundance of MES-like and AC-like tumor cells. Our findings demonstrate that neurosphere and organoid models effectively preserve cellular heterogeneity, genomic alterations, methylation signatures and transcriptomic features, both highly suitable to model glioblastomas complex cellular landscape.

cancer biology↗

bioRxiv2024

TIRE-seq: an Integrated Sample Extraction and Transcriptomics Workflow for High Throughput Perturbation Studies

RNA sequencing (RNA-seq) is widely used in biomedical research, advancing our understanding of gene expression across biological systems. Traditional methods require upstream RNA extraction from biological inputs, adding time and expense to workflows. We developed TIRE-seq (Turbocapture Integrated RNA Expression Sequencing) to address these challenges. TIRE-seq integrates mRNA purification directly into library preparation, eliminating the need for a separate extraction step. This streamlined approach reduces turnaround time, minimizes sample loss, and improves data quality. A comparative study with the widely used Prime-seq protocol demonstrates TIRE-seqs superior sequencing efficiency with crude cell lysates as inputs. TIRE-seqs utility was demonstrated across three biological applications. It captured transcriptional changes in stimulated human T cells, revealing activation-associated gene expression profiles. It also identified key genes driving murine dendritic cell differentiation, providing insights into lineage commitment. Lastly, TIRE-seq analyzed the dose-response and time-course effects of temozolomide on patient-derived neurospheres, identifying differentially expressed genes and enriched pathways linked to the drugs mechanism of action. With its simplified workflow and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies across diverse biological systems.

genomics↗

bioRxiv2023

Matrix selection for the visualization of small molecules and lipids in brain tumors using untargeted MALDI-TOF mass spectrometry imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging allows the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by comparative analysis of lipid and small molecule abundance using liquid chromatography-mass spectrometry and RNA-sequencing assessing differential metabolites between normal and tumor regions. Our findings indicate that the recrystallized cyano-4-hydroxycinnamic acid matrix in positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies.

molecular biology↗

bioRxiv2023

A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq

Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of sample multiplexing reagents can impact data quality and experimental outcomes. In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across diverse sample types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are critical to optimal performance. We also compared the performance of fixed scRNA-Seq kits and highlight the advantages of the Parse Biosciences kit for fragile samples. Highly multiplexed scRNA-Seq experiments require more sequencing resources, therefore we evaluated CRISPR-based destruction of non-informative genes to enhance sequencing value. Our comprehensive analysis provides insights into the selection of appropriate sample multiplexing reagents and protocols for scRNASeq experiments, facilitating more accurate and cost-effective studies.

genomics↗

bioRxiv2017

Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available on https://citrusgreening.org/.

genomics↗