Biology subjects

Palmer, C.

Publications and source records attributed to Palmer, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Respiration and individual differences shape behavioral and inter-brain synchronization

Humans coordinate their actions while their bodies and brains synchronize in social interactions, yet how behavioral, physiological, and neural dynamics interact during interpersonal coordination remains largely unknown. We investigated how respiration and individual differences influence behavioral and inter-brain synchrony in a musical synchronization task, which requires precise temporal alignment. Eighty-eight individuals first produced a familiar melody at their most comfortable rate to measure their spontaneous production rate (SPR). They then synchronized the melody with a randomly assigned unfamiliar partner under natural (unpaced), instructed in-phase, and instructed anti-phase breathing conditions, while hyperscanning 64-channel electroencephalography (EEG), respiration, auditory-motor timing, and perceived social connectedness were recorded. Relative to natural respiration, both in-phase and anti-phase breathing increased inter-brain phase-locking and perceived social closeness but reduced behavioral synchrony; the instructed respiratory phase relationship was mirrored in their inter-brain relative phase. Differences in phase of respiratory cycles (inhalation and exhalation) also influenced coordination: Inhalation was associated with stronger inter-brain synchronization but less precise and stable behavioral coordination than was exhalation. Moreover, Individual differences influenced coordination: Partners with the faster SPR consistently preceded the slower partners and exhibited an alpha-band inter-brain phase advance in synchronization, whereas dyads with similar SPR showed greater behavioral synchrony and smaller inter-brain phase difference. Our findings identify respiration as a previously overlooked factor that organizes behavioral and neural synchronization, while individual intrinsic rhythms constrain how interacting partners align in time. Together, these findings reveal a dynamic interplay between the rhythms of the body and brain during human social interactions.

neuroscience↗

bioRxiv2026

Chemokine and opioid peptide scavenging through constitutive and ligand-induced release of ACKR3-bearing extracellular vesicles

Atypical chemokine receptors (ACKRs) are non-signaling GPCRs that regulate ligand availability, with ACKR3 functioning as a dual scavenger of chemokines and opioid peptides. Here, we demonstrate that following ligand stimulation, besides the canonical internalization, ACKR3 is released on extracellular vesicles (EVs). ACKR3 was also found on EVs released under basal conditions, although to a lesser extent. These observations were confirmed across multiple cellular contexts, including endogenous systems. Mechanistically, basal and ligand-induced EV release are independent of GRKs and {beta}-arrestin but each relies on distinct trafficking routes and C-terminal determinants. Ligand-induced EV release is associated with plasma membrane localization and receptor recycling pathways. In contrast, basal EV release is governed by intracellular sorting processes and influenced by receptor ubiquitination and RAMP3. Functionally, EV-associated ACKR3 retains high-affinity ligand binding, enabling sequestration of CXCL12 and opioid peptides and thereby attenuating their signaling through CXCR4 and MOR. We also show that the release on EVs, in particular under basal conditions, is observed for other receptors such as KOR, CXCR4 and several ACKRs. Collectively, these findings establish EVs as regulators in chemokine and opioid systems and as a previously underappreciated dimension of ACKR3 and more broadly GPCR biology.

Cell Biology↗

bioRxiv2025

Automated filtering of particle images in single particle cryoEM

Continued exponential growth in the number of structures resolved by single particle cryoEM, as seen in the last decade, requires ever more effective data analysis workflows. Datasets are rarely homogeneous, demanding a multistep procedure for discarding outliers. Since individual particles are very noisy, either 2D or 3D averages are normally used for discrimination. This becomes challenging when the 2D classes themselves are heterogeneous, leading to selection of contaminants or discarding useful rare views/poses. The 3D model-based discrimination requires trustworthy 3D maps and a correct assignment of Euler angles, which in turn depends on the quality of the initial data and might not be available at the very early stages of the analysis. We propose a novel deep-learning approach for improving quality of single particle datasets. The two-stage procedure consists of denoising single particle images using Variational AutoEncoder framework followed by particle quality filtering based on the score inferred for every particle by Domain Adaptation Neural Network trained on a large data set of categorised 2D averages. This approach allows an automated scoring of noisy raw images using data patterns learned from the high signal-to-noise ratio, externally derived 2D classes. Consequently, a higher quality data set enters computationally expensive steps of the data analysis, reducing the need for protracted and expensive calculations. Importantly, our method does not require any prior knowledge about the data or existence of a 3D model, making it universally applicable. Tests on publicly available datasets demonstrated that our approach largely outperformed 2D class-based particle discrimination. Smaller subsets of the top-scoring particles selected with our method were required to obtain the author-reported 3D model resolution. When applied to the user data in the automated on-the-fly data processing pipeline, the method rescued 30% of cases, which otherwise would not reach confidence threshold required for making decision to proceed to the 3D model refinement. It also led to general improvements in the quality of the 3D models for many datasets which were selected for the high-resolution processing.

biophysics↗

bioRxiv2025

Atypical activation and molecular glue-like dimerization mechanism of an intrinsically-biased chemokine receptor

CXCR7, also known as atypical chemokine receptor 3 (ACKR3), is a naturally-biased, {beta}-arrestin-coupled seven transmembrane receptor (7TMR) that lacks productive coupling with heterotrimeric G-proteins. Despite a critical involvement in cancer metastasis, cardiovascular pathophysiology, and inflammatory disorders, the molecular basis of non-canonical activation and functional divergence of CXCR7 remains elusive. Here, we present a complete landscape of CXCR7 activation using a series of cryo-EM structures, and discover an atypical activation mechanism that is distinct from prototypical GPCRs. CXCR7 is maintained in a basal conformation by a unique tripartite ionic-lock involving TM5-TM6, in contrast to a broadly conserved TM3-TM6 ionic-lock in GPCRs, which is disrupted upon receptor activation. Importantly, activation of CXCR7 results in a constricted pocket and distinct surface topology on the intracellular side compared to prototypical GPCRs. Serendipitously, we capture novel dimeric arrangements of CXCR7 with an inter-protomer stitching by a native phospholipid serving as a molecular glue, and identify previously unanticipated extrahelical allosteric sites on the receptor. Surprisingly, in an intermediate state structure of CXCR7, the second extracellular loop (ECL2) displays a self-blocking conformation, in stark contrast to ECL2-mediated self-activating mechanism reported recently for some orphan GPCRs. Finally, we unequivocally establish CXCR7 as an atypical opioid receptor via a large peptide library screening and structure elucidation in complex with distinct opioid peptides imparting full receptor activation. In summary, our study elucidates an atypical mechanism of CXCR7 activation, and establishes it as an alternative, non-canonical opioid receptor target with potential for novel pain therapeutics.

biochemistry↗

bioRxiv2025

A single binge ethanol exposure is apoptotic within hours across neurodevelopment and partially regulated by the Myt1l gene.

Ethanol rapidly produces widespread neuronal apoptosis during early development, but this susceptibility declines as the brain matures. In previous research, we found Myt1l (a proneuronal transcription factor) mutations can cause precocious differentiation, neuronal immaturity, and transcriptomic alterations, including many in apoptotic regulators. Therefore, we used a recently developed Myt1l haploinsufficient mouse model to examine this genes effects on ethanol-induced apoptosis across different developmental stages. We discovered that haploinsufficiency can moderately influence vulnerability to ethanol in a complex, age- and cell type-specific manner: apoptosis was reduced on P7, increased P21, but unaffected on P60. Remarkably, we also discovered the previously unrecognized ability of a single binge of ethanol to rapidly increase apoptosis within six hours in early adolescent and adult wild-type mice occurring in microglia and the newborn granule neurons in the hippocampus. This suggests apoptosis is an underappreciated contributor to ethanols neuropathology at older ages and, translated to human use, occurs far more frequently than previously recognized.

neuroscience↗

bioRxiv2025

Respiratory synchrony and individual differences causally influence dyadic interpersonal coordination

Human interpersonal coordination can yield synchronization at multiple timescales, including behavioral (auditory-motor) and physiological (respiratory and cardiac) levels; yet the causal relationship among these levels is poorly understood. By comparing dyadic melody perception and production, we demonstrate that physiological synchrony is not merely a byproduct of shared perception, as it increases significantly during joint production relative to joint perception or to silence. Perturbing dyads behavior or respiration revealed distinct causal effects: respiratory perturbations impaired both dyadic respiratory and behavioral synchrony, whereas auditory-motor perturbations disrupted only dyadic behavioral synchrony. Individual differences further shaped synchrony: partners who shared similar spontaneous rates achieved better behavioral synchrony, and partners with more similar resting heart rates exhibited stronger cardiac synchrony in joint production. These findings disentangle the relationships among levels of human synchrony, reveal directional entrainment processes between respiratory and behavioral synchrony, and highlight the pivotal role of individual differences in interpersonal coordination.

animal behavior and cognition↗

bioRxiv2025

Miro1 knockout inhibits mouse breast cancer tumorigenesis

Miro1 is a mitochondrial outer membrane protein that regulates mitochondrial and peroxisome trafficking, endoplasmic reticulum (ER) association, and mitophagy. Prior studies suggest a role for Miro1 in cell migration and proliferation in both normal and tumor cells. High Miro1 expression is associated with poor overall survival in breast cancer patients. To investigate the role of Miro1 in breast cancer tumorigenesis and metastasis, we established stable Miro1 knockdown (KD) in MDA-MB-231 human triple-negative breast cancer cells using shRNA. Miro1 KD significantly impaired cell proliferation, migration, and invasion in vitro. When implanted into the mammary fat pad of SCID mice, MDA-MB-231 cells formed tumors, whereas Miro1 KD cells showed markedly reduced tumorigenesis. Additionally, we generated a novel transgenic mouse model with inducible, tissue-specific Miro1 deletion in mammary epithelial cells, alongside polyomavirus middle T-antigen (PyVMT) oncogene activation. In this model, wild-type (WT) mice formed tumors at all mammary gland sites, with frequent lung metastases. However, Miro1-deficient mice failed to develop tumors, while heterozygous mice exhibited reduced tumor growth and metastasis. Additionally, these findings identify Miro1 as a key regulator of breast cancer onset and metastatic potential, positioning it as a potential biomarker and therapeutic target.

cancer biology↗

bioRxiv2024

The KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells

Thioneins are cysteine-rich apoproteins that regulate divalent metal homeostasis by virtue of their metal-chelation properties resulting in the ligand-bound metallothionein state. Previous studies show transient upregulation of the metallothionein (MT) gene cluster as part of a complex transcriptional response to a class of histone demethylase tool compounds targeting human Fe2+ dependent ketoglutarate oxygenases KDM6A (UTX) and KDM6B (JmjD3). The prototypic bioactive KDM6 inhibitor GSK-J4 induces apoptotic cell death in multiple myeloma cells and corresponding transcriptomic profiles are dominated by metal and metabolic stress response signatures, also observed in primary human myeloma cells. Here we investigate the hypothesis that metal-chelation by GSK-J4 provides the means for transport and intracellular release of Zn2+ leading to a metallothionein transcriptomic response signature. Live cell imaging of myeloma cells shows transient increases in intracellular free Zn2+ concentrations when exposed to GSK-J4, consistent with a model of inhibitor-mediated metal transport. Comparisons of GSK-J4 and ZnSO4 treatments in the presence or absence of metal chelators show that both treatment conditions induce different transcription factor repertoires with an overlapping MTF1 transcriptional regulation responsible for metallothionein and metal ion transport regulation. The data provide a possible explanation for the observed metal response upon GSK-J4 inhibition however the relationship with the pro-apoptotic mechanism in myeloma cells requires further investigation.

cell biology↗

bioRxiv2024

Miro1 expression alters global gene expression, ERK1/2 phosphorylation, oxidation, and cell cycle progression

Subcellular mitochondrial positioning in cells is necessary for localized energy and signaling requirements. Mitochondria are strategically trafficked throughout the cytoplasm via the actin cytoskeleton, microtubule motor proteins, and adaptor proteins. Miro1, an outer mitochondrial membrane adaptor protein, is necessary for attachment of mitochondria to microtubule motor proteins for trafficking. Previous work showed when Miro1 is deleted (Miro1-/-) from mouse embryonic fibroblasts (MEFs), the mitochondria become sequestered to the perinuclear space, disrupting subcellular energy and reactive oxygen species gradients. Here, we show that Miro1-/- MEFs grow slower compared to Miro1+/+ and Miro1-/- MEFs stably re-expressing the Myc-Miro1 plasmid. Miro1-/- MEFs have a have a cell cycle defect with decreased percentage of cells in G1 and increased cells in the S phase of the cell cycle. We conducted the first ever RNA sequencing experiment dependent upon Miro1 expression and found differential expression in cell proliferation and migration genes upon deletion of Miro1, including the MAP Kinase signaling pathway. We find that ERK1/2 phosphorylation is elevated both spatially (cytoplasm and nucleus) and temporally following serum stimulation in Miro1-/- MEFs. We investigated the expression levels and oxidation of the Dual Specificity Phosphatases (DUSP1-6), ERK1/2 target phosphatases. We found no differences in DUSP1-6 expression and oxidation under asynchronous and synchronized cells. Lastly, we evaluated the oxidation status of ERK1/2 and found an increase in ERK1/2 oxidation in the Miro1-/- MEFs compared to Miro1+/+ and Myc-Miro1. These data highlight transcriptional control based off Miro1 expression and demonstrate the highly dynamic regulation of ERK1/2 upon deletion of Miro1 that may support the observed cell cycle and proliferation defects.

cell biology↗

bioRxiv2023

Stability of Neural Oscillations Supports Auditory-Motor Synchronization

Previous findings suggest that musical training leads to increased coactivation of auditory and motor brain networks, as well as enhanced auditory-motor synchronization. Less is known about the temporal dynamics of auditory-motor network interactions and how these temporal dynamics are shaped by musical training. The current study applied Recurrence Quantification Analysis, a nonlinear technique for characterizing the temporal dynamics of complex systems, to participants neurophysiological activity recorded via electroencephalography (EEG) during an auditory-motor synchronization task. We investigated changes in neural predictability and stability with musical training, and how these changes were related to synchronization accuracy and consistency. EEG was recorded while musicians and nonmusicians first tapped a familiar melody at a comfortable rate, called Spontaneous Production Rate (SPR). Then participants synchronized their taps with an auditory metronome presented at each participants SPR and at rates 15% and 30% slower than their SPR. EEG-based outcomes of determinism (predictability) and meanline (stability) were compared with behavioral synchronization measures. Musicians synchronized more consistently overall than nonmusicians. Both groups of participants showed decreased synchronization accuracy at slower rates, and higher EEG-based determinism (predictability) at slower rates. Furthermore, neural meanline (stability) measures correlated with synchronization consistency across all participants and stimulus rates; as neural stability increased, so did synchronization consistency. Neural stability may be a general mechanism supporting the maintenance of synchronization across rates, which may improve with musical training.

neuroscience↗

bioRxiv2023

Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization

In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical biopsies has been limited due to their large size, general lower tissue quality and high background autofluorescence. Here we report DART-FISH, a versatile padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections at cellular resolution. We introduced an omni-cell type cytoplasmic stain, dubbed RiboSoma that substantially improves the segmentation of cell bodies. We developed a computational decoding-by-deconvolution workflow to extract gene spots even in the presence of optical crowding. Our enzyme-free isothermal decoding procedure allowed us to image 121 genes in a large section from the human neocortex in less than 10 hours, where we successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. Additionally, we demonstrated the detection of transcripts as short as 461 nucleotides, including neuropeptides and discovered new cortical layer markers. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.

genomics↗

bioRxiv2023

Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two subassemblies; Retriever composed of VPS35L, VPS26C and VPS29, and the CCC complex which contains ten subunits COMMD1-COMMD10 and two coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy and in silico predictions we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilised by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a sixteenth subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.

biochemistry↗

bioRxiv2022

Tango for Two: Modeling Synchronization and Social Interaction in Turn-Taking

Important individual differences are observed in peoples abilities to synchronize their body movements with regular auditory rhythms. We investigate whether synchronizing with a regular auditory cue is affected by each persons spontaneous production rate (SPR) and by hearing a partners synchronization in a social context. Musically trained and untrained participants synchronized their tapping with an auditory cue presented at different rates (their own SPR or their partners SPR) and in a Solo or Joint (turn-taking) condition. Linear and nonlinear oscillator models were fit to participants mean asynchronies (signed timing differences between the cued onsets and taps). In Joint turn-taking, participants synchrony was increased when the auditory signal was cued at the participants own SPR, compared with their partners SPR; in contrast, synchronization did not differ across rates in the Solo condition. Asynchronies in the Joint task became larger as the difference between partners spontaneous rates increased; the increased asynchronies were driven by the faster partner who did not slow down to match the rate of their slower partner. Nonlinear delay-coupled models (with time delay, coupling strength, and intrinsic frequency) outperformed linear models (intrinsic frequency only) in accounting for tappers synchronization adjustments. The nonlinear models coupling value increased for musically trained participants, relative to untrained participants. Overall, these findings suggest that both intrinsic differences in partners spontaneous rates and the social turn-taking context contribute to the range of synchrony in the general population. Delay-coupled models are capable of capturing the wide range of individual differences in auditory-motor synchronization.

neuroscience↗

bioRxiv2022

Single-nucleus RNA-seq of normal-appearing brain regions in relapsing-remitting vs. secondary progressive multiple sclerosis

Multiple sclerosis (MS) is an immune-mediated demyelinating disease that alters central nervous system (CNS) functions. Relapsing-remitting MS (RRMS) is the most common form, which can transform into secondary-progressive MS (SPMS) that is associated with progressive neurodegeneration. Single-nucleus RNA sequencing (snRNA-seq) of MS lesions identified disease-related transcriptomic alterations; however, their relationship to non-lesioned MS brain regions has not been reported and which could identify prodromal or other disease susceptibility signatures. Here, snRNA-seq was used to generate high-quality RRMS vs. SPMS datasets of 33,197 nuclei from 8 normal-appearing MS brains, which revealed divergent cell type-specific changes. Notably, SPMS brains downregulated astrocytic sphingosine kinases (SPHK1/2) - the enzymes required to phosphorylate and activate the MS drug, fingolimod. This reduction was modeled with astrocyte-specific Sphk1/2 null mice in which fingolimod lost activity, supporting functionality of observed transcriptomic changes. These data provide an initial resource for studies of single cells from non-lesioned RRMS and SPMS brains.

neuroscience↗

bioRxiv2021

On the hindlimb biomechanics of the avian take-off leap

Although extant land birds take to the air by leaping, generating the initial take-off velocity primarily from the hindlimbs, the detailed musculoskeletal mechanics remain largely unknown. We therefore simulated in silico the take-off leap of the zebra finch, Taeniopygia guttata, a model species of passerine, a class of bird which includes over half of all extant bird species. A 3D computational musculoskeletal model of the zebra finch hindlimb, comprising of 43 musculotendon units was developed and driven with previously published take-off ground reaction forces and kinematics. Using inverse dynamics, the external moments at the ankle, knee, and hip joints were calculated and contrasted to the cumulative muscle capability to balance these moments. Mean peak external flexion moments at the hip and ankle were 0.55 bodyweight times leg length (BWL) each whilst peak knee extension moments were about half that value (0.29 BWL). Muscles had the capacity to generate 146%, 230%, and 212 % of the mean peak external moments at the hip, knee, and ankle, respectively. Similarities in hindlimb morphology and external loading across passerine species suggest that the effective take-off strategy employed by the zebra finch may be shared across the passerine clade and therefore half of all birds.

bioengineering↗

bioRxiv2021

Mapping enzyme catalysis with metabolomic biosensing

Enzymes are represented across a vast space of protein sequences and structural forms and have activities that far exceed the best chemical catalysts; however, engineering them to have novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe a general and scalable approach for characterizing enzyme activity that uses the metabolism of the host cell as a biosensor by which to infer product formation. Since different products consume different molecules in their synthesis, they perturb host metabolism in unique ways that can be measured by mass spectrometry. This provides a general way by which to sense product formation, to discover unexpected products and map the effects of mutagenesis.

bioengineering↗

bioRxiv2021

Screening by deep sequencing reveals mediators of miRNA tailing in C. elegans

microRNAs are frequently modified by addition of untemplated nucleotides to the 3 end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using C. elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2 - here named GLD-2-related 2 (GLDR-2) - is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median=20.7h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.

molecular biology↗

bioRxiv2020

Novel virus-like particle vaccine encoding the circumsporozoite protein of Plasmodium falciparum is immunogenic and induces functional antibody responses

RTS,S is the leading malaria vaccine in development, but has demonstrated only moderate protective efficacy in clinical trials. RTS,S is a virus-like particle (VLP) that uses the human hepatitis B virus as scaffold to display the malaria sporozoite antigen, circumsporozoite protein (CSP). Particle formation requires fourfold excess scaffold antigen, and as a result, CSP represents only a small portion of the final vaccine construct. Alternative VLP or nanoparticle platforms that reduce the amount of scaffold antigen and increase the amount of the target CSP antigen present in particles may enhance vaccine immunogenicity and efficacy. Here, we describe the production and characterization of a novel VLP that uses the small surface antigen (dS) of duck hepatitis B virus to display CSP. The CSP-dS fusion protein successfully formed VLPs without the need for excess scaffold antigen, and thus CSP represented a larger portion of the vaccine construct. Importantly, this is the first report of a dS-based vaccine that formed particles without excess scaffold protein. CSP-dS formed large particles approximately 31-74 nm in size and were confirmed to display CSP on the surface. The CSP-dS VLP was highly immunogenic in mice and induced antibodies to multiple regions of CSP, even when administered at a lower vaccine dosage. Vaccine-induced antibodies demonstrated functional activity, including the ability to interact with complement and Fc{gamma}-receptors, both previously identified as important in malaria immunity. Our novel platform to produce VLPs without excess scaffold protein has wide implications for the future development of innovative vaccines for malaria and other infectious diseases.

immunology↗