Biology subjects

Zhuo, Y.

Publications and source records attributed to Zhuo, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Repetitive transcranial magnetic stimulation targeting motor cortical region induces cell-type-specific transcriptional reprogramming and behavioral recovery in non-human primate model of Rett syndrome

Rett syndrome (RTT), a severe neurodevelopmental disorder caused by mutations in the MECP2 gene, currently lacks effective treatments. The motor cortex is a pivotal hub in RTT and autism spectrum disorders, and its impairments contribute to motor, social, and cognitive deficits. Here we examined the effects of repetitive transcranial magnetic stimulation (rTMS) targeting motor area in non-human primate of RTT (MECP2-mutant monkey) and investigated neuromolecular basis underlying therapeutic effects. We identified a new treatment target, ventral premotor cortex (PMv), for RTT and found that following a 20-day rTMS course, several behavioral and functional connectivity measures showed directional changes. Neuroimaging analyses confirmed that rTMS induced reorganization of large-scale functional connectivity with enhanced functional integration between the somatomotor and the salience networks and normalized coupling between the motor cortex and both the thalamus and the anterior cingulate cortex. Notably, single-nucleus RNA sequencing revealed that rTMS triggered cell-type-specific transcriptional reprogramming: it rescued pathological hyperactivity of excitatory neurons by restoring the expression and regulatory networks of immediate early genes (e.g., FOS, EGR1) and corrected dysregulated intercellular signaling (e.g., NRG, WNT). These findings indicate that targeting motor cortical areas with brain stimulation may treat RTT, which warrants further clinical validation.

neuroscience↗

bioRxiv2026

Cooperative Control of Arrestin Activation By Membrane Lipids And Phosphorylation Barcodes

Arrestins regulate G protein-coupled receptor (GPCR) signaling by binding phosphorylated receptors embedded in lipid bilayers, yet how receptor phosphorylation and membrane composition cooperate to control arrestin activation remains unclear. Here, we reconstitute this interplay using N-terminally palmitoylated phosphopeptides tethered to nanodiscs of defined lipid composition and quantitatively measure arrestin-2 (Arr2) activation and membrane engagement. We find that both receptor phosphorylation and the lipid environment are essential for robust Arr2 activation, with phosphoinositides (PIPs) and other anionic lipids facilitating Arr2 activation and membrane association through distinct mechanisms. Systematic profiling of phosphorylation barcodes derived from atypical chemokine receptor 3 (ACKR3) and vasopressin receptor 2 (V2R) identifies phospho-motifs that potently activate Arr2. Moreover, the position of these motifs relative to the membrane determines Arr2 engagement, supporting a model of regional phosphorylation barcodes. Genome-wide motif analysis further links the phosphorylation barcode to predicted arrestin coupling strength and classification into Class A or Class B GPCRs. Finally, lipidated phosphopeptides inhibit GPCR-Arr2 interactions in live cells and enable structural characterization of Arr2-phosphopeptide complexes by cryo-electron microscopy, establishing a membrane-integrated framework for decoding arrestin response.

biochemistry↗

bioRxiv2025

Label-free Imaging of the Reversible Rhodopsin Dynamics in a Living Eye

Vision begins with photoisomerization of a retinal, triggering further conformational changes, followed by a phototransduction cascade in photoreceptors. Microelectrode recordings revealed an early receptor potential (ERP) signal accompanying these conformational transitions. Such techniques are invasive, obscured by multiple electrical processes in the retina, and in rods, they are limited to the contribution of a small fraction of rhodopsin embedded in the nascent disc membrane and plasma membrane. Recent advances in phase-sensitive OCT (Optoretinography, ORG) enable detection of nanoscale deformations of retinal cells associated with physiological processes. However, in previous ORG studies, focused primarily on cones, cell deformation related to ERP was largely obscured by osmotic swelling and long stimuli did not resolve the isomerization dynamics of photopigments. Here, we demonstrate a very robust electromechanical signature of photoisomerization in rods at microsecond-scale temporal resolution. Green flash induces sub-millisecond-fast contraction of the outer segments by hundreds of nanometers, while subsequent UV flash reverts the activated molecules, producing an opposite response of a similar magnitude. This approach surpasses the sensitivity of electrical methods by integrating the response across all the discs in rod outer segments. Noninvasive and label-free imaging of the rhodopsin dynamics in a living eye opens the door to fundamental studies of visual transduction and to differential diagnosis of the photoreceptors dysfunction.

bioengineering↗

bioRxiv2025

Distinct Membrane Binding Properties of the Two Non-visual Arrestins

Membrane interactions play a crucial role in regulating arrestin activation and its binding to phosphorylated G protein-coupled receptors (GPCRs). Here, we utilize in vitro biophysical approaches and cell-based fluorescence intensity fluctuation analysis to systematically compare the membrane-binding properties of the two highly conserved arrestin subtypes, arrestin-2 and arrestin-3, under basal and stimulated conditions. Our findings reveal that arrestin-2 selectively engages the PI(4,5)P2-containing nanodiscs via its C-edge, whereas arrestin-3 primarily utilizes its finger loop to interact with negatively charged lipids. Notably, while the lipid bilayer alone does not activate arrestin, it synergistically enhances arrestin-2/3 activation in conjunction with a phosphorylated GPCR C-tail. Additionally, the spacing between receptor phosphorylation sites and the lipid bilayer modulates arrestin-membrane assembly. Live cell tracking further demonstrates that arrestin-2 and arrestin-3 exhibit distinct plasma membrane dissociation dynamics. These findings provide novel insights into the mechanisms governing arrestin activation and its functional interplay with membranes.

biochemistry↗

bioRxiv2025

Accumbal acetylcholine signals associative salience

Learning is driven by prediction errors, which determine what is learned, and salience, which controls the learning rate. Dopamine in the nucleus accumbens correlates with prediction errors, but salience mechanisms are less clear. We hypothesized that acetylcholine acts as a salience signal, as it regulates dopamine-induced plasticity. To test this, we recorded acetylcholine and dopamine dynamics in rats across three learning tasks. Our findings reveal a characteristic pattern of evolving neuromodulator responses during learning. First, indiscriminate cholinergic dips appeared, then dopamine responses differentiated based on predicted value, followed by the cholinergic dips also varying by value. Stable performance required this full pattern, and acetylcholine dips could be decoupled from value by changing reward contingencies. The observed acetylcholine dynamics fit an associative salience term predicted by hybrid attentional associative learning models, suggesting that dopamine and acetylcholine act complementarily to determine the content and rate of learning. TeaserAcetylcholine shapes learning rate by signaling the salience of predictive cues.

neuroscience↗

bioRxiv2024

In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicals in vivo simultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+ indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.

neuroscience↗

bioRxiv2024

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics

Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.

genomics↗

bioRxiv2024

Retinal thermometry in-vivo using phase-sensitive optical coherence tomography

Controlling the tissue temperature rise during retinal laser therapy is essential for predictable outcomes, especially at non-damaging settings. We demonstrate a method for determining the temperature rise in the retina using phase-resolved optical coherence tomography (pOCT) in vivo. Measurements based on the thermally induced optical path length changes ({Delta}OPL) in the retina during a 10-ms laser pulse allow detection of the temperature rise with a precision less than 1 {degrees}C, which is sufficient for calibration of the laser power for patient-specific non-damaging therapy. We observed a significant difference in confinement of the retinal deformations between the normal and the degenerate retina: in wild-type rats, thermal deformations are localized between the retinal pigment epithelium (RPE) and the photoreceptors inner segments (IS), as opposed to a deep penetration of the deformations into the inner retinal layers in the degenerate retina. This implies the presence of a structural component within healthy photoreceptors that dampens the tissue expansion induced by the laser heating of the RPE and pigmented choroid. We hypothesize that the thin and soft cilium connecting the inner and outer segments (IS, OS) of photoreceptors may absorb the deformations of the OS and thereby preclude the tissue expansion further inward. Striking difference in the confinement of the retinal deformations induced by a laser pulse in healthy and degenerate retina may be used as a biomechanical diagnostic tool for the characterization of photoreceptor degeneration.

bioengineering↗

bioRxiv2024

Dopamine and acetylcholine correlations in the nucleus accumbens depend on behavioral task states

Dopamine in the nucleus accumbens ramps up as animals approach desired goals. These ramps have received intense scrutiny because they seem to violate long-held hypotheses on dopamine function. Furthermore, it has been proposed that they are driven by local acetylcholine release, i.e., that they are mechanistically separate from dopamine signals related to reward prediction errors. Here, we tested this hypothesis by simultaneously recording accumbal dopamine and acetylcholine signals in rats executing a task involving motivated approach. Contrary to recent reports, we found that dopamine ramps were not coincidental with changes in acetylcholine. Instead, we found that acetylcholine could be positively, negatively, or uncorrelated with dopamine depending on whether the task phase was determined by a salient cue, reward prediction error, or active approach, respectively. Our results suggest that accumbal dopamine and acetylcholine are largely independent but may combine to engage different postsynaptic mechanisms depending on the behavioral task states.

neuroscience↗

bioRxiv2024

The asymmetric transfers of visual perceptual learning determined by the stability of geometrical invariants

We quickly and accurately recognize the dynamic world by extracting invariances from highly variable scenes, a process can be continuously optimized through visual perceptual learning (VPL). While it is widely accepted that the visual system prioritizes the perception of more stable invariants, the influence of the structural stability of invariants on VPL remains largely unknown. In this study, we designed three geometrical invariants with varying levels of stability for VPL: projective (e.g., collinearity), affine (e.g., parallelism), and Euclidean (e.g., orientation) invariants, following the Kleins Erlangen program. We found that learning to discriminate low-stability invariant transferred asymmetrically to those with higher stability, and that training on high-stability invariants enabled location transfer. To explore learning-associated plasticity in the visual hierarchy, we trained deep neural networks (DNNs) to model this learning procedure. We reproduced the asymmetric transfer between different invariants in DNN simulations and found that the distribution and time course of plasticity in DNNs suggested a neural mechanism similar to the reverse hierarchical theory (RHT), yet distinct in that invariant stability--not task difficulty or precision--emerged as the key determinant of learning and generalization. We propose that VPL for different invariants follows the Klein hierarchy of geometries, beginning with the extraction of high-stability invariants in higher-level visual areas, then recruiting lower-level areas for the further optimization needed to discriminate less stable invariants.

neuroscience↗

bioRxiv2023

Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior

Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array and imaging approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits.

neuroscience↗

bioRxiv2023

Improved dual-color GRAB sensors for monitoring dopaminergic activity in vivo

Dopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a vast network of dopaminergic projections. To fully dissect the spatiotemporal dynamics of DA release in both dense and sparsely innervated brain regions, we developed a series of green and red fluorescent GPCR activation-based DA (GRABDA) sensors using a variety of DA receptor subtypes. These sensors have high sensitivity, selectivity, and signal-to-noise properties with subsecond response kinetics and the ability to detect a wide range of DA concentrations. We then used these sensors in freely moving mice to measure both optogenetically evoked and behaviorally relevant DA release while measuring neurochemical signaling in the nucleus accumbens, amygdala, and cortex. Using these sensors, we also detected spatially resolved heterogeneous cortical DA release in mice performing various behaviors. These next-generation GRABDA sensors provide a robust set of tools for imaging dopaminergic activity under a variety of physiological and pathological conditions.

neuroscience↗

bioRxiv2023

An Excitatory Projection from the Basal Forebrain to the Ventral Tegmental Area Underlying Anorexia-like Phenotypes

Adaptation to potential threat cues in feeding regulation is key for animal survival. Maladaptation in balancing internal energy needs and external threat cues may result in eating disorders. However, brain mechanisms underlying such maladaptation remain elusive. Here, we identified that the basal forebrain (BF) sends glutamatergic projections to glutamatergic neurons in the ventral tegmental area (VTA). Glutamatergic neurons in both the BF and the VTA displayed correlated responses to various external stressors. Notably, in vivo manipulation of BF terminals in the VTA revealed that the glutamatergic BFVTA circuit reduces appetite, increases locomotion, and elicits avoidance. In consistence, activation of VTA glutamatergic neurons reduced body weight, blunted food motivation, and caused hyperactivity with behavioral signs of anxiety, all hallmarks of typical anorexia phenotypes. Importantly, activation of BF glutamatergic terminals in the VTA reduced dopamine release in the nucleus accumbens (NAc). Collectively, our results point to overactivation of the glutamatergic BFVTA circuit as a potential cause of anorexia-like phenotypes involving reduced dopamine release.

neuroscience↗

bioRxiv2023

Hepatic conversion of acetyl-CoA to acetate plays crucial roles in energy stresses

Accumulating evidences indicate that acetate is increased in energy stresses such as diabetes mellitus and prolonged starvation. However, it is largely unknown how and where acetate is produced and what is its biological significance. We observed overproduction of acetate in an amount comparable to ketone bodies in patients and mice with diabetes or starvation. Mechanistically, ACOT 12&8 are dramatically upregulated in liver to convert FFA-derived acetyl-CoA to acetate and CoA. This conversion not only provides large amount of acetate which fuels brain preferentially rather than muscle, but also recycles CoA which is required for sustained fatty acid oxidation and ketogenesis. Taken together, we suggest that acetate is an emerging novel "ketone body" and may be used as a parameter to evaluate the progression of energy stress in the future.

biochemistry↗

bioRxiv2023

A multidimensional atlas of human glioblastoma organoids reveals highly coordinated molecular networks and effective drugs

Recent advances in the genomics of glioblastoma (GBM) led to the introduction of molecular neuropathology but failed to translate into treatment improvement. This is largely attributed to the genetic and phenotypic heterogeneity of GBM, which are considered the major obstacle to GBM therapy. Here, we use advanced human GBM organoid (LEGO: Laboratory Engineered Glioblastoma Organoid) and provide an unprecedented comprehensive characterization of LEGO models using single-cell transcriptome, DNA methylome, metabolome, lipidome, proteome, and phospho-proteome analysis. We discovered that genetic heterogeneity dictates functional heterogeneity across molecular layers and demonstrates that NF1 mutation drives mesenchymal signature. Most importantly, we found that glycerol lipid reprogramming is a hallmark of GBM, and several targets and drugs were discovered along this line. We also provide a genotype-based drug reference map using LEGO-based drug screen. This study provides novel human GBM models and a research path toward effective GBM therapy.

cancer biology↗

bioRxiv2022

A toolkit of highly selective and sensitive genetically encoded neuropeptide sensors

Neuropeptides are key signaling molecules in the endocrine and nervous systems that regulate many critical physiological processes, including energy balance, sleep and circadian rhythms, stress, and social behaviors. Understanding the functions of neuropeptides in vivo requires the ability to monitor their dynamics with high specificity, sensitivity, and spatiotemporal resolution; however, this has been hindered by the lack of direct, sensitive and non-invasive tools. Here, we developed a series of GRAB (G protein-coupled receptor activation-based) sensors for detecting somatostatin (SST), cholecystokinin (CCK), corticotropin-releasing factor (CRF), neuropeptide Y (NPY), neurotensin (NTS), and vasoactive intestinal peptide (VIP). These fluorescent sensors utilize the corresponding GPCRs as the neuropeptide-sensing module with the insertion of a circular-permutated GFP as the optical reporter. This design detects the binding of specific neuropeptides at nanomolar concentration with a robust increase in fluorescence. We used these GRAB neuropeptide sensors to measure the spatiotemporal dynamics of endogenous SST release in isolated pancreatic islets and to detect the release of both CCK and CRF in acute brain slices. Moreover, we detect endogenous CRF release induced by stressful experiences in vivo using fiber photometry and 2-photon imaging in mice. Together, these new sensors establish a robust toolkit for studying the release, function, and regulation of neuropeptides under both physiological and pathophysiological conditions.

neuroscience↗

bioRxiv2021

Interferometric imaging of thermal expansion for temperature control in retinal laser therapy

Precise control of the temperature rise is a prerequisite for proper photothermal therapy. In retinal laser therapy, the heat deposition is primarily governed by the melanin concentration, which can significantly vary across the retina and from patient to patient. In this work, we present a method for determining the optical and thermal properties of layered materials, directly applicable to the retina, using low-energy laser heating and phase-resolved optical coherence tomography (pOCT). The method is demonstrated on a polymer-based tissue phantom heated with a laser pulse focused onto an absorbing layer buried below the phantoms surface. Using a line-scan spectral-domain pOCT, optical path length changes induced by the thermal expansion were extracted from sequential B-scans. The material properties were then determined by matching the optical path length changes to a thermo-mechanical model developed for fast computation. This method determined the absorption coefficient with a precision of 2.5% and the temperature rise with a precision of about 0.2{degrees}C from a single laser exposure, while the peak did not exceed 8{degrees}C during 1 ms pulse, which is well within the tissue safety range and significantly more precise than other methods.

bioengineering↗

bioRxiv2020

New and improved GRAB fluorescent sensors for monitoring dopaminergic activity in vivo

The monoamine neuromodulator dopamine (DA) plays a critical role in the brain, and the ability to directly measure dopaminergic activity is essential for understanding its physiological functions. We therefore developed the first red fluorescent GPCR-activation-based DA (GRABDA) sensors and optimized versions of green fluorescent GRABDA sensors following our previous studies. In response to extracellular DA, both the red and green GRABDA sensors have a large increase in fluorescence ({Delta}F/F0 values of 150% and 340%, respectively), with subcellular resolution, subsecond kinetics, and nanomolar to submicromolar affinity. Moreover, both the red and green GRABDA sensors readily resolve evoked DA release in mouse brain slices, detect compartmental DA release in live flies with single-cell resolution, and report optogenetically elicited nigrostriatal DA release as well as mesoaccumbens dopaminergic activity during sexual behavior in freely behaving mice. Importantly, co-expressing red GRABDA with either green GRABDA or the calcium indicator GCaMP6s provides a robust tool for simultaneously tracking neuronal activity and dopaminergic signaling in distinct circuits in vivo.

neuroscience↗