Biology subjects

Zhao, Z.

Publications and source records attributed to Zhao, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

In Utero MRI of Radial Glial Fibers Highlights Their Role in Modulating Fetal Cortical Folding

The process of cortical folding is fundamental to early human brain development. While the differential growth of the cortical layers is a known driver, the biomechanical contribution of key cellular microstructures remains unclear, and there is a lack of direct in vivo markers of cortical microstructures for time-resolved observations. Using a multimodal approach combining in utero and ex vivo fetal brain MRI, histology, and computational mechanical simulation, we investigated whether developmental reorganization of cortical radial microstructures, particularly the radial glial cell (RGC)-associated scaffold, is linked to cortical folding and may modulate its mechanical progression. We characterized this radial organization noninvasively using diffusion MRI-based radial fiber density (FDrad). ex vivo fetal brain MRI and histology supported that regional variations in FDrad were strongly associated with vimentin-labelled radial architecture. Our in utero MRI data revealed closely coordinated developmental changes in cortical FDrad and curvature, with their regional timings and spatial patterns significantly coupled across the cortex. Longitudinal in utero MRI data further supported the synchronized within-individual co-development of FDrad and curvature. Furthermore, biomechanical simulations showed that reducing radial reinforcement modulated differential-growth-driven buckling, producing earlier folding and a greater cortical curvature under otherwise matched model conditions. Collectively, this study introduces FDrad as a noninvasive in utero MRI measure sensitive to radial glial fibers. By integrating spatial, temporal, histological, and computational evidence, our findings suggested a model in which developmental disassembly of the radial scaffold may modulate the mechanical response of the fetal cortex to differential growth, thereby contributing to cortical folding.

neuroscience↗

bioRxiv2026

Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

Current Alzheimer's disease (AD) neuropathological metrics, including Thal phasing, and Braak staging, often do not accurately predict cognitive status: many cognitively resilient individuals have substantial pathological burdens, whereas some patients with dementia show minimal classical AD pathology. Here, we addressed this discrepancy by investigating the molecular mechanisms underlying AD dementia using single-nucleus RNA-sequencing and single-nucleus multiome datasets. To eliminate cross-modality scaling artifacts and compositional biases inherent in neurodegenerative tissues, we normalized the datasets using our novel framework, bypassing scaling issues of conventional methods that may obscure critical biological signals of interest. We identified neuron-specific suppression of nuclear-encoded mitochondrial genes and their upstream mitochondrial biogenesis signaling (MBS) as primary drivers of clinical dementia. By integrating multi-omic quantitative trait loci, genome-wide association studies, and epigenomic profiles, we delineated genetic and epigenetic changes underlying MBS suppression. This study provides a systematic genomic framework for understanding the mechanisms of cognitive resilience.

bioinformatics↗

bioRxiv2026

A Cell-Autonomous Cold Sensor Promotes Lipolysis Through Phase Separation

Temperature is a fundamental determinant of mammalian metabolism. The canonical cold-adaptation pathway involves cold sensing by peripheral sensory neurons, which activate sympathetic outflow, {beta}-adrenergic signaling, and lipolysis in adipose tissue. In contrast, we report here a cell-intrinsic mechanism by which physiologically relevant cooling temperatures (27-31 oC) enhance lipolysis in subcutaneous adipose tissue. Mechanistically, cooling drives liquid-liquid phase separation (LLPS) of perilipin 1 (PLIN1), the dominant lipid droplet coat protein, promoting its condensation and the local recruitment of PKA to the droplet surface. This spatial reorganization selectively amplified PKA-mediated perilipin 1 phosphorylation, CGI-58 release, and ATGL-dependent lipolysis. The process depends on the intrinsically disordered region (IDR) of perilipin1, where four aromatic residues, conserved in endotherms but not in ectotherms, are required for cooling-induced LLPS and lipolysis in vivo. Notably, targeted delivery of an LLPS-competent perilipin 1 variant to the inguinal adipose tissue of mice enhanced local lipolysis and reduced depot mass. Together, these findings uncover a cell-intrinsic thermosensitive mechanism that can tune lipolytic responsiveness, offering a possible strategy for targeted depot-selective fat reduction.

cell biology↗

bioRxiv2026

Stratified Palliobulbar and Midbrain Circuits Control the Timing and Acoustics of Learned Vocalizations

In mammals and birds, production of learned vocalizations depends on prominent projections from the pallium to the brainstem. Although pallial and cortical coding mechanisms for speech and birdsong are becoming increasingly clear, understanding how palliobulbar projections supervise brainstem circuits has remained challenging. Here we identify the functional organization of pallial and brainstem control of learned song in the zebra finch, a songbird in which genetic control of neuronal pathways is now feasible. We find that palliobulbar projections to the medulla and midbrain periaqueductal gray (PAG) arise from largely non-overlapping neuronal populations. Genetic silencing of these pathways reveals that projections to the medulla control the learned acoustic content defining individual song syllables, while projections to the PAG control the respiratory timing needed to sequence syllables. Using large-scale neuronal recordings, we find that song and innate calls are uniquely encoded within the PAG. Dual recordings from the palliobulbar neurons and the PAG suggest hierarchical encoding of expiratory and inspiratory events along this pathway. Lastly, genetic silencing reveals that PAG projections to the medulla are needed for birds to generate learned song and innate calls. Thus, stratified palliobulbar pathways control respiratory-timing and acoustics for song. Yet, without the PAG, they are insufficient to produce any vocalizations.

neuroscience↗

bioRxiv2026

Single-cell analysis of West Nile virus infection in brain organoids identified a serine synthesis enzyme as a determinant of viral neural tropism and a druggable antiviral target

The cellular and molecular determinants of human neuroinvasive West Nile virus (WNV) disease are currently poorly defined. Previous studies of WNV neural infection relied on rodent models and immortalised cell lines that diverge from human brain tissue. Herein, we established a reproducible human cerebral organoid model of WNV infection and profiled it by virus-inclusive single-cell RNA sequencing (scRNA-Seq) to obtain an understanding of WNV-host interactions in the context of human neural tissue. We found that WNV showed preferential tropism to progenitor cells, immature neurons, and astrocytes, while the mature neurons were largely resistant to infection. Astrocytes were identified as the principal source of interferon (IFN) and the main hub of IFN-signalling, whereas mature neurons expressed little viral RNA-sensing machinery or STAT1 and responded weakly to infection and to IFN. The differential gene expression analysis between WNV-permissive and nonpermissive cells demonstrated that virus-susceptible cells had high baseline expression of the serine synthesis and one-carbon metabolism genes PHGDH, SHMT2, and MTHFD2, which were not induced by infection. RNA-interference and pharmacological inhibition of phosphoglycerate dehydrogenase (PHGDH) restricted WNV replication, confirming the requirement of this gene for WNV infection. In addition, the FDA-approved drug disulfiram, known to inhibit PHGDH, also reduced viral replication in neural progenitors and cerebral organoids. Overall, these results provide the first comprehensive single-cell-level characterisation of WNV neural infection in human neural tissue. They identify de novo serine synthesis as a metabolic dependency of WNV in human neural cells that can be targeted as a host-directed antiviral therapy.

microbiology↗

bioRxiv2026

Parrots imitate song and dance with mixed vocal-gestural neural signals

Humans shrug when saying "I don't know" and nod when saying "yes," yet it remains unclear how the brain coordinates vocal and gestural motor systems for learned, multimodal communication. Here we find that budgerigar parrots precisely imitate the fine temporal alignment between song and affiliative headbob gestures. Distinct colonies developed unique vocal-gestural motifs, which reorganized into new shared forms following social re-pairing. Neural recordings from the central nucleus of the anterior arcopallium (AAC), the cortical output of the parrot song system, revealed intermixed representations of vocalizations and head kinematics, including mixed selectivity at the level of single neurons. These findings show that socially learned multimodal communication is implemented by the joint representation of vocal and gestural motor signals within single neurons, revealing neural mechanisms that may extend to frontal cortical regions controlling speech and gesture in humans.

neuroscience↗

bioRxiv2026

A sparse neural code for acoustic targets enables speech-like vocal flexibility in parrots

English speech flexibly recombines 44 phonemes into >20,000 words and limitless phrases. Here we identify a novel neural code supporting combinatorial vocal control in budgerigar parrots. Deep learning based acoustic analyses show that both English imitated and natural warble songs are composed of subsyllabic acoustic elements that are flexibly reused across acoustic contexts, analogous to phoneme reuse in words. Such reuse poses a scaling problem for songbird-inspired timing-based codes, which require distinct neural sequences for distinct syllables even when syllables share acoustic components. We identified neurons in the parrot frontal cortical nucleus MO that exhibit sparse bursts locked to reused acoustic elements independent of syllable identity, timing, or surrounding acoustic context. These results provide the first evidence for a sparse, acoustically-grounded vocal motor code that can be flexibly reused to assemble a large and combinatorial vocal repertoire.

neuroscience↗

bioRxiv2026

Dose-additive and dose-dependent fetal testis toxicity of a nine-phthalate mixture in the rat

Phthalates (ortho-phthalic acid diesters) are used in a variety of manufacturing processes, particularly as non-covalent plasticizers in flexible polyvinyl chloride. Phthalates are male reproductive toxicants that disrupt the development of the fetal testis, resulting in malformed seminiferous cords, multinucleated germ cells (MNGs), and decreased testosterone production. We previously reported that MNGs were a sensitive, dose-dependent marker of dipentyl phthalate (DPEP) germ cell toxicity. To test whether germ cell effects of phthalates are dose-additive, we measured the induction of MNGs by a phthalate mixture. We treated timed pregnant Sprague Dawley rats with an equipotent mixture of nine phthalates, spanning a two-log dose range, from GD 17-21. We found that the phthalate mixture effects on morphogenesis of the testis, assessed through histological analysis of MNGs and seminiferous cord diameter were dose-additive. Consistent with prior results, we also found that the testosterone-reducing effect of the phthalate mixture was dose-additive and dose-dependent. Induction of MNGs had the lowest effective dose of any endpoint that we measured, with a benchmark dose (BMD10) of 9.402 (6.093, 13.13) mg ({sum} all phthalates)/kg/d, which is equivalent to a BMD10 of 3.517 (2.275, 4.919) mg DPEP/kg/d, based on relative potency factors. Quantitative analysis of phthalate metabolites in dam serum showed that the metabolites were present in approximately the same relative concentrations as the parent compounds in the dosing mixture, but with lower levels of monocyclohexyl phthalate and monobenzyl phthalate. Proteomic and spatial transcriptomic analyses showed significant decreases in expression of Leydig cell genes and proteins involved in steroid hormone biosynthesis, as well as enrichment of proteins related to metabolism of lipids and amino acids. Proteomic BMD analysis produced a lowest BMDmedian of 2.156 (0.204, 27.830) mg ({sum} all phthalates)/kg/d, which was within a 4.36-fold margin of the lowest apical endpoint BMD.

pharmacology and toxicology↗

bioRxiv2026

Neural Representations of Visual Anagrams in Macaque Inferotemporal Cortex

Visual recognition requires stable representations of object identity despite large changes in the retinal image. Yet this stability must be selective: some transformations change not only how an image looks, but also what object it appears to depict. Visual anagrams highlight this challenge: a single image can resemble two different objects at different orientations, such as an elephant and a rabbit. Here, we asked how macaque inferotemporal (IT) cortex represents such transformations. We recorded large neuronal populations while presenting visual anagrams and unambiguous exemplars of their two interpretations across rotations. Neurons preferring one exemplar tended to prefer anagram orientations supporting the corresponding interpretation. At each of the two interpretation-relevant canonical angles, population responses more closely resembled those to the matching exemplar than those to the nonmatching exemplar. This matching advantage persisted when both exemplars were presented at the alternative canonical angle. Decoders trained exclusively on exemplars across rotations also tracked the shifts in anagram representations. Visual models showed anagram-exemplar alignment as well, with stronger alignment in models with greater relative shape preference. These findings suggest that transformation tolerance in IT is sensitive to what an image appears to depict, while relative shape preference is associated with similar representational organization in visual models.

neuroscience↗

bioRxiv2026

Glutathione Protects Hematopoietic Stem Cells from Proteotoxic Stress

Glutathione is a redox buffer, best known for preventing oxidative stress and ferroptosis, but rarely studied in stem cells. We studied glutathione function in hematopoietic stem cells (HSCs) by deleting the glutamate-cysteine ligase catalytic subunit (GCLC), which synthesizes glutathione, or glutathione peroxidase 4 (GPX4), which employs glutathione to prevent ferroptosis. GCLC deficiency eliminated glutathione from hematopoietic cells, severely impairing HSC function and hematopoiesis. In contrast, GPX4 deficiency did not affect HSC function and had little effect on hematopoiesis, even after vitamin E depletion, suggesting glutathione has ferroptosis-independent functions in HSCs. Consistent with this, GCLC deficiency increased reactive oxygen species levels in hematopoietic cells. But treatment with antioxidants or ferroptosis inhibitors gave little or no rescue of HSC function despite reducing ROS levels. Rather, GCLC-deficient, but not GPX4-deficient, HSCs exhibited unfolded protein accumulation, proteostatic stress, and cell death marked by elevated p53 levels and Annexin V staining. Deficiency for p53 prolonged the function of GCLC-deficient HSCs after transplantation. Glutathione is thus necessary in HSCs for proteostasis but may be dispensable for ferroptosis inhibition in vivo.

cell biology↗

bioRxiv2026

TRIM21 licenses pancreatic acinar fate by modulating BiP phase state through VCP-dependent retrotranslocation

The endoplasmic reticulum (ER) chaperone BiP/GRP78 sits at the center of the proteostasis network, coordinating unfolded protein response (UPR) signaling and supporting oncogenic programs of plasticity, metastasis, immune evasion, and chemoresistance. While BiP undergoes liquid-liquid phase separation in vitro, whether mammalian cells dynamically tune this physicochemical behavior to prevent functional exhaustion or pathological condensation under sustained ER stress has remained unclear. Here, we identify the E3 ubiquitin ligase TRIM21 as a phase-state regulator that suppresses BiP's liquid-to-solid phase separation, clearing, and preventing insoluble aggregates-thereby controlling BiP's localization and availability to sustain the adaptive UPR under ER stress. We found that during ER stress, BiP is prone to liquid-to-solid phase separation, a transition that renders the chaperone dysfunctional. TRIM21 is recruited to BiP, where it directly polyubiquitinates BiP at specific K547/553/554/556 sites with K6-, K27-, K33-, and K63-linked chains; VCP recognizes these marks and extracts BiP from the ER lumen via ER-associated degradation (ERAD), coupling ubiquitin tagging to retrotranslocation. This preserves chaperone availability and sustains adaptive UPR-a homeostatic mechanism broadly relevant to UPR-driven diseases. In vivo, genetic ablation of Trim21 in KrasG12D/+; Pdx1Cre/+ mice triggers aberrant BiP solidification while curtailing acinar-to-ductal transdifferentiation and tumorigenesis; notably, TRIM21 co-localizes with BiP condensates in pre-malignant human pancreatic lesions, underscoring the clinical relevance of this regulatory axis. Our findings define the TRIM21-BiP axis as a phase-control system at the interface of proteostasis and stress adaptation, offering a new framework with translational potential.

cell biology↗

bioRxiv2026

Stem cell factor acts locally in the bone marrow to promote stem and progenitor cell maintenance

Stem cell factor (SCF) from Leptin Receptor-expressing (LepR+) mesenchymal stromal cells and endothelial cells is required for hematopoietic stem and progenitor cell maintenance in bone marrow. Consistent with this, Scf is highly expressed by LepR+ cells and at lower levels by endothelial cells in bone marrow. However, endothelial cells outside the bone marrow produce circulating SCF, raising the question of whether the SCF that promotes stem and progenitor cell maintenance is produced inside or outside bone marrow. We found that Scf deletion in spleen and liver endothelial cells reduces SCF levels in the blood without affecting stem or progenitor numbers in the bone marrow. Moreover, deletion of Scf from mesenchymal cells in the long bones, but not vertebrae, of Prx1Cre; Scf fl/fl mice depletes stem and progenitor cells in long bones but not vertebrae. SCF thus acts locally within the bones in which it is made to promote stem and progenitor cell maintenance.

cell biology↗

bioRxiv2026

Loss of TCA cycle turning promotes stem cell function

The citric acid cycle (TCA cycle) is the common terminal pathway for the oxidation of all nutrients. Citrate oxidation to oxaloacetate produces CO2, and citrate synthase (CS) uses nutrient-derived acetyl groups to regenerate citrate and fuel cycle turning. However, the essentiality of cycle fueling and turning in vivo remains unclear. Here we use hematopoiesis, the most proliferative system in the body, as a model to show that, contrary to common assumptions, TCA cycle turning is dispensable for respiration, survival, and proliferation of stem and progenitor cells in vivo, and its loss promotes stem cell function. Hematopoietic-specific Cs deletion in adult mice blocked citrate cycling without reducing the frequency of hematopoietic stem (HSC) and progenitor cells. HSCs and progenitor cells adapted to TCA cycle loss by markedly increasing nutrient consumption and biosynthesis. Disruption of cycle turning increased HSC regeneration, myeloid progenitor proliferation, and myelopoiesis in vivo. HSCs without a turning TCA cycle outcompeted wild-type HSCs within the same environment. The effect of CS deletion on HSC function was not phenocopied by genetic ablation of cytosolic citrate use and was rescued by ablation of glutamine use in biosynthesis. Therefore, TCA cycle turning restrains nutrient uptake, biosynthesis, cell proliferation, and stem cell function. These results suggest an explanation for the reduction in cycle activity observed in many normal proliferating cells and cancer cells.

biochemistry↗

bioRxiv2026

Loss of TDP-43 function drives cryptic circular RNAs in neurodegenerative diseases

TAR DNA-binding protein 43 (TDP-43) is a key pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and a critical regulator of RNA splicing. While loss of TDP-43 induces aberrant splicing in linear transcripts, its impact on circular RNA (circRNA) biogenesis remains unexplored. Here, we show that TDP-43 depletion in human neurons induces widespread circRNA changes, especially upregulation of a distinct class of cryptic circRNAs that arise specifically upon loss of TDP-43. Some of these cryptic circRNAs incorporate cryptic exons derived from intronic sequences. Notably, these cryptic circRNAs exhibit greater stability than their corresponding linear RNA isoforms and accumulate progressively in neurons. Moreover, cryptic circRNAs are elevated in postmortem brain tissues from ALS, FTD and Alzheimer's disease (AD) patients. These findings reveal a previously unrecognized role for TDP-43 in repressing cryptic circRNA formation and establish these circRNAs as stable molecular signatures of TDP-43 dysfunction.

neuroscience↗

bioRxiv2026

Designed nutrient-gradient phenotyping enables predictive ionomics of tropical leafy greens

Accurate prediction of edible-leaf mineral composition is challenging because tissue ionomes integrate nutrient supply, plant identity, growth dilution, water-balance regulation and cumulative environmental exposure. We combined a designed nutrient-gradient experimental framework with machine learning to predict leaf ionome using 1,163 Chinese spinach (Amaranthus dubius) and Chinese broccoli (Brassica oleracea Alboglabra Group) plants grown across 16 designed nutrient-gradient experiments in a semi-controlled tropical greenhouse. Targeted perturbations of N, P, K, Ca, Mg, Fe and Mo were combined with cumulative transpiration, integrated microclimate, shoot dry weight and laboratory quantification of 12 harvested-leaf mineral targets. The resulting ionome was broad, non-Gaussian and species dependent, with coordinated off-target shifts also evident for minerals whose supplied concentrations were held constant. We benchmarked AutoGluon and TabPFN using five-fold leakage-free, distribution-balanced grouped cross-validation, in which all biological replicates from each dosing condition were withheld together. Across previously unseen nutrient conditions, pooled out-of-fold R2 ranged from 0.72 to 0.92, with broadly comparable performance between architectures. Learning curves showed rapid early gains for several targets but persistent condition-level generalization gaps for total reduced nitrogen, K, Mn and Zn. Model-agnostic Shapley additive explanations identified target-specific combinations of nutrient inputs, plant type, substrate, cumulative environment and physiological traits, while cross-model attribution agreement varied among minerals. Finally, reduced-feature models were tested on an independent grower-operated cohort of 99 plants. Calibration was closest for NO3, Mg and B, whereas Mn and Na showed substantial external bias. These results establish leakage-aware predictive ionomics as a robust framework for post-harvest lab-free crop mineral estimation while defining the calibration and sensing requirements for commercial deployment.

plant biology↗

bioRxiv2026

Diffusion MR Microscopy of the Human Hippocampus at 50 μm Resolution at 14.1 T for 3D Virtual Histology

Bridging the gap between macroscopic neuroimaging and microscopic histology remains a challenge in neuroscience. Here, we present a technical feasibility study of diffusion MR microscopy (dMRM) in the ex vivo human hippocampus using a 14.1 T ultrahigh-field MRI system. Mid-hippocampal blocks from control and Alzheimers disease (AD) patients were acquired at 50 x 50 x 100 {micro}m3, representing, to our knowledge, the highest resolution reported for human brain diffusion MRI. At a spatial scale approaching cellular dimensions, dMRM maps and tractography showed close correspondence with immunohistological markers of axons and dendrites. The acquired data delineated six hippocampal laminae, distinguished the inner and outer molecular layers, and preserved short, lamina-specific trajectories that became attenuated or blurred at 100 {micro}m resolution. Tractography further depicted the major components of the hippocampal tri-synaptic circuit--the perforant path, mossy fibers, and Schaffer collaterals in 3D. In the AD specimen, dMRM revealed reduced laminar contrast, local discontinuities, and altered radial and tangential fibers that were paralleled by pathological staining. With the 3D nondestructive characterization of human brain microstructure and circuitry, ex vivo dMRM showed its potential toward the goal of 3D virtual histology.

neuroscience↗

bioRxiv2026

Sleep spindle state-dependent motor cortical plasticity induction by EEG-triggered ripple burst TMS

Background: Sleep spindles are fundamental for plasticity and memory consolidation. Here we sought to target different spindle states in sleeping healthy participants with real-time EEG-burst repetitive transcranial magnetic stimulation (rTMS) at hippocampal ripple frequency, and test the spindle state-dependent induction of corticospinal and sensorimotor cortical plasticity. We hypothesized that the spindle-trough is a particularly critical state for plasticity induction because hippocampal ripples are naturally nested in the spindle-trough, reflecting replay of memory traces and facilitating memory consolidation. Methods: Fourteen participants underwent four experimental nights, in which rTMS was applied either at the spindle-trough, spindle-peak, spindle random phase or during spindle-free epochs. Readouts of plasticity were changes in resting-state EEG (rsEEG) power, motor evoked potential (MEP) amplitude, local mean field amplitude (LMFA, for the N45 and P60 potential components), immediate response slope (IRS) and TMS-related time frequency response (TFR), tested 10 and 30 min after the end of the rTMS interventions upon awakening, and compared to pre-sleep baseline. Results: Spindle-trough rTMS resulted in pre- to post-sleep decreases of rsEEG beta-band power, MEP amplitude, P60-LMFA, IRS and TFR in the alpha-band, and an increase in the N45-LMFA. None of the other spindle state-dependent rTMS interventions resulted in consistent plastic changes. Conclusions: Targeting the spindle-trough with ripple-burst rTMS stands out in consistently leading to long-term depression-like changes across a broad array of corticospinal and sensorimotor cortical excitability readouts. This opens the intriguing opportunity of targeted manipulation of human sleep physiology for improving specific behavioral processes, such as memory consolidation.

neuroscience↗

bioRxiv2026

Lateralized Tenm4 expression biases visual performance and modulates axonal growth and pre-synapse size in retinal ganglion cells

The precise wiring of neuronal connections is a striking feature of the central nervous system and is critical for correct brain function. During vertebrate visual development, retinal ganglion cells (RGCs) establish synaptic connections with postsynaptic cells in the optic tectum, a process that is in part conferred by cell adhesion molecules. However, a complete understanding of the retinotectal wiring mechanism is lacking. Here, we show that the synaptic adhesion molecule Teneurin-4 (Tenm4) is expressed by RGCs and their postsynaptic tectal cell targets in a left-right side-specific manner in zebrafish. Loss of tenm4 leads to defects in presynaptic structures in RGCs and further affects their axonal growth and arbor complexity. Functional assessment of RGC responses to visual stimuli showed a general increase in response amplitude in mutant animals. Visual behavioral analysis revealed a deficit with a strong left-right asymmetrical component in mutant larvae. Our findings demonstrate that tenm4 plays an important role in sensorimotor circuit assembly, extending to neural activities and visual acuity.

neuroscience↗