Biology subjects

Zhao, Z.

Publications and source records attributed to Zhao, Z..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

A photostable genetically encoded voltage indicator for imaging neural activities in tissue and live animals

Genetically encoded voltage indicators (GEVIs) enable noninvasive, high-speed monitoring of electrical activity but are constrained by limited brightness and rapid photobleaching under continuous illumination. Here, we present Vega, a highly photostable green fluorescence GEVI with both high sensitivity ({Delta}F/F = -33% per 100 mV) and fast response (1.34 ms). Under one-photon excitation at 1 W/cm2, Vega exhibits more than 20-fold slower photobleaching than the spectrally similar GEVI, Ace-mNeon2. In acute mouse brain slice, Vega enabled wide-field high-fidelity recording of action potentials from 51 neurons simultaneously. In pancreatic islets, it revealed heterogeneous {beta}-cell activation and intercellular coupling in response to glucose elevation. Finally, one-photon imaging in awake mice demonstrated stable cortical voltage mapping in vivo. Vega thus overcomes the longstanding photostability-performance trade-off, enabling chronic, high-fidelity voltage imaging across preparations.

bioengineering↗

bioRxiv2025

Neural hierarchy for coding articulatory dynamics in speech imagery and production

Mental imagery is a hallmark of human cognition, yet the neural mechanisms underlying these internal states remain poorly understood. Speech imagery--the internal simulation of speech without overt articulation--has been proposed to partially share neural substrates with actual speech articulation. However, the precise feature encoding and spatiotemporal dynamics of this neural architecture remain controversial, constraining the understanding of mental states and the development of reliable speech imagery decoders. Here, we leveraged high-resolution electrocorticography recordings to investigate the shared and modality-specific cortical coding of articulatory kinematic trajectories (AKTs) during speech imagery and articulation. Applying a linear model, we identified robust neural dynamics in frontoparietal cortex that encoded AKTs across both modalities. Shared neural populations across the middle premotor cortex, subcentral gyrus, and postcentral-supramarginal junction exhibited consistent spatiotemporal stability during the integrative articulatory planning. In contrast, modality-specific populations for speech imagery and articulation were somatotopically interleaved along the primary sensorimotor cortex, revealing a hierarchical spatiotemporal organization distinct from shared encoding regions. We further developed a generalized neural network to decode multi-population neural dynamics. The model achieved high syllable prediction accuracy for speech imagery (79% median accuracy), closely matching the performance of speech articulation (81%). This model robustly extrapolated AKT decoding to untrained syllables within each modality while demonstrating cross-modal generalization across shared populations. These findings uncover a somato-cognitive hierarchy linking high-level supramodal planning with modality-specific neural manifestation, revolutionizing an imagery-based brain-computer interface that directly decodes thoughts for synthetic telepathy.

neuroscience↗

bioRxiv2025

Impact of Peptide Initial Configuration and Membrane Composition on Melittin's Pore-Forming Ability under Unbiased All-Atom Molecular Dynamics Simulations

The rising challenge of antimicrobial resistance has accelerated the search for alternative therapeutics. Antimicrobial peptides (AMPs), a class of naturally occurring defense molecules found across diverse species, are promising candidates. Despite their potent membrane-disrupting activity, the atomic details of the pore formation process remain insufficiently understood. In this study, we employed all-atom molecular dynamics (MD) simulations to investigate the pore formation process of melittin under different initial configurations. Simulations were conducted using three different membrane systems: a pure POPC bilayer, a mammalian membrane model (DOPC:Cholesterol, 9:1), and a bacterial membrane model (DOPE:DOPG, 3:1). For each system, we examined four different starting configurations, in which six melittin peptides were arranged in a star-like pattern. Our results demonstrated that the pore formation process strongly depends on the initial peptide configuration. In one specific initial arrangement (termed as Conf.I), pore formation consistently occurred within 100 nanoseconds, regardless of membrane composition. Furthermore, the simulations revealed that pore formation was more challenging in the mammalian membrane model and even more so in the bacterial membrane model, in comparison with the pure POPC bilayer. These findings are in line with previously reported minimum inhibitory concentration (MIC) and the 50% hemolysis concentration (HC50) of melittin in the literature. Additionally, we identified lysine-7 (K7) as the key residue in determining whether a stable pore can form. In configurations where the K7 side chain formed electrostatic interactions with the phosphate group of a lipid, melittin were anchored to the membrane surface, thereby preventing pore formation. In contrast, simulations of melittin mutants K7A and K7Q showed no such anchoring effect, and thus pore formation was possible in multiple initial configurations. Notably, the K7Q mutation showed a preference for pore formation in bacterial membranes over mammalian membranes, suggesting that reducing toxicity while maintaining antimicrobial efficacy is possible.

biochemistry↗

bioRxiv2025

Bioinformatics classification of the MgtE Mg2+ channel and de novo protein design for the stabilization of its novel subclass

MgtE channels play crucial roles in Mg{superscript 2} homeostasis and are implicated in bacterial survival under antibiotic exposure. Previous structural and biophysical studies have predominantly focused on the Thermus thermophilus MgtE, leaving the structural and mechanistic diversity of MgtE family proteins largely unexplored. In this study, using a genome mining approach, we identified diverse MgtE homologs, including a novel subclass termed the "mini-N type," which lacks the canonical cytoplasmic N and CBS domains but possesses a unique small N-like domain. Despite extensive expression screening, mini-N type homologs could not be stably purified. To address this issue, we designed a series of de novo proteins and determined their crystal structures. A selected de novo protein was fused to a mini-N type MgtE, enabling successful purification and preliminary cryo-EM imaging. Our findings demonstrate that de novo designed protein fusions can serve as powerful tools for stabilizing and purifying otherwise unstable membrane proteins, opening new avenues for the structural and functional studies of otherwise inaccessible membrane proteins.

biophysics↗

bioRxiv2025

A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography

Developing high-resolution reference maps of disease-susceptible spatial niches is a critical step to mitigating the profound effects of lung disease. Here, we present an integrated multimodal single-nucleus human lung atlas (snHLA) profiling 746,047 nuclei from 49 mapped lung blocks spanning clinically relevant distal airways, alveoli, and interstitium across 11 healthy adults. Integrating snRNA-seq and SNARE-seq2, which co-assays chromatin accessibility and gene expression from the same nucleus, we resolved 70 molecularly distinct populations and captured 332,846 accessible chromatin regions, nominating new transcriptional regulators of human lung cell diversity. Spatial transcriptomics using MERFISH mapped 25 cell populations across 7 structural neighborhoods and multiplexed immunofluorescence localized cell subtypes and distal airway-defining protein markers, expanding and validating distinct lung structure-specific cell populations. This open access snHLA and companion Cell Type and Marker Gene Dictionary with anatomically aligned nomenclature delivers a foundational resource at an unprecedented resolution to interrogate the origins of lung pathophysiology.

cell biology↗

bioRxiv2025

Decoding protein-peptide interactions using a large, target-agnostic yeast surface display library

Protein-peptide interactions underlie key biological processes and are commonly utilized in biomedical research and therapeutic discovery. It is often desirable to identify peptide sequence properties that confer high-affinity binding to a target protein. However, common approaches to such characterization are typically low throughput and only sample regions of sequence space near an initial hit. To overcome these challenges, we built a yeast surface displayed library representing [~]6.1 x 109 unique peptides. We then performed screens against diverse protein targets, including two antibodies, an E3 ubiquitin ligase, and an essential membrane-bound bacterial enzyme. In each case, we observed motifs that appear to drive peptide binding and we identified multiple novel, high-affinity clones. These results highlight the librarys utility as a robust and versatile tool for discovering peptide ligands and for characterizing protein-peptide binding interactions more generally. To enable further studies, we will make the library freely available upon request.

bioengineering↗

bioRxiv2025

A Reductive Uric Acid Degradation Pathway in Anaerobic Bacteria

Uric acid is a key intermediate in purine degradation across diverse organisms, while its accumulation in humans leads to inflammation and gout disease. Aerobic organisms degrade uric acid via a well-known "oxidative pathway" involving dearomatization of the purine core catalyzed by uric acid oxidases or dehydrogenases. The ability to degrade uric acid is also widespread in anaerobic bacteria, including gut bacteria, although the mechanisms are incompletely understood. Here, we report the biochemical characterization of a recently identified uric acid degradation gene cluster from Escherichia coli, and show that it encodes a "reductive pathway" for uric acid degradation. In this pathway, uric acid is first reduced to isoxanthine (2,8-dioxopurine) by a xanthine dehydrogenase homolog (XdhD), followed by dearomatization of the purine core catalyzed by a flavin-dependent reductase (YgfK). Stepwise cleavage of the pyrimidine and imidazole rings forms 2,3-diureidopropionate, and stepwise cleavage of the 2- and 3-ureido groups then forms 2,3-diaminopropionate, which is cleaved by a pyridoxal 5-phosphate-dependent lyase (YgeX) to pyruvate and ammonia. Detection of isoxanthine in clinical serum samples suggests it is a physiologically relevant circulating metabolite. A probiotic E coli Nissle strain was engineered for constitutive overexpression of the gene cluster, and oral administration in a uricase-knockout hyperuricemic mouse model significantly reduced the serum uric acid level and alleviated associated kidney injury, suggesting a potential route towards uricolytic probiotics.

biochemistry↗

bioRxiv2025

Estrogen-related receptor alpha promotes skeletal muscle regeneration and mitigates muscular dystrophy

Skeletal muscle regeneration in chronic muscle diseases such as Duchenne Muscular Dystrophy (DMD) has remained clinically unsurmountable. Estrogen-related receptor alpha (ERR) plays a critical role in adult skeletal muscle metabolism and exercise fitness. Whether ERR activation can drive muscle regeneration and mitigation of dystrophy in DMD is not known. We have investigated ERR signaling in pre-clinical models of acute muscle injury and DMD. ERR is induced in differentiating C2C12 myoblast and regenerating muscle. ERR silencing suppressed proliferation and differentiation in C2C12 myoblasts. RNA sequencing revealed that angiogenic factor and proliferation genes were downregulated by ERR knockdown in proliferating cells, whereas oxidative mitochondrial and differentiation regulator genes were downregulated in differentiating cells. In accordance with in vitro findings, transgenic ERR overexpression in rodent skeletal muscle stimulates muscle regeneration after acute BaCl2 injury, which is accompanied by enhanced angiogenesis and mitochondrial biogenesis. Notably, ERR and its angiogenic and metabolic target gene expression is suppressed in muscle stem cells (MuSCs) derived from dystrophic muscles in mdx mice, coinciding with proliferation and differentiation defect in these cells. Loss of ERR and its target gene expression was recapitulated in adult dystrophic mdx muscles. Consequently, muscle specific ERR overexpression in mdx mice restored angiogenic and metabolic gene expression, induced vascular and oxidative remodeling, alleviated baseline muscle damage, and boosted regeneration after BaCl2 injury in dystrophic muscle. Our studies demonstrate a pro-regenerative role of ERR and its deficiency in dystrophic muscles and its MuSCs. ERR restoration could be a therapeutic strategy for DMD through angio-metabolic gene program.

physiology↗

bioRxiv2025

Direct interoceptive input to the insular cortex shapes learned feeding behavior

The insular cortex (insula) is an interoceptive hub, which senses internal states such as hunger, thirst, pain, and emotions. Previous studies suggest that the insula directly senses internal states, but the mechanisms remain elusive. We identified a population of leptin receptor-positive cells with a unique morphology in the insula (INSLepR). Based on leptins known role in signaling adiposity, we hypothesized that INSLepR neurons detect internal states to regulate food intake and body weight. Accordingly, we found that intra-insula leptin administration or optogenetic stimulation of INSLepR neurons impacts feeding behavior. Moreover, INSLepR neuron activity encodes feeding bouts in an internal-state dependent manner, and leptin alters insula neural dynamics in response to feeding, while also reshaping the transcriptome. Taken together, our data supports a model for direct interoceptive input to the insula, in which INSLepR cells integrate adiposity level signals to regulate feeding and body weight in a learned manner.

neuroscience↗

bioRxiv2025

Triple-N Dataset: Non-human Primate Neural Responses to Natural Scenes

Understanding the neural mechanisms of visual perception requires data that encompass both large-scale cortical activity and the fine-grained dynamics of individual neurons. While the Natural Scenes Dataset (NSD) has provided substantial insights into visual processing in humans (Allen et al., 2022), its reliance on functional magnetic resonance imaging (fMRI) limits the exploration of individual neuron contributions. To bridge this gap, we present a new dataset: the Triple-N (Non-human Primate Neural Responses to Natural Scenes) dataset, which extends the NSD framework to non-human primates, incorporating single-neuron activity and fMRI recorded from the inferotemporal (IT) cortex. Using Neuropixels probes, we recorded neural responses from five macaques as they passively viewed 1,000 shared NSD images. The dataset includes 59 sessions across 27 sub-regions, capturing over 30,000 visual responsive units. Many recordings were obtained from fMRI-defined category-selective regions, such as face-, body-, scene-, and color-selective areas. Our dataset enables in-depth exploration of neural responses at multiple levels - from population dynamics to single-neuron activity, providing new insights into various aspects of visual processing, including the heterogeneity of object selectivity within functional regions and the temporal dynamics of responses to natural images. Furthermore, the dataset enables joint cross-species analyses, by integrating the macaque neural recordings with human fMRI data, offering a framework for comparing and aligning visual representations across primate species. Overall, our dataset provides a valuable resource for advancing our understanding of visual perception, bridging the gap between large-scale neuroimaging and fine-grained electrophysiological signals, while also facilitating the development of computational models of the high-level visual system.

neuroscience↗

bioRxiv2025

EGFR activation correlates with intracranial pressure and outcome in a mixed intracranial bleeding porcine model

Intracranial hypertension is a major driver of secondary injury after acute subdural hematoma (ASDH), yet how mechanical stress is translated into neuroinflammatory signaling remains poorly understood. Here, we identify a mechanosensitive astrocyte signaling pathway that links elevated intracranial pressure (ICP) to inflammatory amplification in the injured brain. Using a clinically relevant porcine ASDH model combined with mechanistic studies in human iPSC-derived astrocytes, we demonstrate that sustained ICP elevation induces bilateral neuroinflammation together with coordinated upregulation of mechanosensitive ion channels and receptor tyrosine kinase (RTK) pathways. Integrative analysis of molecular and physiological datasets identified astrocytes as the principal cellular responders to ICP and revealed epidermal growth factor receptor (EGFR) as the astrocyte-associated RTK most strongly correlated with ICP dynamics, inflammatory chemokine expression, and survival. Pharmacological activation of the mechanosensitive channel Piezo1 in human astrocytes was sufficient to trigger EGFR internalization, site-specific phosphorylation, and ERK signaling, promoting structural remodeling and robust induction of pro-inflammatory mediators including CCL2, IL-6, and IL-8. Conversely, EGFR inhibition attenuated inflammatory signaling while enhancing astrocytic programs associated with water handling and edema containment. In vivo, increased expression of EGFR ligands together with elevated EGFR phosphorylation supported sustained pathway engagement following ASDH, and correlation analyses linked Piezo1 expression and EGFR activation with ICP severity and adverse outcome. Together, these findings define a mechanotransduction axis in which astrocytic Piezo1 signaling integrates mechanical stress with EGFR-dependent neuroimmune responses, positioning EGFR as a translationally accessible target to modulate inflammation-driven secondary brain injury.

neuroscience↗

bioRxiv2025

PIBE: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics

We developed a parallel ion beam etching device that simultaneously thins hundreds of sections on a whole 4-inch wafer at 20 nm steps, enabling sub-centimeter volumetric imaging with high axial resolution. Compared with traditional volume electron microscopy, PIB preserves in-situ continuity within sections and simplifies inter-section registration. Its high axial resolution facilitates reliable neuron segmentation and tracing with reduced proofreading, providing an efficient route toward ultra-large-scale connectomics, such as whole-mouse-brain reconstruction.

neuroscience↗

bioRxiv2025

MARQO pipeline resolves multiparametric cellular and spatial organization in cancer tissue lesions

Multiplex immunostaining analysis remains fragmented, underperforming, and labor-intensive despite tissue proteomic methodologies achieving ever-increasing marker complexity. Here we propose an open-source, semi-supervised automated pipeline that streamlines start-to-finish, single-cell resolution analysis of whole-slide tissue, named Multiplex-imaging Analysis, Registration, Quantification, and Overlaying (MARQO). We compared and validated MARQO using Multiplex Immunohistochemical Consecutive Staining on a Single Slide (MICSSS) using human tumor and adjacent normal tissue samples. Performance was compared with manually-curated pathologist determinations and quantification of multiple markers. We also optimized MARQO to analyze diverse tissue sizes (whole tissue, biopsy, tissue microarray) and staining approaches (singleplex immunohistochemistry, 20-color multiplex immunofluorescence) to determine marker co-expression patterns in multiple human solid cancer types. Lastly, we validated CD8 T cell enrichment in hepatocellular carcinoma responders to neoadjuvant cemiplimab in a phase II clinical trial, further demonstrating MARQOs ability to provide spatially-resolved in situ mechanisms by providing multiplex whole-slide single-cell resolution data.

immunology↗

bioRxiv2025

Evolutionary Consequences of Unusually Large Pericentric TE-rich Regions in the Genome of a Neotropical Fig Wasp

Transposable elements (TEs), despite generally being considered deleterious, represent a substantial portion of most eukaryotic genomes. Specific genomic regions, such as telomeres and pericentromeres, are often densely populated with TEs. In these regions, which tend to be gene-poor, reduced recombination shelters the genome from the deleterious effects of TEs. Here, we describe unusually large and continuous pericentromeric TE-rich regions in all chromosomes of the genome assembly of Pegoscapus hoffmeyeri Sp. A (511.79 Mbp), a Neotropical fig wasp that is the obligate pollinator of Ficus obtusifolia. The identified pericentromeric TE-rich regions span nearly half (46%) of the genome, and harbor over 40% of all annotated genes, including 30% of conserved BUSCO genes. We present evidence that low recombination in these TE-rich regions generates strong bimodal molecular evolution patterns genome-wide. Patterns of nucleotide diversity and protein-coding gene evolution in TE-rich regions are consistent with a reduced efficiency of selection and suggestive of strong Hill-Robertson effects. A significant reduction in third codon position GC content (GC3) in TE-rich regions emerged as the most distinctive gene feature differentiating genes in TE-rich regions from those in the rest of the genome, a pattern that likely results from the absence of GC-biased gene conversion. This remarkable binary compartmental genome organization in the genome of P. hoffmeyeri provides a unique example of how genome organization with compartmental TE distribution can lead to context-dependent gene evolution shaped by common evolutionary forces.

genomics↗

bioRxiv2025

SIMIT-seq: a bead-free, scalable microfluidic platform for single cell mRNA sequencing with ultrahigh cell-indexing rate

SIMIT-seq is a bead-free, scalable microfluidic platform designed for high-efficiency single-cell mRNA sequencing. Conventional microfluidic-based single-cell RNA sequencing platforms rely heavily on barcoded beads and intricate co-encapsulation schemes, often constrained by double Poisson limitations and the complexities of bead synthesis. In contrast, SIMIT-seq eliminates the need for beads entirely by employing a deterministic, orthogonal barcoding strategy within a two-dimensional micro-well array. This platform achieves an impressive single-cell indexing rate of 96.6% without the need for complex microfluidic operations. Here, we describe the design and fabrication of the SIMIT-seq platform, outline its workflow for transcript capture and library preparation, and demonstrate its application in profiling K562 cells. Our results validate both the high fidelity of molecular barcode immobilization and the systems capability to support downstream single-cell mRNA sequencing. SIMIT-seq offers a cost-effective and scalable alternative for single-cell transcriptomics, providing a promising foundation for future single-cell omics applications.

bioinformatics↗

bioRxiv2025

Personalized Brain Morphometric Feature as a Transdiagnostic Predictor of Psychopathology: Insights from Dual Systems Models

BackgroundAdolescents are particularly vulnerable to developing psychopathological symptoms, yet neurobiological markers that can identify these vulnerabilities in a personalized and interpretable manner remain limited. Dual Systems Models suggest that this vulnerability may result from asynchronous development of neural systems subserving cognitive-control and socioemotional functions. Given that rigorous empirical evidence is sparse, this study aimed to quantify developmental imbalances and evaluate their predictive value for psychopathology. MethodsBased on Dual Systems Models, the dorsolateral prefrontal cortex (DLPFC) and ventral striatum (VS) were selected as key regions for the two brain systems, respectively. Using longitudinal data from the Adolescent Brain Cognitive Development (ABCD) study (baseline: n=11,238, ages 9.92{+/-}0.625 years; 2-year follow-up: n=7,870, ages 12.2{+/-}0.652 years; 4-year follow-up: n=2972, ages 14.1{+/-}0.693 years), we derived a personalized imbalance score based on brain morphometric features, including surface area, thickness and gray-matter volume. Nested linear mixed models were employed to assess associations between the imbalance scores and psychopathology. Additionally, generalized additive models were used to capture developmental trajectories of the imbalance scores and explore potential non-linear associations with psychopathology. To examine reproducibility, data from the Lifespan Human Connectome Project in Development study (HCP-D, N=652, ages 8-21 years) were interrogated. ResultsThe imbalance score, quantified as the difference between VS volume and DLPFC surface area, exhibited strong reliability and validity. During adolescence, the score exhibited a declining trend, with decreasing growth rates and variability between individuals. The score was positively associated with externalizing symptoms and showed a U-shaped relationship with internalizing symptoms. These findings were replicated in the HCP-D sample. ConclusionsThe novel neuroanatomical imbalance score empirically supports Dual Systems Models and may function as a transdiagnostic marker for internalizing and externalizing psychopathology. These findings enhance understanding of the neurodevelopmental mechanisms underlying adolescent psychopathology and offer potential implications for precision prevention and intervention strategies.

developmental biology↗

bioRxiv2025

Large-scale single-neuron recording using the uFINE array in human cortex

Monitoring neural population activity at single-cell resolution is essential for driving fundamental research and clinical innovations. However, translating advanced recording techniques from animal models to humans remains a significant challenge. Flexible neural electrodes have recently emerged as powerful tools for large-scale single-unit recordings due to their superior biocompatibility and high recording density. Here, we demonstrate reliable, high-density single-unit recordings during intraoperative procedures in human patients using ultra-Flexible Implantable Neural Electrode (uFINE) arrays. The uFINE array exhibited sufficient mechanical robustness to maintain structural integrity throughout surgical operations. We successfully recorded 616 single units from 10 patients, with up to 135 single units simultaneously recorded. The flexibility of uFINE array minimized signal disturbances from brain pulsations, enabling stable and continuous single-unit detection. Stimulus and response tuning were observed at the level of individual neurons in awake patients. This uFINE-based recording approach offers unique opportunities to investigate human-specific cognitive functions and develop next-generation brain-machine interfaces.

bioengineering↗

bioRxiv2025

Loss of transcriptional factor Zbtb33 fails to induce clonal hematopoiesis in mice but plays a role in tumor immunity

Clonal hematopoiesis (CH) is an early indicator of hematologic malignancies, driven by mutations in hematopoietic stem cells (HSCs) such as TET2 or TP53. Mutations in ZBTB33 have been implicated in MDS and suggested as a potential driver of CH. However, the role of ZBTB33 in hematopoiesis and its involvement in CH remains unclear. We generated a Zbtb33-knockout mouse strain to elucidate its role in hematopoiesis and the immune system. Our findings indicate that hematopoiesis in Zbtb33-defecient mice appeared grossly normal, and competitive bone marrow transplantation assays demonstrated that loss of Zbtb33 in HSCs did not confer expansional advantage. Introducing the Zbtb33 mutation into Tet2- or Tp53-mutation background yielded no synergistical effects. Tumor challenging assays suggested that Zbtb33 influences cancer immunity response, rather than directly driving CH or myeloid malignancies. In summary, ZBTB33 deficiency was insufficient to induce clonal hematopoiesis but may have a regulatory role in tumor microenvironment. Statement of significanceClonal hematopoiesis (CH) is linked to mutations in hematopoietic stem cells, but the role of Zbtb33 in CH remains unclear. To investigate this, we examined the function of Zbtb33 under physiological conditions and in response to external stimuli. Additionally, we explored whether Zbtb33 mutations cooperate with other genetic mutations to drive clonal hematopoiesis. Key pointsO_LILoss of Zbtb33 fails to induce clonal hematopoiesis and does not synergize with Tet or Tp53 mutations. C_LIO_LIHowever, it plays a significant role in regulating cancer immunity and the tumor microenvironment. C_LI

immunology↗