Biology subjects

Zhang, L. I.

Publications and source records attributed to Zhang, L. I..

10 recordsLinked to original sources

bioRxiv2026

Multi-scale spatial transcriptomic atlas of the whole mouse spinal cord

The spinal cord coordinates sensory, motor and autonomic functions through diverse neuronal and non-neuronal populations, yet how molecularly defined cell types are organized across its full extent remains incompletely understood. Here we use Stereo-seq to generate a genome-wide, single-cell-resolution spatial atlas of the whole adult mouse spinal cord. Profiling 322,827 cells across 81 anatomically registered transverse sections spanning cervical, thoracic, lumbar and sacral levels, we resolve 12 major cell classes and 94 transcriptomic subclusters. Major cell classes occupy characteristic anatomical territories conserved along the rostrocaudal axis, whereas individual subclusters exhibit reproducible laminar, mediolateral and segment-associated distributions. Transcriptome-wide analysis identifies coordinated spatial gene-expression modules that delineate anatomical domains independently of predefined cell-type labels. Notably, oligodendrocyte subtypes exhibit a distinct and reproducible laminar organization within spinal cord white matter across spinal levels, revealing finer structural subdivisions beyond conventional anatomical descriptions. Integrating cell-type identities with local spatial organization further defines hierarchical domains that recapitulate canonical anatomy while resolving finer subdivisions within established regions. Together, these findings define a multi-scale cellular architecture linking transcriptomic diversity, spatial gene-expression programs and anatomical organization throughout the spinal cord.

neuroscience↗

bioRxiv2026

Glutamatergic Neurons in caudal Pontine Reticular Nucleus (PRNc) Mediate Backward Locomotion in mice

Locomotion is essential for animals to adaptively navigate their environment. However, despite extensive investigation into neural mechanisms underlying forward movement, the brain circuits controlling backward locomotion, a critical motor behavior for navigating confined spaces and avoiding threats, remain poorly understood. Here, using a specially designed behavioral paradigm for backward locomotion in mice, we find that glutamatergic neurons in the caudal pontine reticular nucleus (PRNc) are selectively activated during backward, but not forward, locomotion. Activity increase of these neurons is temporally aligned with backward movement, with its amplitude correlated with speed. Optogenetic manipulations further demonstrate that these neurons are both sufficient and necessary for initiating and sustaining backward walking. Moreover, anatomical tracing reveals that the PRNc broadly integrates bilateral cortical and subcortical inputs and projects extensively to brain-wide and spinal cord networks. These findings suggest PRNc as a previously unrecognized brainstem center in direction-specific locomotor control circuits. Key findings of this work and our initial identification of this brainstem locomotor node were presented at the Society for Neuroscience Annual Meeting in November, 15th, 2025 (SfN Neuroscience 2025, San Diego, CA; Program No. PSTR027.02).

neuroscience↗

bioRxiv2026

TRACE: End-to-end temporal inference and annotation of animal behaviors from video

Quantitative analysis of animal behavior is fundamental to neuroscience and ethology but remains constrained by the scalability, subjectivity, and limited reproducibility of manual annotation. Many automated approaches infer behavior through intermediate representations such as pose trajectories, whereas direct video modeling retains motion, appearance, and context, but its accuracy and efficiency remain incompletely established. Here we introduce V-TRACE (Video-based Temporal Recognition and Annotation of Continuous Ethograms of Animal Behavior), an end-to-end platform with a graphical user interface for behavioral detection and annotation. V-TRACE combines transformer-based video encoders with a multi-scale temporal module to model behavioral dynamics across a broad range of durations. Its modular design supports interchangeable encoder architectures within a common detection pipeline to produce frame-resolved behavioral identities and derive temporal boundaries from continuous recordings. Across datasets spanning species and experimental contexts, V-TRACE demonstrates high accuracy and high-throughput inference, enabling scalable, efficient, and context-aware animal behavior analysis directly from video.

animal behavior and cognition↗

bioRxiv2023

Integrative mapping of spatial transcriptomic and amyloid pathology in Alzheimer's disease at single-cell resolution

Alzheimers disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Despite decades of research, the underlying molecular and cellular changes of AD remain unresolved, especially in terms of the spatial structure of gene expression changes that correlates with pathology, e.g. amyloid beta (A-beta) plaques. Recent advances in imaging-or sequencing-based single-cell spatial transcriptomics have allowed a systematic dissection of molecular and cell architectures in the brain and other tissues. In this study, we employed the recently developed Stereo-seq technology to spatially profile the whole-genome transcriptomics in the 5xFAD mouse model and established the methodology to analyze the specific neuronal transcriptomic changes spatially correlated with amyloid pathology at single cell resolution. More specifically, we developed a pipeline for integrative image- and non-image-based cell segmentation, VoxelMorph-based non-linear alignment, and Unet-based object detection to achieve reliable transcriptomics analysis at the single-cell resolution, and investigated the spatial relationship between diverse neuronal clusters and A-beta depositions. This work has demonstrated the potential of using the Stereo-seq technology as a powerful tool to investigate AD and other complex neurological disorders.

neuroscience↗

bioRxiv2020

The mouse cortico-basal ganglia-thalamic network

The cortico-basal ganglia-thalamic loop is one of the fundamental network motifs in the brain. Revealing its structural and functional organization is critical to understanding cognition, sensorimotor behavior, and the natural history of many neurological and neuropsychiatric diseases. Classically, the basal ganglia is conceptualized to contain three primary information output channels: motor, limbic, and associative. However, given the roughly 65 cortical areas and two dozen thalamic nuclei that feed into the dorsal striatum, a three-channel view is overly simplistic for explaining the myriad functions of the basal ganglia. Recent works from our lab and others have subdivided the dorsal striatum into numerous functional domains based on convergent and divergent inputs from the cortex and thalamus. To complete this work, we generated a comprehensive data pool of [~]700 injections placed across the striatum, external globus pallidus (GPe), substantia nigra pars reticulata (SNr), thalamic nuclei, and cortex. We identify 14 domains of SNr, 36 in the GPe, and 6 in the parafascicular and ventromedial thalamic nuclei. Subsequently, we identify 6 parallel cortico-basal ganglia-thalamic subnetworks that sequentially transduce specific subsets of cortical information with complex patterns of convergence and divergence through every elemental node of the entire cortico-basal ganglia loop. These experiments reveal multiple important novel features of the cortico-basal ganglia network motif. The prototypical sub-network structure is characterized by a highly interconnected nature, with cortical information processing through one or more striatal nodes, which send a convergent output to the SNr and a more parallelized output to the GPe; the GPe output then converges with the SNr. A domain of the thalamus receives the nigral output, and is interconnected with both the striatal domains and the cortical areas that filter into its nigral input source. This study provides conceptual advancement of our understanding of the structural and functional organization of the classic cortico-basal ganglia network.

neuroscience↗

bioRxiv2020

High-throughput whole-brain mapping of rhesus monkey at micron resolution

Whole-brain mesoscale mapping of primates has been hindered by large brain size and the relatively low throughput of available microscopy methods. Here, we present an integrative approach that combines primate-optimized tissue sectioning and clearing with ultrahigh-speed, large-scale, volumetric fluorescence microscopy, capable of completing whole-brain imaging of a rhesus monkey at 1 {micro}m x 1 {micro}m x 2.5 {micro}m voxel resolution within 100 hours. A progressive strategy is developed for high-efficiency, long-range tracing of individual axonal fibers through the dataset of hundreds of terabytes, establishing a "Serial sectioning and clearing, 3-dimensional Microscopy, with semi-Automated Reconstruction and Tracing" (SMART) pipeline. This system supports effective connectome-scale mapping of large primates that reveals distinct features of thalamocortical projections of the rhesus monkey brain at the level of individual axonal fibers.

neuroscience↗

bioRxiv2019

Anterograde Trans-Synaptic AAV Strategies for Probing Neural Circuitry

Elucidating the organization and function of neural circuits is greatly facilitated by viral tools that spread transsynaptically. Adeno-associated virus (AAV) has been shown to exhibit anterograde transneuronal spread. However, the synaptic specificity of the spread and its broad application in various neural circuits remain to be explored. Here, using anatomical, functional, and molecular approaches, we provide strong evidence for the specifically preferential spread of AAV1 to post-synaptically connected neurons. Besides glutamatergic synapses made onto excitatory and inhibitory neurons, AAV1 also transsynaptically spreads through GABAergic synapses and effectively tags spinal cord neurons receiving long-distance projections from various brain regions, but exhibits little or no spread through neuromodulatory projections (e.g. serotonergic, cholinergic, and noradrenergic). Combined with newly designed intersectional and sparse labeling strategies, AAV1 can be utilized to categorize neurons according to their input sources, morphological and molecular identities. These properties make AAV a unique anterograde transsynaptic tool for establishing a comprehensive cell-atlas of the brain.

neuroscience↗

bioRxiv2019

Track-Control, an automatic video-based real-time closed-loop behavioral control toolbox

Approaches of optogenetic manipulation of neuronal activity have boosted our understanding of the functional architecture of brain circuits underlying various behaviors. In the meantime, rapid development in computer vision greatly accelerates the automation of behavioral analysis. Real-time and event-triggered interference is often necessary for establishing a tight correlation between neuronal activity and behavioral outcome. However, it is time consuming and easily causes variations when performed manually by experimenters. Here, we describe our Track-Control toolbox, a fully automated system with real-time object detection and low latency closed-loop hardware feedback. We demonstrate that the toolbox can be applied in a broad spectrum of behavioral assays commonly used in the neuroscience field, including open field, plus maze, Morris water maze, real-time place preference, social interaction, and sensory-induced defensive behavior tests. The Track-Control toolbox has proved an efficient and easy-to-use method with excellent flexibility for functional extension. Moreover, the toolbox is free, open source, graphic processing unit (GPU)-independent, and compatible across operating system (OS) platforms. Each lab can easily integrate Track-Control into their existing systems to achieve automation.

animal behavior and cognition↗

bioRxiv2019

Connectivity characterization of the mouse basolateral amygdalar complex

The basolateral amygdalar complex (BLA) is implicated in behavioral processing ranging from fear acquisition to addiction. Newer methods like optogenetics have enabled the association of circuit-specific functionality to uniquely connected BLA cell types. Thus, a systematic and detailed connectivity profile of BLA projection neurons to inform granular, cell type-specific interrogations is warranted. In this work, we applied computational analysis techniques to the results of our circuit-tracing experiments to create a foundational, comprehensive, multiscale connectivity atlas of the mouse BLA. The analyses identified three domains within the classically defined anterior BLA (BLAa) that house target-specific projection neurons with distinguishable cell body and dendritic morphologies. Further, we identify brain-wide targets of projection neurons located in the three BLAa domains as well as in the posterior BLA (BLAp), ventral BLA (BLAv), lateral (LA), and posterior basomedial (BMAp) nuclei. Projection neurons that provide input to each nucleus are also identifed. Functional characterization of some projection-defined BLA neurons were demonstrated via optogenetic and recording experiments. Hypotheses relating function to connection-defined BLA cell types are proposed.

neuroscience↗

bioRxiv2018

A genetically-encoded fluorescent acetylcholine indicator

Acetylcholine (ACh) regulates a diverse array of physiological processes throughout the body, yet cholinergic transmission in the majority of tissues/organs remains poorly understood due primarily to the limitations of available ACh-monitoring techniques. We developed a family of G-protein-coupled receptor activation-based ACh sensors (GACh) with sensitivity, specificity, signal-to-noise ratio, kinetics and photostability suitable for monitoring ACh signals in vitro and in vivo. GACh sensors were validated with transfection, viral and/or transgenic expression in a dozen types of neuronal and non-neuronal cells prepared from several animal species. In all preparations, GACh sensors selectively responded to exogenous and/or endogenous ACh with robust fluorescence signals that were captured by epifluorescent, confocal and/or two-photon microscopy. Moreover, analysis of endogenous ACh release revealed firing pattern-dependent release and restricted volume transmission, resolving two long-standing questions about central cholinergic transmission. Thus, GACh sensors provide a user-friendly, broadly applicable toolbox for monitoring cholinergic transmission underlying diverse biological processes.

neuroscience↗