神经科学

Amyotrophic lateral sclerosis (ALS) is characterized by early and spatially restricted pathology in motor axons, including distal degeneration and accumulation of aggregation-prone proteins such as TDP-43. However, a major limitation in the field has been the lack of approaches that enable robust, quantitative, and compartment-specific analysis of these early axonal events, particularly in human-relevant systems. Here, we describe an integrated experimental and analytical framework that enables quantitative dissection of axonal degeneration and protein aggregation, specifically within distal motor axons. By combining compartmentalized human co-cultures with a dedicated image analysis strategy, this approach enables selective and quantitative analysis of pathological processes specifically within axons, independent of surrounding tissues such as muscle and other cellular compartments. This framework captures both structural degeneration and protein aggregation dynamics at subcellular resolution, enabling spatially resolved quantitative analysis of disease-relevant changes along axons. Importantly, the analytical framework is not limited to TDP-43 but is broadly applicable to diverse aggregation-prone proteins, thereby providing a generalizable platform to study axonal pathology across neurodegenerative diseases. Together, this work provides a scalable approach for investigating axonal pathology as an early and measurable feature of neurodegeneration, with potential applications in mechanistic studies and therapeutic targeting in ALS and related disorders.

Social behavior is highly dynamic and context-dependent, yet many commonly used rodent social assays rely on short testing periods and simplified measures of proximity or investigation. Here, we present a detailed protocol for constructing and using the immersive social interaction assay (ISIA), a behavioral paradigm designed to capture prolonged, voluntary social interactions in freely moving mice. The ISIA apparatus consists of two modified standard rodent home-cage chambers connected by a 3D-printed tube with an adjustable inner diameter. This design enables flexible experimental control: a removable restrictor can confine a head-bar-implanted focal mouse to one chamber while permitting a freely moving conspecific to traverse the full apparatus, enabling assessment of social motivation. Animals can be recorded over extended time windows with familiar or novel conspecifics, in their home territory or in novel environments, and under varying thermal or enrichment conditions, while expressing a broad repertoire of affiliative and aggressive behaviors, including huddling and aggression. The apparatus can be readily integrated with machine learning–based tracking and behavioral classification pipelines for high-throughput analysis. This protocol describes step-by-step construction, setup, and experimental implementation of the ISIA, from apparatus construction and head-bar implantation to video-based behavioral analysis, with the goal of facilitating broader adoption of ethologically relevant behavioral assays in neuroscience research.

Acid ceramidase (aCDase) is a lysosomal amidase that catalyzes the hydrolysis of sphingolipids (SphL), including ceramides and glucosylceramides. Altered expressions of aCDase are associated with several pathological conditions, such as cancer, inflammation, pain, and pulmonary disorders. aCDase activity is reduced in Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, diabetes, and cardiovascular disease. Recent reports suggest that aCDase inhibition may be an emerging strategy for treating several SphL-related neurodegenerative conditions, such as Krabbe, Gaucher, and Parkinson’s disease, due to its role in the accumulation of glycosphingolipids. Therefore, the development of a tissue-based aCDase activity assay has potential applications in clinical diagnostics and drug discovery, enabling the evaluation of the onset and progression of disease from biological samples of patients, drug-target engagement analysis, and identification of biomarkers. Here, we report a detailed protocol for detecting aCDase activity in tissue lysates, using Rbm14-12 as a specific fluorogenic substrate for aCDase. Assay protocol optimization, including a procedure for the preparation and storage of tissue lysates and the identification of optimal protein tissue lysate amounts and substrate concentrations based on kinetic enzymatic parameter analyses, is described.

Expressing large DNA constructs in the native three-dimensional brain microenvironment remains technically challenging. Although viral vectors provide high transduction efficiency and cell-type selectivity, their genetic payload capacity is limited. Various non-viral approaches have been used in brain tissue, but they may compromise tissue viability or require specialised equipment, such as biolistic delivery or electroporation. We present an adapted protocol for delivering the large DNA vector encoding the optical PIEZO1 sensor GenEPi into brain tissue to enable sensor expression in pyramidal neurons. By applying DNA–Lipofectamine liposomes directly to the slice surface, we achieved efficient, minimally invasive transfection of pyramidal neurons in the CA1 and CA3 regions of organotypic hippocampal slices. PIEZO1 sensor expression was detectable as early as 7 days after transfection, increased with longer tissue maintenance, and was sustained for 3–4 weeks in vitro. This protocol describes a cost-effective, non-invasive approach that preserves cell viability and enables investigation of PIEZO1-mediated mechanotransduction in a native brain microenvironment.

Progressive neurodegeneration linked to the accumulation of misfolded proteins is a hallmark of several neurodegenerative disorders, including Parkinson’s disease, Huntington’s disease, and Alzheimer’s disease. Dysfunction in the protein homeostasis machinery correlates with pathology. The chaperone protein DNAJB6 is expressed in neurons and oligodendrocytes and has been shown to play a key role in preventing amyloid aggregation by binding to amyloidogenic proteins and facilitating their refolding or degradation, in cooperation with other chaperones. Here, we describe a simple and feasible assay that enables high-throughput screening for DNAJB6 activity in a plate reader format. We use genetically engineered HEK293 cells that stably express DNAJB6 fused to either CFP or YFP. These cells can be plated into multi-well plates, and the fluorescence resonance energy transfer (FRET) signal can be measured for analysis of DNAJB6 dimerization, which is linked to DNAJB6 activity. The protocol can be used for drug screening and to identify compounds that increase DNAJB6 dimerization, and can serve as a starting point for finding new medicines that act through modulating DNAJB6 activity.

Retinopathy of prematurity (ROP), a retinovascular disease, is a leading cause of childhood blindness worldwide. Given the constraints of studying molecular mechanisms in preterm infants, reproducible animal models are important to understand ROP pathophysiology. Mouse and rat oxygen-induced retinopathy (OIR) models are the most commonly used and recapitulate key vascular features seen in ROP. However, these models are susceptible to inherent variability that limits reproducibility, including inter-litter variability, consistency of oxygen delivery across experiments, retinal dissection technique, and immunohistochemistry. Here, we describe a comprehensive protocol for performing the most common mouse and rat OIR models, and procedures such as eye enucleation, retinal dissection and flat mounting, isolectin GS-IB4 staining, whole retina stitched fluorescence imaging from Z-stacks, and quantification of vascular features. This protocol provides important materials and procedural details to increase the reproducibility of the mouse and rat OIR models.

Phosphatase and tensin homolog-induced kinase 1 (PINK1) is a serine/threonine kinase that plays a key role in mitophagy initiation. Loss-of-function autosomal recessive mutations in PINK1 cause early onset Parkinson’s disease (EOPD). Current approaches for studying PINK1 function depend on bulk techniques that can only provide snapshots of activity and could miss the dynamics and cell-to-cell heterogeneity of PINK1 activity or provide an indirect readout of PINK1 activity. Here, we present a protocol using our newly developed phase separation–based PINK1 biosensor (PINK1-SPARK) to observe real-time activity of endogenous PINK1 in single cells. Following transfection of live cells with PINK1-SPARK, cells are treated with mitochondrial depolarizing agents and visualized using widefield or confocal fluorescence microscopy, either following the same cells over time for time-lapse imaging of PINK1 activity or end-point measurements. Thus, PINK1-SPARK is a new tool that enables the measurement of PINK1 activity in single live cells, allowing for further elucidation of the role of PINK1 in mitophagy and cell function.

Persistent neural activity underlies fundamental brain functions such as memory, decision-making, and emotion. Despite its importance, experimental paradigms that enable quantitative analysis of persistent behavioral responses remain limited. Here, we describe a protocol to induce and measure a persistent locomotor response by applying a brief alternating current (AC) electric stimulus to the nematode Caenorhabditis elegans. This method reliably evokes a prolonged increase in locomotion speed that persists for minutes after stimulus termination and can be quantified by video tracking. Because C. elegans has a fully mapped connectome and is amenable to genetic and neurophysiological manipulation, this protocol provides a useful platform for dissecting the molecular and neural mechanisms underlying persistent behavioral responses. Electrically induced persistent locomotion serves as a simple, robust, and quantifiable behavioral readout for studying the regulation of neural persistence in vivo.

Standardized laboratory assays are essential for generating reproducible and comparable data in toxicology. Although acute contact and oral toxicity tests are widely applied in pesticide risk assessment, these approaches have rarely been adapted for social vespids. Vespa velutina nigrithorax, an invasive hornet in Europe and East Asia, is commonly managed through chemical control, yet treatment efficacy may vary depending on the route of exposure and other biological factors. This protocol describes a standardized method to assess acute contact and oral toxicity of chemical compounds in adult V. v. nigrithorax workers under controlled laboratory conditions. Hornets are collected in the field, individually housed, and exposed either to topical applications on the thorax or to spiked food sources. Mortality is monitored over 48–96 h and analyzed using appropriate statistical approaches to estimate lethal endpoints. This protocol enables comparison among compounds and exposure routes and provides a practical framework for toxicity screening in hornets.

Whole-mount techniques are widely used in medical and biological research to analyze protein expression and tissue organization in intact specimens. Traditional approaches for protein localization include section-based immunohistochemistry and in situ hybridization; however, these methods can be limited by tissue disruption and loss of spatial context. Whole-mount protocols generally involve tissue fixation, permeabilization, and staining with specific probes, but their effectiveness varies depending on the antigen–antibody combination and the specimen type. Consequently, no universal protocol is suitable for all experimental conditions. This protocol presents a detailed whole-mount immunostaining protocol for evaluating tyrosine hydroxylase (TH) expression, a key marker of dopaminergic neurons, in zebrafish (Danio rerio) larvae. The procedure outlines critical steps from sample preparation to staining optimization to ensure reproducible and specific signal detection. This approach enables accurate visualization and analysis of dopaminergic neuron distribution in intact larvae. The protocol offers a reliable and adaptable approach that preserves tissue integrity, enables three-dimensional visualization, and is particularly well-suited for developmental and neurobiological studies using zebrafish larvae.