Despite substantial progress in preclinical cannabinoid research, translational studies on cannabis use disorders (CUD) are still insufficient due to the absence of robust, validated animal models that fully recapitulate the multifactorial clinical phenotype of human CUD. The complex nature of CUD and the incomplete understanding of its underlying neurobiological mechanisms contribute to the limited availability of effective treatments. To address this gap, we developed an operant conditioning-based mouse model that enables the identification of individual vulnerability or resilience to CUD development. This highly translational model is based on the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5) criteria for substance use disorders. The model allows the assessment of addiction-like behaviors by evaluating three behavioral domains: 1) persistence of responding during periods of cannabinoid unavailability, 2) motivation for cannabinoid seeking measured using a progressive ratio schedule, and 3) compulsivity, assessed when cannabinoid reward is paired with an aversive consequence such as a mild electric foot shock. A major strength of this paradigm is its ability to quantify two phenotypic traits proposed as predisposing factors for addiction vulnerability and two parameters related to craving. In addition, the model is specifically designed to evaluate genetic and circuit-level manipulations using chemogenetic approaches, with minor modifications required by surgical viral-vector delivery. Using this protocol, we can determine whether altering the excitability of specific neural networks promotes resilience or vulnerability to developing cannabinoid addiction. Elucidating these mechanisms is expected to facilitate the identification of novel and more effective therapeutic interventions for CUD. Key features • Operant conditioning-based mouse model to study cannabis use disorders (CUD) based on DSM-5 substance use disorder criteria. • Enables assessment of addiction-like behaviors across persistence, motivation (progressive ratio), and compulsivity under punishment, allowing stratification of vulnerable versus resilient individuals. • Quantifies phenotypic traits linked to cannabinoid addiction vulnerability and behavioral signatures associated with craving for cannabinoids. • Compatible with genetic and circuit-level manipulations to test how specific neural networks modulate CUD-related behaviors.

Extracellular vesicles (EVs) are critical mediators of cell-cell communication and play a key role in male reproductive biology by modulating sperm function. This protocol describes a robust and reproducible workflow for isolating EVs from ram seminal plasma using size-exclusion chromatography (SEC) and assessing their uptake by ram spermatozoa. In contrast to ultracentrifugation-based methods, SEC provides a gentle and more efficient isolation approach that preserves EV integrity and functionality. A central innovation of this protocol is the use of carboxyfluorescein succinimidyl ester (CFSE)-labeled seminal plasma EVs (SP-EVs) to evaluate their incorporation into sperm cells through two complementary detection platforms: (i) flow cytometry with standard resolution and (ii) confocal microscopy, for spatial confirmation of EV-sperm interactions. By bridging the gap between EV isolation and functional analysis, this protocol provides a valuable tool for investigating the role of EV-cell interactions. Specifically, it offers potential applications in male fertility preservation, biomarker discovery, and the development of EV-based therapeutic strategies in reproductive medicine. Key features • Provides a gentle, SEC-based EV isolation method optimized for ram seminal plasma, suitable for preserving vesicle integrity in studies of male reproductive biology. • Integrates EV purification with functional assays, enabling direct evaluation of EV-sperm interactions through confocal microscopy and flow cytometry. • Includes a reproducible CFSE-labeling strategy tailored for seminal plasma EVs, ensuring consistent detection of vesicle uptake by ram spermatozoa. • Designed for applications in fertility research, offering a workflow compatible with biomarker discovery, cryopreservation studies, and development of EV-based reproductive interventions.

Laccase2 (Lac2), a member of the phenoloxidase (PO) family, is an essential oxidase for melanin pigmentation in insects. The identification of the in vivo spatial distribution of Lac2 is crucial for understanding the molecular mechanisms underlying color pattern formation. However, it is technically difficult to determine the distribution because Lac2 expression peaks at late pupal stages, when adult cuticle sclerotization has already begun. Here, we report a simple and rapid protocol for estimating the distribution of endogenous PO proteins, prophenoloxidases (proPOs) and phenoloxidases (POs), in insect tissues. In this method, the spatial distribution of endogenous PO proteins is estimated based on staining patterns formed by dopamine melanin synthesis in tissues incubated in a solution containing isopropanol and dopamine. We validated that tissues collected at approximately 80% of the total pupal duration yielded staining patterns corresponding to adult melanin-forming regions in three insect species. By comparing staining patterns across developmental stages, this protocol enables estimation of the timing of color pattern formation. Furthermore, the contrast between stained and unstained regions within the same tissue allows region-specific sampling, thereby facilitating an investigation of the underlying molecular mechanisms regulating spatial PO distribution. Taken together, this method facilitates the study of melanin biosynthesis and enables the identification of the genes involved in regulating color pattern formation. This protocol does not require antibodies, transgenic lines, or specialized equipment and can be completed within a short time frame. Its effectiveness has been validated in multiple coleopteran and lepidopteran species, demonstrating its broad applicability as a versatile tool for studying insect pigmentation and color pattern formation. Key features • A simple tissue staining protocol to estimate the spatial distribution of endogenous PO proteins without the use of antibodies or transgenic lines. • Comparing staining patterns across different developmental stages to estimate both the spatial distribution of PO proteins within tissues and the timing of color pattern formation. • RNAs can be extracted from the tissue after staining, enabling gene expression analyses between stained and unstained regions. • This protocol has been validated in two coleopteran species and one lepidopteran species, demonstrating broad applicability across diverse insect taxa.

Super-resolution imaging of synapses in intact brain tissue remains challenging because light scattering, photobleaching, and limited probe penetration, along with antigen accessibility within the densely packed postsynaptic densities (PSDs), constrain resolution and labeling efficiency. Here, we present a protocol utilizing thin brain cryosections and tau-stimulated emission depletion (STED) nanoscopy to visualize the intricate nano-architecture of excitatory synapses in situ. Slicing the brain into 6 μm sections allows for highly efficient and even penetration of probes throughout sections while ensuring that the resolution is not significantly impacted by the imaging depth of the tissue. We outline step-by-step instructions for labeling pre- and postsynaptic nano-architecture using antibodies and nanobodies, highlighting how fixative choice influences the labeling efficiency of synaptic proteins. While this protocol is compatible with both confocal and super-resolution imaging, when combined with rapid image acquisition times of tau-STED, it enables clear separation of key synaptic features in three dimensions with minimal photobleaching. Thus, this approach enables robust multiplex imaging of fluorescently labeled synaptic proteins in the brain, providing exceptional spatial resolution for visualization and quantification of synaptic nanoarchitecture in its native environment. Key features • Detailed protocol for in situ 3D STED microscopy with ~50 nm XY and ~100 nm Z resolution. • Optimized strategies for labeling pre- and postsynaptic nano-architecture using antibodies and nanobodies, including guidance on fixative choice. • Unified workflow for visualizing synaptic morphology and nanoarchitecture to uncover molecular synaptic diversity in the brain at the nanoscale.

Small ubiquitin-related modifiers (SUMOs) are covalently conjugated onto the proteome and serve as signaling molecules in many aspects of eukaryotic cell biology, from S. cerevisiae and C. elegans to H. sapiens. The conjugatable SUMO variants, SUMO1 and the almost identical SUMO2 and SUMO3 (designated SUMO2/3), are processed by an E1(SAE1:SAE2)-E2(UBC9)-E3 enzyme cascade to produce SUMO-modified proteins. The prerogative of the SUMO biology field is to identify and study the specific proteins undergoing SUMOylation, which grants us insights into the biological pathway of interest. This protocol was developed using the human osteosarcoma cell line U2OS to enable the investigation of SUMO conjugates in mitosis, the cell division phase of the cell cycle. We enrich the cell population for mitotic cells, which are isolated and subjected to stringent lysis conditions involving a high concentration of SDS and DTT in RIPA buffer, to promote complete protein denaturation. The lysates in high SDS RIPA buffer are diluted to reduce the overall SDS concentration and undergo conventional immunoprecipitation using SUMO1- or SUMO2/3-specific antibodies bound to protein A/G agarose beads. The samples are then compatible with downstream readouts such as western blots and mass spectrometry. This protocol detects endogenous SUMOylated proteins and avoids exogenous SUMO overexpression, which can alter SUMO conjugate formation. Furthermore, this denaturing protocol ensures only SUMOylated proteins are immunoprecipitated, and not their interactors. Key features • Purifies endogenous SUMO-modified proteins by building on Becker et al. [1]. • Enriches and isolates cells in mitosis using nocodazole and mitotic shake-off. • 1% SDS RIPA lysis promotes robust denaturation ahead of SUMO-specific immunoprecipitation. • Compatible with downstream readouts such as western blots and mass spectrometry.

Cyanobacteria have been widely used as model organisms in photobiochemical research and have recently been exploited as hosts in numerous pilot studies to produce valuable biochemicals via genetic and metabolic modifications. Analyzing cellular RNA is a suitable method for studying genetic changes in cells. Several methods have previously been reported for cyanobacterial RNA extraction. However, the majority of these methods rely heavily on phenol and chloroform, which are hazardous. Additionally, these methods are time-consuming and difficult to perform. Using Synechocystis sp. PCC 6803 as a model, this study developed a novel method for extracting total ribonucleic acid (RNA) using standard centrifugation techniques and laboratory chemicals such as citric acid, ethylenediaminetetraacetic acid, sodium dodecyl sulfate, sodium chloride, and tri-sodium citrate dihydrate to extract RNA from cyanobacterial cells. This method does not necessitate the use of hazardous chemicals, especially phenol and chloroform. Furthermore, it is cost-effective since it does not require expensive chemicals. The results of the quantification, purity, and integrity checks show the effectiveness of this method for extracting good-quality RNA. Furthermore, RT-qPCR results demonstrate that the quality of the extracted RNA is suitable for downstream applications. Key features • Simple and efficient RNA extraction method. • Requires less than an hour to extract total RNA. • Provides high-quality RNA suitable for downstream applications. • This method might be used to extract RNA from other cyanobacteria and algae.

Organic solvent-based tissue clearing methods are widely used for whole-brain imaging but often compromise endogenous fluorescence. Existing protocols, such as iDISCO and fluorescence-preserving variants, have improved optical transparency but still present trade-offs between fluorescence retention, tissue stability, and workflow complexity. Here, we present MDISCO, a modified iDISCO-based clearing protocol designed to enhance preservation of endogenous fluorescence while maintaining high transparency and stable tissue morphology. MDISCO is directly compared with FDISCO+, an established fluorescence-preserving protocol, for the preservation of endogenous tdTomato and YFP. Performance across clearing steps is evaluated by measuring brain weight, anteroposterior and mediolateral dimensions, and optical transparency before and after solvent clearing and refractive index matching. Fluorescence preservation is assessed using whole-brain light-sheet microscopy with standardized imaging parameters to enable direct comparison. This protocol provides an accessible and high-throughput, reproducible workflow for solvent-based clearing with robust endogenous fluorescence preservation, offering clear advantages for whole-brain 3D imaging of genetically encoded fluorescent reporters. Key features • Preserves endogenous tdTomato and YFP fluorescence in whole mouse brains without signal amplification through immunolabeling. • Improves optical clarity and cellular resolvability while maintaining anatomical integrity. • Supports high-throughput "clearing" of whole-tissue samples.

Extracellular vesicles (EVs) are nanoscale particles secreted by all cells and present in all biological fluids, where they carry molecular cargo reflective of health and disease states. Their diagnostic potential is often obscured by the high abundance of non-EV proteins and lipoproteins (e.g., albumin, apolipoproteins) that complicate proteomic analysis of primary biofluids, such as ascites fluid. Conventional isolation strategies face a persistent trade-off between EV purity and yield. To overcome this, a magnetic bead-based protocol (Mag-Net) to enrich EVs according to electrochemical surface charge using strong anion-exchange chemistry (SAX) was adapted for proteomics. Our workflow is specifically adapted to ascites fluid from human or murine sources. This approach effectively separates EVs from high-abundance proteins and lipoproteins, enabling proteomic profiling from as little as 2 μL of ascites fluid. Demonstrated in both murine and human ovarian cancer models, Mag-Net offers a reproducible, scalable, and automation-ready solution for EV isolation from various biofluids.Key features• Extracellular vesicles (EVs) from murine and human ascites fluid are effectively enriched using Mag-Net beads.• EVs are effectively captured and eluted from Mag-Net beads to support Raman spectroscopy, nanoparticle tracking analysis, and atomic force microscopy.• EV isolation by Mag-Net provides robust proteomic depth obtained by mass spectrometry.• Robust proteomic data can be obtained from input volumes ranging from 2 to 100 μL of ascites.

Breast cancer (BC) is the most frequently diagnosed malignancy in women and a leading cause of cancer-related mortality worldwide. Current clinical management relies on molecular classification—based on estrogen receptor (ER), progesterone receptor (PR), HER2, and Ki67 expression—to guide prognosis and therapy. Triple-negative breast cancer (TNBC), which lacks ER, PR, and HER2 expression, represents 15%–20% of cases and is characterized by aggressive behavior, early recurrence, and a paucity of targeted treatment options. These challenges underscore the urgent need for improved preclinical models that better recapitulate tumor biology to accelerate therapeutic discovery. While conventional monolayer (2D) cultures have contributed significantly to cancer research, they fail to mimic critical features of the three-dimensional (3D) tumor microenvironment (TME), thereby limiting clinical translation. To address this gap, 3D spheroid models have emerged as a powerful intermediary, more accurately replicating in vivo conditions such as cell–cell and cell–matrix interactions, nutrient and oxygen gradients, and the development of hypoxic cores. These features make spheroids a physiologically relevant platform for studying complex processes like metastasis, drug resistance, and treatment response. Here, we present a robust, simple, and cost-effective protocol for generating uniform 3D spheroids. Our method enables consistent monitoring of spheroid formation and growth over time, with quantitative, image-based size analysis to ensure reproducibility and scalability. Designed for flexibility, the protocol is broadly applicable across diverse cell types, effectively bridging the gap between traditional 2D cultures and complex in vivo studies. By providing an accessible and reliable model of the 3D TME, this protocol opens new avenues for high-throughput drug screening, mechanistic studies of tumor progression, and the advancement of personalized medicine strategies in breast cancer and beyond.Key features• Employs a cost-effective, lab-made agarose coating to create non-adherent surfaces in standard 96-well plates.• Optimized for reproducible spheroid formation from the aggressive MDA-MB-231 triple-negative breast cancer cell line.• Requires a brief orbital shaking step to promote homogeneous cell aggregation and formation of a single central spheroid per well.• Generates measurable spheroids within 96 h using only basic cell culture equipment and an orbital shaker.• Provides a clear workflow from spheroid formation to quantitative size analysis, using freely available (ImageJ) and widely used (GraphPad Prism) software.

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for exploring cellular heterogeneity and host–pathogen interactions. This protocol details the Zika virus (ZIKV)-targeted scRNA-seq workflow for preparing high-quality single-cell suspensions from the whole brain tissues of neonatal mice, high-quality single-cell sorting, cDNA reverse transcription, amplification, ZIKV enrichment and host transcriptome library preparation, and sequencing dataset integration in downstream analysis to complete the quantification of ZIKV RNA in individual cells.Key features• Preparation of high-quality single-cell suspensions from the whole brain tissues of neonatal mice.• ZIKV-specific magnetic beads for using the ZIKV and host cell RNA capture.• ZIKV enrichment and host transcriptome library construction, providing a framework for quantifying viral load within individual cells.• Integration of viral enrichment and host transcriptomic datasets enables the visualization and quantification of ZIKV at single-cell resolution.