Immunofluorescence assay for demyelination, remyelination, and proliferation in an acute cuprizone mouse model

Here, we present a protocol to assess demyelination in the corpus callosum of an acute cuprizone mouse model, which is routinely used to induce demyelination for studying myelin regeneration in the rodent brain. We describe the tracing of neural stem cells via intraperitoneal injection of tamoxifen into adult Gli1CreERT2;Ai9 mice and the induction of demyelination with cuprizone diet. We also detail EdU administration, cryosectioning of the mouse brain, EdU labeling, and immunofluorescence staining to examine proliferation and myelination. For complete details on the use and execution of this protocol, please refer to Radecki et al. (2020).1.

Inducing primary brainstem gliomas in genetically engineered mice using RCAS/TVA retroviruses and Cre/loxP recombination

Genetically engineered mice are commonly used to model brainstem gliomas in pre-clinical research. One technique for inducing primary tumors in these genetically engineered mice involves delivering viral vectors containing the code for gene-editing proteins. We present a protocol for generating primary brainstem gliomas using the RCAS-TVA retroviral delivery system and the Cre/loxP gene editing system. We describe steps for transfecting and harvesting chicken fibroblast cells, intracranially injecting cells into mice, imaging primary tumors, and treating primary tumors with focal, image-guided brain irradiation. For complete details on the use and execution of this protocol, please refer to Deland et al. (2021).1.

An updated protocol for in vitro bovine embryo production

Cattle embryos represent a useful model for understanding parts of human embryogenesis due to various biological similarities. We describe a protocol to mature and fertilize bovine oocytes followed by culture of resulting presumptive zygotes up until the blastocyst stage. Our protocol features a unique procedure for washing and moving oocytes and zygotes between their respective dishes using a cell strainer. A thorough troubleshooting section will help users optimize embryo development with cleavage and blastocyst rates exceeding 70% and 20%, respectively. For complete details on the use and execution of this protocol, please refer to Wooldridge and Ealy (2019).1.

Generation of 3D ex vivo mouse- and patient-derived glioma explant slice model for integration of confocal time-lapse imaging and spatial analysis

Development of spatial-integrative pre-clinical models is needed for glioblastoma, which are heterogenous tumors with poor prognosis. Here, we present an optimized protocol to generate three-dimensional ex vivo explant slice glioma model from orthotopic tumors, genetically engineered mouse models, and fresh patient-derived specimens. We describe a step-by-step workflow for tissue acquisition, dissection, and sectioning of 300-μm tumor slices maintaining cell viability. The explant slice model allows the integration of confocal time-lapse imaging with spatial analysis for studying migration, invasion, and tumor microenvironment, making it a valuable platform for testing effective treatment modalities. For complete details on the use and execution of this protocol, please refer to Comba et al. (2022).1.

Isolation of slow-cycling cancer cells from lung patient-derived xenograft using carboxyfluorescein-succinimidyl ester retention-mediated cell sorting

The slow-cycling subpopulation plays an important role in anticancer drug resistance and tumor recurrence. Here, we describe a clinically relevant patient-derived xenograft model and a carboxyfluorescein succinimidyl ester dye that is diluted in a cell proliferation-dependent manner. We detail steps to separate active-cycling cancer cells and slow-cycling cancer cells (SCCs) in heterogeneous cancer populations to confirm their different cellular properties. This protocol can be used to distinguish SCCs, investigate their biology, and develop strategies for anticancer therapeutics. For complete details on the use and execution of this protocol, please refer to Cho et al. (2021).¹.

Generation of liver metastases in a mouse model using ultrasound-guided intravenous injection

Here, we present a protocol to generate a murine model of liver metastasis by directly injecting tumor cells into the portal vein under ultrasound guidance. We describe steps for animal and cell preparation and two techniques for injecting tumor cells. One technique is freehand, while the other technique is device-assisted using a 3D-printed prototype device. Finally, we describe tumor surveillance with bioluminescent imaging.

Protocol for analyzing root halotropism using split-agar system in Arabidopsis thaliana

Plant roots sense salt gradients in soil to avoid saline environments through halotropism. Here, we present a protocol to study halotropism with an optimized split-agar system that simulates the salt gradient in soil. We describe steps for preparation of the split-agar system, measurement of Na⁺, and observation of root bending. We then detail segmentation of root cells and visualization of microtubules and cellulose synthases. This system is simple to operate and has broader applications, such as hydrotropism and chemotropism. For complete details on the use and execution of this protocol, please refer to Yu et al. (2022).¹.

Protocol to establish a genetically tractable synthetic symbiosis between Sodalis praecaptivus and grain weevils by insect egg microinjection

We present a protocol to establish a synthetic symbiosis between the mCherry-expressing Sodalis praecaptivus and the grain weevil host, Sitophilus zeamais. We describe steps to isolate grain weevil eggs, followed by microinjecting the bacterial symbiont into insect eggs using a modified Drosophila injection protocol, which leads to localization of bacteria in female insect ovaries. We then detail larval transplantation and visualization of bacteria in live insects using a fluorescence dissection microscope to assess the transgenerational transmission to offspring in weevils. For complete details on the use and execution of this protocol, please refer to Su et al. (2022).¹.

Immunization of MERS-CoV-2-infected mice with a sublethal dose of MERS-CoV or VRP-MERS-S

Here, we detail the immunization of mice with a sublethal dose of MERS-CoV or two doses of replication-incompetent alphavirus replicon particles expressing MERS-CoV spike protein. We then describe steps to determine the outcome of immunization by challenging immunized mice with a lethal dose of MERS-CoV, as well as by detecting virus-specific neutralizing antibody and virus-specific T cell response via neutralization assay and flow cytometry, respectively. This protocol can be used to evaluate other CoV infections or vaccine-induced immune responses. For complete details on the use and execution of this protocol, please refer to Zheng et al. (2021).1.

Protocol to obtain high-quality single-cell RNA-sequencing data from mouse liver cells using centrifugation

High-quality single-cell RNA-sequencing data of liver cells, especially hepatocytes, are challenging due to cell death associated with hepatocyte isolation using fluorescence-activated cell sorting (FACS). Here, we present a protocol to obtain viable hepatocytes and nonparenchymal liver cells for scRNA-seq, using centrifugation. We detail steps for liver wash and enzyme perfusion, followed by in vitro dissociation of liver cells and gradient centrifugation. We further describe hepatocytes harvesting for subsequent viability check and scRNA-seq. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021) and Mederacke et al. (2015).

Protocol for intranasal chemoprevention delivery in a urethane mouse lung cancer model

Mouse iloprost lung cancer chemoprevention studies typically use oral delivery. Here, we present a protocol for intranasal iloprost delivery within a urethane lung adenocarcinoma mouse model. We detail steps for intraperitoneal urethane injection in mice, followed by nine-week monitoring, intranasal iloprost treatment, and lungs harvesting for analysis. This iloprost delivery approach parallels an ongoing phase II clinical trial of inhaled iloprost for lung cancer chemoprevention. This protocol diversifies options for chemoprevention studies and offers a relevant and translatable model. For complete details on the use and execution of this protocol, please refer to Sompel et al. (2022).

A behavioral assay to test sensory-cue-guided oriented flight in monarch butterflies under controlled conditions

Many animals use sensory cues to guide movement. Testing animals under conditions in which cues can be isolated and manipulated is key for understanding the function of cues. Here, we present a protocol to assess the flight of migratory monarch butterflies (Danaus plexippus). We describe procedures to optimize and conduct trials, especially under indoor conditions. This protocol facilitates testing monarchs in various experimental conditions including during their subjective night when they are not normally flying. For complete details on the use and execution of this protocol, please refer to Parlin et al. (2022).¹.

Protocol for mouse optogenetic fMRI at ultrahigh magnetic fields

Mouse optogenetic functional magnetic resonance imaging (opto-fMRI) is critical for linking genes and functions and for mapping cell-type-specific neural circuits in the whole brain. Herein, we describe how opto-fMRI images can be reliably obtained in anesthetized mice with minimal distortions at ultrahigh magnetic fields. The protocol includes surgical and anesthesia procedures, animal cradle modification, animal preparation and setup, animal physiology maintenance, and pilot fMRI scanning. This protocol will enable reproducible mouse opto-fMRI experiments. For complete details on the use and execution of this protocol, please refer to Jung et al. (2021),¹ Jung et al. (2022),² and Moon et al. (2021).³.

Generation of orthotopic patient-derived xenograft models for pancreatic cancer using tumor slices

Orthotopic patient-derived xenograft models recapitulate the genomic complexity of the original tumor and some aspects of local microenvironment, useful for rapid development and validation of personalized treatment strategies. Here, we precisely describe a protocol for generating tumor slices from human or murine-derived pancreatic cancer. They are then implanted directly into the murine pancreas, monitored using ultrasound, with a 90% success rate. This assay creates a clinically relevant in vivo model facilitating personalized treatment development.

Protocol to visualize distinct motoneuron pools in adult zebrafish via injection of retrograde tracers

In adult zebrafish, slow, intermediate, and fast muscle fibers occupy distinct regions of the axial muscle, allowing the use of retrograde tracers for selective targeting of the motoneurons (MNs) innervating them. Here, we describe a protocol to label distinct MN pools and tissue processing for visualization with confocal laser microscopy. We outline the different steps for selective labeling of primary and secondary MNs together with spinal cord fixation, isolation, mounting, and imaging. For complete details on the use and execution of this protocol, please refer to Pallucchi et al. (2022)¹ and Ampatzis et al. (2013).².

Protocol to colonize gnotobiotic mice in early life and assess the impact on early life immune programming

Understanding how changes in gut microbiota in early life impact immune programming can be difficult to study due to variations in the assembly of the microbiota. In this protocol, we describe how to colonize gnotobiotic/germ-free mice in early life with different microbiota community types (e.g., PAMI and PAMII). We detail several assays to determine whether differential colonization alters immune programming in early life. We also describe how to propagate mouse fecal microbiota transplant material if the donor fecal sample is limited. For complete details on the use and execution of this protocol, please refer to Lynn et al. (2021).¹.

Identification and functional characterization of potential oncofetal targets in human hepatocellular carcinoma

Here, we present a detailed protocol for the identification of potential oncofetal targets for hepatocellular carcinoma (HCC) patients through a hepatocyte differentiation model and a sorafenib refractory cell-line-derived xenograft model. We describe the procedures of tumor sphere formation, organoid generation, and subcutaneous tumor formation for functional studies. We then detail the procedures of immunohistochemistry and immunofluorescence for examination of changes in lineage-specific markers. Finally, we describe the development of antibody-based therapeutics targeting tumor lineage plasticity in HCC. For complete details on the use and execution of this protocol, please refer to Kong et al. (2021).¹.

Single-cell dissociation of the model cnidarian sea anemone Exaiptasia diaphana

The sea anemone Exaiptasia diaphana (Aiptasia) is a versatile model in studying cellular mechanisms that govern cnidarian-Symbiodiniaceae symbiosis, the foundation of coral reef ecosystems. Here, we provide a protocol to efficiently dissociate adult Aiptasia tissue into a single-cell suspension using enzymatic digestion. We detail steps including washing animals, dissociating tissue with pronase digestion, and evaluating dissociated single cells using fluorescence imaging. This procedure can be applied to other cnidarians, including coral polyps. For complete details on the use and execution of this protocol, please refer to Jinkerson et al. (2022).¹.

Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing

Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq3) enables high-throughput single-nucleus transcriptomic profiling of multiple samples in one experiment. Here, we describe an optimized protocol of mouse kidney nuclei isolation and sci-RNA-seq3 library preparation. The use of a dounce tissue homogenizer enables nuclei extraction with high yield. Fixed nuclei are processed for sci-RNA-seq3, and self-loaded transposome Tn5 is used for tagmentation in library generation. The step-by-step protocol allows researchers to generate scalable single-cell transcriptomic data with common laboratory supplies at low cost. For complete details on the use and execution of this protocol, please refer to Li et al. (2022).¹.

Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae

Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. ¹ and Ball et al..².

Measuring ventral nerve cord stiffness in live flat-dissected Drosophila embryos by atomic force microscopy

Drosophila is an amenable system for addressing the mechanics of morphogenesis. We describe a workflow for characterizing the mechanical properties of its ventral nerve cord (VNC), at different developmental stages, in live, flat-dissected embryos employing atomic force microscopy (AFM). AFM is performed with spherical probes, and stiffness (Young's modulus) is calculated by fitting force curves with Hertz's contact model. For complete details on the use and execution of this protocol, please refer to Karkali et al. (2022).

Adaptable toolbox to characterize Alzheimer's disease pathology in mouse models

Here, we describe a highly adaptable toolbox for characterizing and analyzing molecular and histopathological changes in Alzheimer's disease (AD) mouse models. We detail optimized and streamlined approaches from sample preparation to image analysis to facilitate reproducible analyses. We also describe the extraction and measurement of the soluble Aβ level by sandwich ELISA in the cortex and hippocampus of AD mouse models before and after plaque deposition. Finally, we outline the steps for image quantification and analysis using Imaris and ImageJ. For complete details on the use and execution of this protocol, please refer to Huang et al. (2021).¹.

Protocol for recording and analyzing spontaneous locomotion in Drosophila

The quantitative analysis of locomotion is used to study many biological processes. Here, we describe how to record the locomotion of up to 50 Drosophila individuals and process the resulting video files using FlyTracker. We detail the use of modifiable MatLab scripts to process structure array files generated by FlyTracker. We have applied this to study Drosophila movement during aging, but it could be used to address a variety of research questions. For complete details on the use and execution of this protocol, please refer to Barwell et al. (2021).¹.

Specific and efficient gene knockout and overexpression in mouse interscapular brown adipocytes in vivo

The classical Cre-LoxP system is time consuming. Here we detail a protocol that leverages Rosa26-LSL-Cas9;Adiponectin-Cre mice to restrict Cas9 expression in adipocytes. This enables specific deletion of target genes in brown adipocytes within 6 weeks by local injection of AAV-sgRNA into interscapular brown adipose tissue. We also describe an adiponectin-promoter-driven AAV vector to express sgRNA-resistant cDNA-encoded protein for subsequent rescue. This protocol thus provides an efficient means to specifically knockout and overexpress genes in brown adipocytes in vivo. For complete details on the use and execution of this protocol, please refer to Xue et al. (2022).¹.

Quantitative phenotypic screens of Aspergillus niger mutants in solid and liquid culture

This protocol describes procedures for quantifying Aspergillus niger growth in both solid and liquid culture. Firstly, by comparing radial growth between mutant and progenitor isolates on solid agar supplemented with sublethal stressors, susceptibility coefficients can be calculated. Secondly, analysis of macromorphological growth types in liquid culture allows full quantification of how a gene of interest affects submerged growth. By combining these assays, an extensive and quantitative dataset of how a gene of interest impacts growth in this fungus is possible. For complete details on the use and execution of this protocol, please refer to Cairns et al. (2019)¹ and Cairns et al. (2022).².