Protocol for image-based small-molecule screen to identify neuroprotective compounds for dopaminergic neurons in zebrafish

Whole-organism-based screen holds promise for discovering biologically active compounds. However, high-content imaging is challenging due to the difficulty of positioning live animals and individual variability of neuron counts. Here, we present a protocol to identify neuroprotective compounds for dopaminergic neurons in zebrafish using an image-based small-molecule screen. We describe steps for raising larvae, agarose embedding, and treatment to induce neurodegeneration. We then detail procedures for live confocal imaging, image processing, and data analysis. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).1.

Protocol for FRAP-based estimation of nuclear import and export rates in single yeast cells

Here, we present a protocol for estimating nuclear transport parameters in single cells. We describe steps for performing four consecutive fluorescence recovery after photobleaching experiments, fitting the obtained data to an ordinary differential equations model, and statistical analysis of the fittings using a specialized R package. This protocol permits the estimation of import and export rates, nuclear or cytosolic fixed fractions, and total number of molecules. For complete details on the use and execution of this protocol, please refer to Durrieu et al.1.

Protocol to generate traceable CAR T cells for syngeneic mouse cancer models

The efficacy of chimeric antigen receptor (CAR) T cell immunotherapy is limited by insufficient infiltration and activation of T cells due to the immunosuppressive tumor microenvironment. Preclinical studies with optimized mouse CAR T cells in immunocompetent mouse cancer models will help define the mechanisms underlying immunotherapy resistance. Here, we present a protocol for preparing mouse T cells and generating CAR T cells. We then detail procedures for testing their therapeutic efficacy and tracking them in a syngeneic mouse glioma model. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.

Ex vivo two-photon imaging of whole-mount skeletal muscles to visualize stem cell behavior

Quiescent skeletal muscle stem cells (MuSCs) are morphologically and functionally heterogeneous and exhibit different lengths of cellular extensions, which we call protrusions. Here, we present a protocol for ex vivo two-photon imaging of MuSCs in their native environment. We describe steps for muscle dissection, fixation, embedding, imaging, and analysis of datasets. This protocol allows the examination of MuSC morphology and protrusions at the single-cell level as well as stem cell numbers. For complete details on the use and execution of this protocol, please refer to Ma et al. (2022).1.

Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing

The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.

Analyzing engram reactivation and long-range connectivity

Here, we present a protocol for marking engram cells to efficiently measure reactivation levels and their projection pathways. We describe steps for genetic manipulation utilizing transgenic mice and viral infections, labeling engram cells, and a modified version of CLARITY, a tissue-clearing technique. This protocol can be adapted to various research inquiries that involve assessing the overlap of cell populations and uncovering novel long-range connectivity pathways. For complete details on the use and execution of this protocol, please refer to Refaeli et al. (2023).1.

Protocol for tail vein injection in Xenopus tropicalis tadpoles

Functional studies in post-embryonic Xenopus tadpoles are challenging because embryonic perturbations often lead to developmental consequences, such as lethality. Here, we describe a high-throughput protocol for tail vein injection to introduce fluorescent tracers into tadpoles, which we have previously used to effectively inject morpholinos and molecular antagonists. We describe steps for safely positioning tadpoles onto agarose double-coated plates, draining media, injecting into the ventral tail vein, rehydrating plates, and sorting tadpoles by fluorescence with minimal injury for high-throughput experiments. For complete details on the use and execution of this protocol, please refer to Kakebeen et al.,1 Patel et al.,2 and Patel et al.3.

Protocol to monitor cardiac function and hemodynamics in septic rodents

Septic cardiomyopathy is associated with high mortality in septic patients, characterized by reversible systolic and diastolic dysfunction. It is essential to monitor cardiac function and hemodynamic changes in septic animals. Here, we present a protocol to monitor cardiac function and hemodynamics in septic rodents. We describe steps for performing cecal ligation and puncture on rodents to induce sepsis, acquiring two-dimensional echocardiographic and M-mode ultrasonic images, and assessing mean arterial pressure in septic animals. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.

Protocol for analyzing the movement and uptake of isotopically labeled signaling molecule azelaic acid in Arabidopsis

Understanding the generation, movement, uptake, and perception of mobile defense signals is key for unraveling the systemic resistance programs in flowering plants against pathogens. Here, we present a protocol for analyzing the movement and uptake of isotopically labeled signaling molecule azelaic acid (AZA) in Arabidopsis thaliana. We describe steps to assess 14C-AZA uptake into leaf discs and its movement from local to systemic tissues. We also detail the assay for uptake and movement of 2H-AZA from roots to the shoot. For complete details on the use and execution of this protocol, please refer to Cecchini et al.1,2.

Establishing a mouse model of lung metastases using ultrasound-guided right heart ventricle injection

We report a technique to generate a murine model of lung metastases by selectively injecting tumor cells into the right heart ventricle under ultrasound guidance. First, we describe cell preparation and reference animal preparation as previously described. We then detail the technique using a previously described 3D-printed instrument stabilization device. Finally, we describe tumor growth surveillance using bioluminescent imaging. For complete details on the use and execution of this protocol, please refer to Labora et al.1.

Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing

Here, we present a protocol to generate B cell restricted mouse models of loss-of-function genetic drivers typical of lymphoproliferative disorders, using stem cell engineering of murine strains carrying B cell restricted Cas9 expression. We describe steps for preparing lentivirus expressing sgRNA-mCherry, isolating hematopoietic stem and progenitor cells, and in vitro transduction. We then detail the transplantation of engineered cells into recipient mice and verification of gene edits. These mouse models represent versatile platforms to model complex disease traits typical of lymphoproliferative disorders. For complete details on the use and execution of this protocol, please refer to ten Hacken et al.,1 ten Hacken et al.,2 and ten Hacken et al.3.

Protocol for the generation of Symbiodiniaceae mutants using UV mutagenesis

Genetic approaches are limited in the dinoflagellate family, Symbiodiniaceae, causing a bottleneck in the discovery of useful mutants toward the goal of preventing future coral bleaching events. In this protocol, we demonstrate the application of UV exposure, coupled with downstream phenotypic screening and mutant isolation, to form a UV mutagenesis pipeline. This pipeline provides an avenue to generate Symbiodiniaceae mutants to help link genotype to phenotype, as well as address previously unanswered questions surrounding relationships with host organisms, like coral. For complete details on the use and execution of this protocol, please refer to Jinkerson et al. (2022).1.

Protocol for the in vitro isolation and culture of mature adipocytes and white adipose tissue explants from humans and mice

White adipose tissue (WAT) explants culture allows the study of this tissue ex vivo, maintaining its structure and properties. Concurrently, isolating mature adipocytes facilitates research into fat cell metabolism and hormonal regulation. Here, we present a protocol for obtaining, isolating, and processing mature adipocytes, alongside the cultivation of WAT explants from humans and mice. We describe steps for WAT retrieval, culturing of WAT explants, WAT digestion, and adipocytes separation. We then detail procedures for culturing isolated mature adipocytes. For complete details on the use and execution of this protocol, please refer to Villanueva-Carmona et al. (2023).1.

Protocol for live imaging of transferred mouse bone marrow cells by two-photon microscopy

The in situ behavior of living cells can be visualized by two-photon microscopy. Here, we present a protocol for the live imaging of transferred mouse bone marrow cells by two-photon microscopy. We describe steps for staining and injecting target cells into mice, fixing the skull bone to a head holder and stage, and 4D imaging bone marrow using multi-photon microscopy. We then detail procedures for creating images and analyzing cells. For complete details on the use and execution of this protocol, please refer to Sudo et al. (2021).1.

Protocol for implementing medial forebrain bundle stimulation as a reward for perceptual tasks in mice

Training mice to perform perceptual tasks is a vital part of integrative neuroscience. Replacing classical rewards like water with medial forebrain bundle (MFB) stimulation allows experimenters to avoid deprivation and obtain higher trial numbers per session. Here, we provide a protocol for implementing MFB-based reward in mice. We describe steps for MFB electrode implantation, efficacy testing, and stimulation calibration. After these steps, MFB reward can be used to facilitate sensory discrimination task training and enable nuanced characterization of psychophysical abilities. For complete details on the use and execution of this protocol, please refer to Verdier et al. (2022).1.

Protocol for screening facultative parthenogenesis in Drosophila

Most species of sexually reproducing Drosophila are capable of some degree of facultative parthenogenesis, which involves the initiation of development in an unfertilized egg. Here, we present an optimized protocol to screen facultative parthenogenesis in Drosophila. We describe steps for the collection and maintenance of virgin flies. We then detail offspring screening for the analysis of parthenogenesis. This protocol can be applied to different Drosophila strains and can be adapted for the analysis of parthenogenesis in other animals. For complete details on the use and execution of this protocol, please refer to Sperling et al.1.

A protocol for measuring the sexual receptivity of female Drosophila

Female receptivity in mating is crucial for successful copulation, but protocols for quantifying female behaviors reflecting receptivity are scarce compared to the analysis of male behaviors. Here, we present a protocol for assessing the sexual receptivity of female Drosophila that considers behaviors from both sexes. We describe steps for preparing and loading flies into a courtship chamber, video recording the behaviors of the pairs, and analyzing their behavioral displays. This protocol includes behavior recognition criteria suitable for typical laboratory settings. For complete details on the use and execution of this protocol, please refer to Yang et al. (2023).1.

Protocol for cytokine and uterine immune cell characterization in a mouse model of LPS-induced preterm birth

Inflammation-driven preterm birth (PTB) is modeled in mice using lipopolysaccharide (LPS) challenge. Here, we present a protocol for cytokine and uterine immune cell characterization in a mouse model of LPS-induced PTB. We describe steps for LPS challenge, in vivo cytokine capture assay, and isolation of uterine immune cells for flow cytometry. These techniques allow examination of systemic inflammation in vivo and immune cell characterization at the maternal-fetal interface, facilitating exploration of inflammatory dynamics in mouse models of PTB susceptibility. For complete details on the use and execution of this protocol, please refer to Doll et al.1.

Surgical protocol for pulmonary artery banding in mice to generate a model of pressure-overload-induced right ventricular failure

Right ventricular failure (RVF) is the leading cause of death in patients with pulmonary hypertension. Here, we present a protocol for pulmonary artery banding in mice to generate a model of pressure-overload-induced RVF. We describe steps for anesthesia of mice, endotracheal intubation, and pulmonary artery banding surgery. We then detail procedures for phenotyping and analysis. Our approach does not involve complete blockage of the pulmonary flow during clip placement and is, therefore, associated with low intraoperative mortality. For complete details on the use and execution of this protocol, please refer to Veith et al. (2020).1.

Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses

Here, we present Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping, a user-friendly pipeline for the registration and analysis of whole-brain images in larval zebrafish. We describe steps for pre-processing, registration, quantification, and visualization of whole-brain phenotypes in zebrafish mutants of genes associated with neurodevelopmental and neuropsychiatric disorders. By utilizing BioImage Suite Web, an open-source software package originally developed for processing human brain imaging data, we provide a highly accessible whole-brain mapping protocol developed for users with general computational proficiency. For complete details on the use and execution of this protocol, please refer to Weinschutz Mendes et al. (2023).1.

Protocol to investigate the neural basis for copulation posture of Drosophila using a closed-loop real-time optogenetic system

In internal fertilization animals, maintaining a copulation posture facilitates the process of transporting gametes from male to female. Here, we present a protocol to investigate the neural basis for copulation posture of fruit flies using a closed-loop real-time optogenetic system. We describe steps for using deep learning analysis to enable optogenetic manipulation of neural activity only during copulation with high efficiency. This system can be applied to various animal behaviors other than copulation. For complete details on the use and execution of this protocol, please refer to Yamanouchi et al. (2023).1.

Protocol for orthotopic single-lung transplantation in mice as a tool for lung metastasis studies

The transplantation model provides the opportunity to assess the relevance of a molecule of interest for tumor cell extravasation by using a respective genetically modified donor animal. Here, we present a protocol for orthotopic single-lung transplantation in mice as a tool for lung metastasis studies. We describe steps for animal preparation, lung transplantation, and tumor cell injection. We then detail procedures for the direct comparison of tumor cell spreading between the genetically modified left lung and the naive right lung parenchyma. For complete details on the use and execution of this protocol, please refer to Giannou et al. (2023).1.

Protocol to build a drug-testing pipeline using large populations of Drosophila melanogaster

As a small animal that recapitulates many fundamental aspects of human disease, Drosophila lends itself to probing the biological activity of molecules and drug candidates. Here, we present a protocol to build a drug-testing pipeline in Drosophila. We describe steps for generating synchronous populations of Bicaudal C mutants by genetic crossing and wild-type fly culturing for controlled compound administration and exemplary phenotypic assays. For complete details on the use and execution of this protocol, please refer to Millet-Boureima et al.,1 Millet-Boureima et al.,2 and Gamberi et al.3.

Protocol for tissue processing and paraffin embedding of mouse brains following ex vivo MRI

Combining histology and ex vivo MRI from the same mouse brain is a powerful way to study brain microstructure. Mouse brains prepared for ex vivo MRI are often kept in storage solution for months, potentially becoming brittle and showing reduced antigenicity. Here, we describe a protocol for mouse brain dissection, tissue processing, paraffin embedding, sectioning, and staining. We then detail registration of histology to ex vivo MRI data from the same sample and extraction of quantitative histological measurements.

Quantitative live-cell imaging of Candida albicans escape from immune phagocytes

Population-level dynamics of host-pathogen interactions can be characterized using quantitative live-cell imaging. Here, we present a protocol for infecting macrophages with the fungal pathogen Candida albicans in vitro and quantitative live-cell imaging of immune and pathogen responses. We describe steps for detailed image analysis and provide resources for quantification of phagocytosis and pathogen escape, as well as macrophage membrane permeabilization and viability. This protocol is modifiable for applications with a range of pathogens, immune cell types, and host-pathogen mechanisms. For complete details on the use and execution of this protocol, please refer to Olivier et al.1.