Immunostaining of tumor-infiltrating immune-cell-related markers and cytokines in the tumor fractional radiation model of host PD-L1-deficient mice

In this protocol, we describe how to explore immune function in radiation-induced anti-tumor abscopal effect (ATAE) in PD-L1-deficient (PD-L1^-/-) mice. We detail steps for primary and abscopal tumor model establishment in mice, tumor fractional irradiation scheme, and isolation of single cells from tumor tissues. Furthermore, we describe the analysis of the proportion of immune cells infiltrated in tumors and the specific staining of cytokines released from immune cells to confirm the ability of CD8+ T cells in killing tumors. For complete details on the use and execution of this protocol, please refer to Zhao et al. (2022).¹.

An analysis pipeline to compare explorative locomotion across fish species

Recently, we introduced a powerful approach that leverages differences in swimming behaviors of two closely related fish species to identify previously unreported locomotion-related neuronal correlates. Here, we present this analysis approach applicable for any species of fish to compare their short and long timescale swimming kinematics. We describe steps for data collection and cleaning, followed by the calculation of short timescale kinematics using half tail beats and the analysis of long timescale kinematics using mean square displacement and heading decorrelation. For complete details on the use and execution of this protocol, please refer to Rajan et al. (2022).¹.

A protocol for establishing a male G×E schizophrenia mouse model

Schizophrenia pathogenesis involves both genetic and environmental factors (G×E). Here, we present a protocol to prepare a schizophrenia rodent model with a specific G×E pair. We describe the breeding of Bdnf-e6-/- mice with genetic deficiency in promoter-VI-driven BDNF expression. We then detail the procedure to expose the mice to postnatal environmental stress including hypoxia, social isolation, and corticosterone. This model better represents the etiology of schizophrenia and thus may facilitate basic research and drug development for schizophrenia. For complete details on the use and execution of this protocol, please refer to Chen et al. (2022).¹.

Protocol for gene characterization in Aspergillus niger using 5S rRNA-CRISPR-Cas9-mediated Tet-on inducible promoter exchange

This protocol presents an efficient genetic strategy to investigate gene function in the fungus Aspergillus niger. We combined 5S rRNA-CRISPR-Cas9 technology with Tet-on gene switch to generate conditional-expression mutants via precisely replacing native promoter with inducible promoter. We describe the design and DNA preparation for sgRNAs and donor DNA. We then detail the steps for DNA co-transformation into A. niger protoplasts by PEG-mediated transformation, followed by homozygote isolation. Finally, we describe the genome verification and strain validation of the isolates. For complete details on the use and execution of this protocol, please refer to Zheng et al. (2019).¹.

Non-invasive chimeric HaloTag labeling to study clustering and diffusion of membrane proteins

As live imaging plays an increasingly critical role in cell biology research, the desire to label and track individual protein molecules in vivo has been growing. To address this, in this protocol we describe steps for sparse labeling using two different HaloTag ligand dyes in C. elegans. This labeling approach is simple, is non-invasive, and preserves the view of the bulk protein population. We further describe how to carry out single-particle tracking experiments and extract information about particle diffusion behavior. For complete details on the use and execution of this protocol, please refer to Chang and Dickinson (2022).¹.

Protocol to measure ß-galactosidase in Drosophila extracts using a CPRG assay

The quantification of ß-galactosidase activity is routinely required by laboratories worldwide. We present a cost-effective, highly replicable, simple technique for quantifying ß-galactosidase-specific activity from crude extracts made from whole organisms or dissected tissues or cells. Extracts are prepared and measured without the need for any specialized equipment, and tissue is ground manually by pestle and measured by colorimetric CPRG and Bradford assays. This protocol describes the assay using Drosophila extracts but could be applied to any biological system of interest. For complete details on the use and execution of this protocol, please refer to Seroude et al. (2002),¹ Poirier et al. (2008),² and Barwell et al. (2017).³.

Generation of iPSC-based human-mouse microglial brain chimeras to study senescence of human microglia

Here, we provide a step-by-step protocol for generating human induced pluripotent stem cell (hiPSC)-based microglial mouse brain chimeras. In addition, we detail steps for intracerebral injection of pathological tau and magnetic cell isolation of human microglia from chimeric mouse brains for single-cell RNA sequencing. Human microglia developed in chimeric mouse brains recapitulate the pathophysiology of microglia in human brain tissue, offering unprecedented opportunities to study human microglial senescence in vivo. For complete details on the use and execution of this protocol, please refer to (Jin et al., 2022b).

A protocol to characterize zebrafish LGP2 as a dual regulator of IFN response during viral infection

Here, we present a protocol to characterize zebrafish LGP2 as a dual regulator of interferon (IFN) response. We detail in vivo assays using time-lapse comparison of IFN response between wild-type and lgp2 knockout zebrafish following spring viraemia of carp virus (SVCV) infection. We also describe in vitro assays including titration of infection duration in SVCV-infected fish cells to determine changes in IFN response. This protocol is effective to illuminate a regulatory switch of LGP2 in fish cells toward virus infection. For complete details on the use and execution of this protocol, please refer to Gong et al. (2022).¹.

High-throughput genetic screening of meiotic commitment using fluorescence microscopy in Saccharomyces cerevisiae

Simple genetic screens in budding yeast have identified many conserved meiotic regulators. However, the identification of genes involved in specific steps of meiosis may require a more complex genetic screen that allows visualization of meiosis. Here, we describe a high-throughput protocol using fluorescence microscopy to systematically screen an overexpression library to identify genes involved in meiotic commitment. We also explain how this protocol can be adapted for identifying proteins that function at different stages of meiosis.

For complete details on the use and execution of this protocol, please refer to Gavade et al. (2022).

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Step-by-step protocol to identify budding yeast genes involved in meiotic commitment

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Protocol for high-throughput yeast transformations in 96-well plates

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Protocol for meiotic induction in 96-well plates

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Description of how to analyze meiotic cells using fluorescence microscopy

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples

Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene V4 region sequencing, and bioinformatic analyses. This protocol includes detailed instructions and example outputs to ensure accurate, reproducible results and data visualization. Comprehensive troubleshooting and limitation sections address technical and statistical issues that may arise when profiling microbiota. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2022).

Using fluorescent indicators for in vivo quantification of spontaneous or evoked motor neuron presynaptic activity in transgenic zebrafish

In this protocol, we describe steps that utilize the optical clarity of the zebrafish larvae and the stereotyped motor neuron axon structure in the trunk to measure spontaneous or evoked motor neuron axon activity. This activity is detected with transgenic fluorescent indicators introduced into the larvae by zygotic injection. Fluorescent indicator intensity changes in the small neuromuscular junctions are quantified to measure the presynaptic calcium activity and consequent synaptic vesicle release. For complete details on the use and execution of this protocol, please refer to Mandal et al. (2020).

An optimized protocol for assessing changes in mouse whole-brain activity using opto-fMRI

Functional magnetic resonance imaging (fMRI) in mouse brain, paired with spatially and temporally defined manipulations, offers a powerful tool to causally explain the effect of specific neuronal activity on brain network dynamics. Here, we present an optimized protocol to measure cell-type-specific contributions to changes in whole-brain dynamics in mice using optogenetics (opto)-fMRI. This protocol details the injection of ChR2-expressing AAV, the implantation of optical fiber, the steps to perform opto-BOLD (blood-oxygenation-level-dependent) fMRI recording, and data analysis. For complete details on the use and execution of this protocol, please refer to Grimm et al. (2021).

Protocol for renal ischemia-reperfusion injury by flank incisions in mice

Ischemia-reperfusion injury (IRI) contributes to acute kidney injury (AKI) and development of chronic kidney disease. We describe an IRI protocol for mice via flank incisions approach, using a pedicle clamp to cause ischemic injury. Compared with trans-abdominal approach, it is technically easier with lesser fluid loss and organ injury. Technical challenges during the dissection of renal pedicles are highlighted. For complete details on the execution of this protocol, please refer to Lai et al. (2014).

Environmental enrichment and exercise housing protocols for mice

Here, we present a protocol that allows comparison of the effects of the standard home cage, environmentally enriched home cage with additional super-enrichment, and the exercise (running wheels only) home cage in laboratory mice. We first describe the steps to assemble these three types of cages, respectively. We then detail the assembly of super-enrichment arenas, which provide additional stimulation beyond that provided by home-cage enrichment. This protocol can help to improve reproducibility of results from studies involving environmental enrichment and exercise by offering consistent housing conditions between laboratories. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2021).

CRISPR/Cas9-mediated tissue-specific knockout and cDNA rescue using sgRNAs that target exon-intron junctions in Drosophila melanogaster

In this protocol, we take CRISPR/Cas9 and Gal4/UAS approaches to achieve tissue-specific knockout in parallel with rescue of the knockout by cDNA expression in Drosophila. We demonstrate that guide RNAs targeting the exon-intron junction of target genes cleave the genomic locus of the genes, but not UAS-cDNA transgenes, in a tissue where Gal4 drives Cas9 expression. The efficiency of this approach enables the determination of pathogenicity of disease-associated variants in human genes in a tissue-specific manner in Drosophila. For complete details on the use and execution of this protocol, please refer to Yap et al. (2021).

Simultaneous recording of neuronal and vascular activity in the rodent brain using fiber-photometry

Coupling of hemodynamic responses to neuronal activity is the foundation of several functional neuroimaging techniques. Here, we provide three fiber-photometry approaches to simultaneously measure neuronal and vascular signals in the rodent brain using a spectrometer-based system. Two out of these three approaches allow the removal of hemoglobin (Hb)-absorption artifacts and restore the underlying neuronal activity. This technique is applicable to different fluorescent sensors and provides a more accurate measurement of hemodynamic response function in any location of the rodent brain. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).

Protocols for measuring cold-evoked neural activity and cold tolerance in Drosophila larvae following fictive cold acclimation

Here, we outline protocols to study cold acclimation in Drosophila from a neurobiological perspective, starting with fictive cold acclimation using a custom-built optogenetics-housing apparatus we call the OptoBox. We also provide detailed steps for single-unit electrophysiological recordings from larval cold nociceptors and a high-throughput cold-tolerance assay. These protocols expand the toolkit for the study of insect cold acclimation and nociception. For complete details on the use and execution of this protocol, please refer to Himmel et al. (2021).

Protocol to downregulate GABAergic-astrocyte signaling via astrocyte-selective ablation of GABAB receptor in adult mice

Here, we present a protocol to selectively downregulate GABA_B receptor (GABA_BR) expression in astrocytes of mouse medial prefrontal cortex (mPFC). We first describe the procedure of surgeries and viral injections. We then detail genetic, histological, and functional characterizations of astrocytic GABA_BR ablation using RT-PCR, imaging, and behavioral assays. The use of GABA_B flox mice can be easily adapted to generate astrocyte-selective GABA_BR ablation in different brain areas and postnatal stages, leading to local downregulation of GABAergic-astrocyte signaling without developmental issues. For complete details on the use and execution of this protocol, please refer to Mederos et al. (2021).

Protocol for culturing and imaging of ectodermal cells from Xenopus

The Xenopus embryo provides an advantageous model system where genes can be readily transplanted as DNA or mRNA or depleted with antisense techniques. Here, we present a protocol to culture and image the cell biological properties of explanted Xenopus cap cells in tissue culture. We illustrate how this protocol can be applied to visualize lysosomes, macropinocytosis, focal adhesions, Wnt signaling, and cell migration. For complete details on the use and execution of this protocol, please refer to Tejeda-Muñoz et al. (2022).

In vivo gain-of-function cDNA library screening for colonization genes in a mouse model of pulmonary metastasis

We provide a protocol for gain-of-function (GOF) cDNA screen of genes that foster cancer cell colonization of secondary tissues, the last and most lethal step of the metastasis cascade. We present techniques for cDNA viral library preparation and delivery leading up to the recovery of colonization-promoting sequences in a proof-of-concept DU145-based mouse model of pulmonary metastasis. Adapted to other cDNA libraries and cancer models, this approach would prove widely useful in enumerating intrinsic genetic determinants underlying metastatic colonization.

For complete details on the use and execution of this protocol, please refer to Tu et al. (2021).

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Colonization is the last and most lethal bottleneck step of the metastasis cascade

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Gain-of-function (GOF) cDNA screen was adapted to probe cancer colonization of lung

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DU145 cells harboring GOF prostate cDNA library generated pulmonary macro-metastases

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Genomic PCR of macro-colonies exposed inserted cDNAs of potential colonization genes

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

A modified surgical procedure using minimally invasive ileocolic vein perfusion in a mouse intrahepatic islet transplant model

Murine intrahepatic islet transplantation is a clinically relevant but technically challenging surgical procedure because of frequent lethal postoperative bleeding. Here, we describe a protocol for mouse pancreatic islet isolation, purification, and culture. Besides, we also describe a protocol for intrahepatic islet transplantation through the ileocolic vein. Intrahepatic islet transplantation through the ileocolic vein, as opposed to traditional islet perfusion via the main portal vein, has the advantage of improving recovery after surgery and may facilitate islet survival and function in preclinical settings. For complete details on the use and execution of this protocol, please refer to Shrestha et al. (2020).

Synthesis of 124I-labeled epichaperome probes and assessment in visualizing pathologic protein-protein interaction networks in tumor bearing mice

Epichaperomes are disease-associated pathologic scaffolds composed of tightly bound chaperones and co-chaperones. They provide opportunities for precision medicine where aberrant protein-protein interaction networks, rather than a single protein, are detected and targeted. This protocol describes the synthesis and characterization of two 124I-labeled epichaperome probes, [124I]-PU-H71 and [124I]-PU-AD, both which have translated to clinical studies. It shows specific steps in the use of these reagents to image and quantify epichaperome-positivity in tumor bearing mice through positron emission tomography. For complete details on the use and execution of this protocol, please refer to Bolaender et al. (2021), Inda et al. (2020), and Pillarsetty et al. (2019).

Protocol to assess the effect of disease-driving variants on mouse brain morphology and primary hippocampal neurons

Genetic variants that affect neurological function will often produce changes visible at the level of gross morphology, either of the whole brain or of specific neuronal types. Here we describe how to perfuse and dissect the brain in preparation for Nissl staining. Then we outline steps for culturing mouse primary hippocampal neurons to evaluate dendritic arborization (Sholl analysis). For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).

Single-sister labeling in the C. elegans germline using the nucleotide analog EdU

Reciprocal exchanges between genetically identical sister chromatids (sister chromatid exchanges or SCEs) have been challenging to study. Here, we describe a protocol that utilizes a pulse/chase of the thymidine analog 5-ethyl-3′-deoxyuridine (EdU) in combination with click chemistry and antibody labeling to selectively label sister chromatids in the C. elegans germline. Labeling has no discernable effects on meiosis, allowing for cytological quantification of SCEs. This protocol can be combined with a variety of imaging approaches, including STED, confocal and super-resolution.

For complete details on the use and execution of this protocol, please refer to Almanzar et al. (2021).

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Pulse/chase labeling of individual sister chromatids in the C. elegans germline

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Can be readily combined with immunofluorescence or other labeling techniques

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Wide fluorophore support suited for confocal, STED and super-resolution imaging ima

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Variable chase times allows visualization of single sisters throughout meiosis

Incorporation of reporter genes into mitochondrial DNA in budding yeast

Many aspects of mitochondrial gene expression are still unknown, which can be attributed to limitations in molecular tools. Here, we present a protocol to introduce reporter genes into the mitochondrial genome of budding yeast, Saccharomyces cerevisiae. Mitochondrially encoded reporter constructs can be used to interrogate various aspects of mitochondrial gene expression. The power of this technique is exemplified by a mitochondrially encoded nanoluciferase, which allows to monitor levels of mitochondrial translation under a variety of growth conditions.