Protocol for expression of murine milk using modified human breast pump parts

Understanding the nutritional and immunomodulatory components of breast milk is crucial to developing novel mechanisms to optimize neonatal health. Here, we present a protocol to express and isolate murine milk in sufficient quantities for further analysis of components and bioactivity. We describe steps for separating dams from pups, administering intraperitoneal anesthetic and oxytocin, and expressing milk using a minimally modified and readily available commercial breast pump parts. For complete details on the use and execution of this protocol, please refer to Meyer et al. (2022).1.

Protocol for extracting live blastoderm cells from embryos of annual killifish

The implementation of in vitro approaches using undifferentiated embryonic cells from annual killifish to complement existing in vivo developmental studies has been hindered by a lack of efficient isolation techniques. Here, we present a protocol to isolate annual killifish blastoderm cells, at the epiboly and early dispersion phase, from embryos. We describe steps for hair removal, embryo cleaning, dechorionation, and cell purification. This protocol may also be used to develop strategies to isolate cells from embryos presenting similar challenges.

Using the single-cell imaging system and orthotropic footpad injection to establish mouse models for experimental and spontaneous melanoma metastasis

Metastasis, a complex process, is responsible for most deaths in patients with cancer. Clinically relevant research models are indispensable to advancing our understanding of metastatic mechanisms and developing new treatments. We here describe detailed protocols to establish mouse models for melanoma metastasis using the single-cell imaging system and orthotropic footpad injection. The single-cell imaging system permits the tracking and quantification of early metastatic cell survival, while the orthotropic footpad transplantation mimics aspects of the complex metastatic process. For complete details on the use and execution of this protocol, please refer to Yu et al.1,2.

Inoculation of Arabidopsis seedlings with Ralstonia solanacearum in sterile agar plates

Ralstonia solanacearum invades plants through their roots and causes devastating bacterial diseases in multiple crops. Here, we present a versatile inoculation assay in Arabidopsis thaliana seedlings grown in sterile agar plates. We describe steps for plant preparation, bacterial inoculation, tissue sampling, and bacterial quantification. This protocol can be used for accurate assessment of bacterial colonization and observation of plant response to infection. For complete details on the use and execution of this protocol, please refer to Dindas et al. (2022).1.

Kidney capsule transplantation of chemically treated embryonic murine tooth germs

Subcapsular transplantation of developing tissues and organs into the richly vascularized murine kidney provides the necessary trophic support, thus ensuring proper completion of their growth.1,2,3 Here, we provide a protocol for kidney capsule transplantation that allows the full differentiation of embryonic teeth previously exposed to chemicals. We describe steps for dissection and in vitro culture of embryonic teeth, followed by transplantation of tooth germs. We then detail harvesting of kidneys for further analysis. For complete details on the use and execution of this protocol, please refer to Mitsiadis et al.4.

Modified Capillary Feeder assay using micro-tips to measure real-time feeding in Drosophila

Capillary Feeder assay (CAFE) is a real-time feeding assay used in Drosophila that employs micro-capillaries, which are costly. Here, we present a modified version of the assay by replacing micro-capillaries with micro-tips, hence ensuring the same principle with cost reduction by 500 times. We developed a mathematical approach to measure volume for the conical shaped micro-tips. In this protocol, we describe step-by-step procedures of pre-assay setup along with fly rearing; assay setup included with detailed analysis for volume calculations. For further verification and use of this protocol, please refer to Segu and Kannan.1.

Differential systemic decellularization in vivo to study molecular changes in each vasculature layer in murine models of disease

Vascular dysfunction underlies the onset and progression of many life-threatening diseases, highlighting the need for improved understanding of its molecular basis. Here, we present differential systemic decellularization in vivo (DISDIVO), a protocol that enables systemic and independent study of the molecular changes in each vasculature layer in murine models of disease. We describe steps for anesthesia, perfusion surgery, and exsanguination. We then detail detachment and collection of glycocalyx and decellularization and collection of both endothelial and smooth muscle cells. For complete details on the use and execution of this protocol, please refer to Serra et al., Gallart-Palau et al., and Vinaiphat et al.1,2,3.

CRISPR generation of CSF1R-G795A human microglia for robust microglia replacement in a chimeric mouse model

Chimeric mouse models have recently been developed to study human microglia in vivo. However, widespread engraftment of donor microglia within the adult brain has been challenging. Here, we present a protocol to introduce the G795A point mutation using CRISPR-Cas9 into the CSF1R locus of human pluripotent stem cells. We also describe an optimized microglial differentiation technique for transplantation into newborn or adult recipients. We then detail pharmacological paradigms to achieve widespread and near-complete engraftment of human microglia. For complete details on the use and execution of this protocol, please refer to Chadarevian et al. (2023).1.

Protocol for culturing the endocrine junctional zone of the mouse placenta in serum-free medium

The lack of a suitable explant culture system restricts the study of factors secreted by the mouse placenta into maternal circulation. Here, we present a protocol for culturing the endocrine junctional zone of the mouse placenta, free from the decidua and labyrinthine layers in serum-free medium. We describe steps for dissecting and separating layers, dicing tissue, and culture setup. We then detail medium processing for downstream analysis. This model allows the investigation of placental signals that may regulate maternal physiology. For complete details on the use and execution of this protocol, please refer to Yung et al. (2023).1.

Protocol for evaluation of tumor-derived exosome-induced cancer cell metastasis in a mouse model

Exosomes mediate intracellular communication between cancer cells and the local/distant microenvironment, which promotes systemic dissemination of cancer. Here, we present a protocol for tumor-derived exosome isolation and in vivo metastasis evaluation in a mouse model. We describe steps for isolating and characterizing exosomes, establishing a metastatic mouse model, and injecting exosomes into mouse. We then detail hematoxylin and eosin staining and analysis. This protocol can be used to investigate exosome function and identify unexplored metastatic regulators related to exosome biogenesis. For complete details on the use and execution of this protocol, please refer to Lee et al. (2023).1.

Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq

Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.

Two-step CRISPR-Cas9 protocol for transposable element deletion in D. melanogaster natural populations

We present a protocol for generating a precise deletion, without altering the genetic background of the strain, of a transposable element (TE) in a natural population of Drosophila melanogaster using two steps of CRISPR-Cas9 homology-directed repair. We describe steps for replacing the TE by a fluorescent marker and for subsequent marker removal using single-guide RNAs, repair plasmids, and microinjection. We also detail steps for screening the deletion of the TE and generating a homozygous mutant strain. For complete details on the use and execution of this protocol, please refer to Merenciano and Gonzalez.1.

Isolation and profiling of viable tumor cells from human ex vivo glioblastoma cultures through single-cell transcriptomics

Single-cell RNA-sequencing (scRNA-seq) is becoming a ubiquitous method in profiling the cellular transcriptomes of both malignant and non-malignant cells from the human brain. Here, we present a protocol to isolate viable tumor cells from human ex vivo glioblastoma cultures for single-cell transcriptomic analysis. We describe steps including surgical tissue collection, sectioning, culturing, primary tumor cells inoculation, growth tracking, fluorescence-based cell sorting, and population-enriched scRNA-seq. This comprehensive methodology empowers in-depth understanding of brain tumor biology at the single-cell level. For complete details on the use and execution of this protocol, please refer to Ravi et al.1.

Protocol for diagnosing Erwinia amylovora infection using a fluorescent probe

Current fire blight diagnosis techniques are DNA based and require specialized equipment and expertise, or they are less sensitive. Here, we present a protocol for diagnosing fire blight using the fluorescent probe, B-1. We describe steps for Erwinia amylovora culture, implementing a fire blight-infected model, and E. amylovora visualization. This protocol allows for detection of fire blight bacteria of up to 102 CFU/mL on plants or objects in just 10 s with a simple application including spraying and swabbing. For complete details on the use and execution of this protocol, please refer to Jung et al.1.

Protocols for transgenesis at a safe harbor site in the Xenopus laevis genome using CRISPR-Cas9

We have established a new transgenesis protocol based on CRISPR-Cas9, "New and Easy XenopusTransgenesis (NEXTrans)," and identified a novel safe harbor site in African clawed frogs, Xenopus laevis. We describe steps in detail for the construction of NEXTrans plasmid and guide RNA, CRISPR-Cas9-mediated NEXTrans plasmid integration into the locus, and its validation by genomic PCR. This improved strategy allows us to simply generate transgenic animals that stably express the transgene. For complete details on the use and execution of this protocol, please refer to Shibata et al. (2022).1.

Protocol to locally express cxcl12a during zebrafish olfactory organ development by combining IR-LEGO with live imaging

Temporal and spatial regulation of gene expression is crucial for proper embryonic development. Infrared laser-evoked gene operator (IR-LEGO) can provide information for various developmental processes. Here, we present a protocol to locally express cxcl12a during zebrafish olfactory organ development1 using a combination of IR-LEGO and live imaging. We describe steps for implementing IR-LEGO, biological sample preparation, live imaging, data collection, and analysis. This protocol can be applied to virtually any genetically modified experimental organism.

Protocol for isolation of mouse pre-implantation embryos for gene expression analysis

Visualizing and quantifying the numerous factors that regulate murine pre-implantation embryonic development is technically challenging. Here, we present a protocol for the isolation of pre-implantation embryos at multiple stages of embryonic development to study gene expression. We describe steps for isolating RNA and cDNA synthesis from a small number of embryos. We then detail an immunofluorescence assay for the detection and localization of protein of interest by confocal microscopy in the pre-implantation embryos. For complete details on the use and execution of this protocol, please refer to Varghese et al.1.

Using Taxol-sensitized budding yeast to investigate the effect of microtubule stabilization on anaphase onset

The microtubule (MT)-stabilizing drug Taxol (paclitaxel) is a commonly used tool to investigate MT dynamics and MT-dependent processes. Here, we present a protocol for using Taxol-sensitized budding yeast to investigate the effect of microtubule stabilization on anaphase onset. We describe steps for establishing a log phase culture, synchronizing cells in G1, arresting in metaphase, and releasing cells into Taxol. We then detail procedures for imaging and scoring anaphase onset. This protocol facilitates maintenance and reproducibility in testing drug-sensitized and Taxol-sensitized yeast strains. For complete details on the use and execution of this protocol, please refer to Proudfoot et al.1.

Synthesis of fluorinated triphenylphosphonium analogs that improve cancer cell selectivity and in vivo detection

Triphenylphosphonium (TPP+) compounds like mito-metformin (MMe) target cancer cells by exploiting their hyperpolarized mitochondrial membrane potential. Here, we present a protocol for synthesizing TPP+ analogs with selectivity for mammalian cancer cells, reduced toxicity, and quantifiability using fluorine-19 nuclear magnetic resonance (19F-NMR). We describe steps for treating mammalian cells with mitochondria-targeted compounds, treating and preparing mouse tissue with these compounds, and 19F-NMR detection of MMe analogs in cells and tissue. TPP+-conjugated metformin analogs include para-methoxy (pMeO-MMe) and para-trifluoromethyl MMe (pCF3-MMe) and meta-trifluoromethyl MMe (mCF3-MMe).

Protocol to minimize the confounding effect of cold stress on socially isolated mice using thermoneutral housing

Social isolation, a risk factor for mortality and various disease states, in mice remains poorly understood, due in part to under-consideration of housing temperature and the murine thermoneutral zone. Here, we present a housing protocol to minimize the confounding effect of chronic cold stress on socially isolated mice that are unable to socially thermoregulate. We describe steps for allocating mice to group housing or social isolation conditions, housing mice in thermoneutral cabinets, feeding mice with high-fat diet, and measuring body weight, food intake, and metabolic indicators. For complete details on the use and execution of this protocol, please refer to Queen et al..1.

Protocol for human brain organoid transplantation into a rat visual cortex to model neural repair

Human stem-cell-derived organoids represent a promising substrate for transplantation-based neural repair. Here, we describe a protocol for transplanting forebrain organoids into an injured adult rat visual cortex. This protocol includes surgical details for craniectomy, aspiration injury, organoid transplantation, and cranioplasty. This platform represents a valuable tool for investigating the efficacy of organoids as structured grafts for neural repair. For complete details on the use and execution of this protocol, please refer to Jgamadze et al.1.

A protocol for visualization of murine in situ neurovascular interfaces

Mapping cranial vasculature and adjacent neurovascular interfaces in their entirety will enhance our understanding of central nervous system function in any physiologic state. We present a workflow to visualize in situ murine vasculature and surrounding cranial structures using terminal polymer casting of vessels, iterative sample processing and image acquisition, and automated image registration and processing. While this method does not obtain dynamic imaging due to mouse sacrifice, these studies can be performed before sacrifice and processed with other acquired images. For complete details on the use and execution of this protocol, please refer to Rosenblum et al.1.

Measuring the transcriptome-wide effects of aging on murine adipocytes using RNAseq

Adipose tissue plays a central role in age-related diseases. While RNAseq protocols exist for many tissues, few data have been generated with this technology to explore gene expression in adipocytes, particularly during aging. Here, we present a protocol to analyze the transcriptional changes that occur in adipose tissue during normal and accelerated aging in mouse models. We describe steps for genotyping, diet control, euthanasia, and dissection. We then detail RNA purification and genome-wide data generation and analysis. For complete details on the use and execution of this protocol, please refer to De Cauwer et al. (2022) iScience. Sep 16;25(10):105149.

Protocol for neonatal respiratory syncytial virus infection in mice and immune analysis of infected lungs and bronchoalveolar lavage fluid

Respiratory syncytial virus (RSV) infection in infants and toddlers is a major public health problem. Here, we provide a protocol for neonatal RSV infection in mice and immune analysis of infected lungs and bronchoalveolar lavage (BAL) fluid. We describe steps for anesthesia and intranasal inoculation, weight monitoring, and whole lung collection. We then detail BAL fluid immune and whole lung analyses. This protocol can be used for neonatal pulmonary infection with other viruses or bacteria.

Protocol to study projection-specific circuits in the basal ganglia of adult mice using viral vector tracing, optogenetics, and patch-clamp technique

Analysis of synaptic strength and plasticity provides functional insights of complicated neural circuits. Here, we describe steps for cell- and projection-specific optogenetic manipulation of divergent basal ganglia circuits using anterograde and retrograde viral vectors. We quantitatively analyze synaptic function of these circuits utilizing a patch-clamp technique. This protocol is applicable to probe potential circuit targets for treatment of brain diseases. For complete details on the use and execution of this protocol, please refer to Ji et al.1.