Protocol for using UV stimuli to evoke prey capture strikes in head-fixed zebrafish larvae

Hunting in larval zebrafish begins with eye convergence and orienting turns, proceeds to approach swims, and ends with the strike, where larvae consume the prey. Here, we describe a protocol to present UV stimuli to zebrafish, which greatly increases the occurrence of hunting initiation and strikes. We also describe how we record and analyze strike behavior in head-fixed larvae. Our goals are to increase the robustness of prey capture and to allow other labs to implement the strike behavioral assay. For complete details on the use and execution of this protocol, please refer to Khan et al. (2023).1.

Protocol for induction of heterosynaptic long-term potentiation in the mouse hippocampus via dual-opsin stimulation technique

Cholecystokinin (CCK) is the most abundant neuropeptide that broadly regulates the physiological status of animals. Here, we present a two-color laser theta burst stimulation (L-TBS) protocol for simultaneous activation of Schaffer collateral and perforant pathway in the hippocampus of CCK Cre mice. We describe steps for heterosynaptic long-term potentiation induction by L-TBS. This technique allows for the examination of the neurotransmitter roles in synaptic modulation and facilitates the exploration of pathological mechanisms in genetic models of brain disorders in mice. For complete details on the use and execution of this protocol, please refer to Su et al.1.

Protocol for cross-platform characterization of human and murine extracellular vesicles and particles

Characterization of isolated extracellular vesicles and particles (EVPs) is crucial for determining functions and biomarker potential. Here, we present a protocol to analyze size, number, morphology, and EVP protein cargo and to validate EVP proteins in both humans and mice. We describe steps for nanoparticle tracking analysis, transmission electron microscopy, single-EVP immunodetection, EVP proteomic mass spectrometry and bioinformatic analysis, and EVP protein validation by ExoELISA and western blot analysis. This allows for EVP cross-validation across different platforms. For complete details on the use and execution of this protocol, please refer to Hoshino et al.1.

Protocol for ovariectomy and estradiol replacement in mice

Ovariectomy, involving the surgical removal of ovaries, and estradiol replacement facilitate the understanding of sexual dimorphism-related physiological changes, encompassing reproductive biology, metabolism, and hormone-related diseases. In this study, we present a protocol for conducting ovariectomy and estradiol replacement in mice. We describe steps for performing sham and ovariectomy operations, outline preoperative preparations, and provide details on postoperative care, including analgesia administration and the removal of surgical clips. Additionally, we elaborate on the procedures for performing vehicle and estradiol injections. For complete details on the use and execution of this protocol, please refer to Luengo-Mateos et al.1.

Protocol to study microcircuits in the medial entorhinal cortex in mice using multiple patch-clamp recordings and morphological reconstruction

Multiple patch-clamp recordings and morphological reconstruction are powerful approaches for neuronal microcircuitry dissection and cell type classification but are challenging due to the sophisticated expertise needed. Here, we present a protocol for applying these techniques to neurons in the medial entorhinal cortex (MEC) of mice. We detail steps to prepare brain slices containing MEC and perform simultaneous multiple whole-cell recordings, followed by procedures of histological staining and neuronal reconstruction. We then describe how we analyze morphological and electrophysiological features. For complete details on the use and execution of this protocol, please refer to Shi et al.1.

Establishing a 3D culture system for early organogenesis of monkey embryos ex vivo and single-cell transcriptome analysis of cultured embryos

Creating in vitro culture platforms for monkey embryos is crucial for understanding the initial 4 weeks of early primate embryogenesis. Here, we present a protocol to culture cynomolgus monkey embryos in vitro for 25 days post-fertilization and to delineate the key developmental events of gastrulation and early organogenesis. We describe steps for culturing with a 3D system, immunofluorescence analysis, single-cell RNA sequencing, and bioinformatic analysis. For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1.

Integrative detection of genome-wide translation using iRibo

Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading frames. We describe the process of using iRibo to generate a species' translatome from a set of ribosome profiling samples using S. cerevisiae as an example. For complete details on the use and execution of this protocol, please refer to Wacholder et al. (2023).1.

Isolating mononuclear cells from fetal bone and liver for metabolic, functional, and immunophenotypic analyses in nonhuman primates

Studying fetal hematopoiesis is challenging as hematopoiesis transitions from the liver to bone marrow. Obtaining human samples is not possible, and small animal models may not provide sufficient biological material. Here, we present a protocol for isolating hematopoietic cells from the nonhuman primate fetal liver and bone. We describe steps for using cells from the same fetus for fluorescence lifetime imaging microscopy to measure metabolism, assessing cellular function, and flow cytometry for immunophenotyping at the single-cell level. For complete details on the use and execution of this protocol, please refer to Nash et al. (2023).1.

Protocol for xenografting of BxPC-3 pancreatic tumors using a chorioallantoic membrane model

The chorioallantoic membrane (CAM) model is an increasingly attractive model for the study of human tumors. However, concise techniques for the use of pancreatic ductal adenocarcinoma BxPC-3 xenografts in CAM assays are not yet available. Here, we present a protocol for the induction of BxPC-3 xenograft tumors with high grafting efficiency. We describe steps for embryo incubation, egg handling, and grafting, each of which has been optimized to prevent fungal contamination and minimize mortality.

Generation of post-surgical minimal residual disease models to investigate metastasis in soft tissue sarcoma patient-derived orthotopic xenografts

Despite optimal multimodal treatment including surgical resection, 50%-80% of high-grade soft tissue sarcoma (STS) patients metastasize. Here, we present a protocol for the generation and use of post-surgical minimal residual disease models to investigate metastatic relapse in STS patient-derived xenografts. We describe steps for orthotopic engraftment of high-grade STS patient-derived tumor tissue. We then detail procedures for primary tumor resection with broad, negative resection margins and follow-up until metastases using MRI. For complete details on the use and execution of this protocol, please refer to Fischer et al. (2023).1.

Protocol for screening α-synuclein PET tracer candidates in vitro and ex vivo

Alpha-synuclein (α-Syn) positron emission tomography (PET) imaging is a valuable approach for diagnosing and monitoring synucleinopathies-related diseases, such as Parkinson disease. Here, we present a protocol for screening potential α-Syn PET tracers using in vitro and ex vivo approaches. We describe steps for employing recombinant pre-formed fibrils and conducting screening procedures on neuronal models, mouse models, and patients' brain tissue sections to assess the specificity and selectivity of the candidate compounds. For complete details on the use and execution of this protocol, please refer to Xiang et al. (2023).1.

Protocol for transplanting pancreatic islets into the parametrial fat pad of female mice

Although the male epididymal fat pad is an effective site for islet transplantation, females lack this tissue. Here, we present a protocol to assess the parametrial fat pad (PFP) adjacent to the uterine horn in females as an alternative site for islet transplantation. We describe steps for islet isolation from the pancreas, counting, transplantation into PFP, and monitoring for engraftment. Transplantation into PFP is minimally invasive, time efficient, and supports long-term engraftment of syngeneic islets and rejection of allogeneic islets. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).1.

Protocol for culturing and functionally manipulating planarian neoblasts using SiR-DNA-based flow cytometry

Neoblasts are the only cells capable of proliferation in planarians. The traditional flow cytometry protocol using Hoechst inhibits the cell cycle. Here, we present a protocol for culturing and functionally manipulating planarian neoblasts using SiR-DNA-based flow cytometry. We describe steps for cell dissociation and staining, flow cytometry, and cell collection and culture. We then detail procedures for Nanoluciferase mRNA transfection. This protocol facilitates further investigations into the pluripotency and regeneration mechanisms within neoblasts. For complete details on the use and execution of this protocol, please refer to Lei et al.1.

Protocol for assessing myogenic tone and perfusion pressure in isolated mouse kidneys

The isolated perfused kidney is a classic ex vivo preparation for studying renal physiology in general and vascular function. Here, we present a protocol for assessing myogenic tone in isolated mouse kidneys as well as vasodilatory and vasoconstrictive responses, expressed as perfusion pressure. We describe steps for pre-operative preparation, kidney and renal artery isolation, and connection of renal artery with glass cannula. We then detail how to measure pressure changes in perfused kidneys and the myogenic tone. For complete details on the use and execution of this protocol, please refer to Cui et al.1.

Protocol to create a murine subcutaneous air pouch for the study of monosodium urate crystal-induced gout

Monosodium urate (MSU) crystal deposition in articular joints and bursal tissue causes acute joint inflammation, which is a hallmark of gout. Here, we describe the steps necessary to create a subcutaneous air pouch on the back of mice that resembles this bursa-like space with a synovial lining-like membrane. We then detail the injection of MSU crystals into this pouch, which induces a localized inflammatory response reminiscent of gout and approaches to quantify the inflammatory response. For complete details on the use and execution of this protocol, please refer to Devi et al. (2023),1 de Almeida et al. (2022),2 and Ratsimandresy et al. (2017).3.

Protocol for the establishment and characterization of an endometrial-derived epithelial organoid and stromal cell co-culture system

Postnatal development of the uterus involves the specification of undifferentiated epithelium into uterine-type epithelium. That specification is regulated by stromal-epithelial interactions as well as intrinsic cell-specific transcription factors and gene regulatory networks. Here, we present a co-culture system to study the effects of stromal-derived factors on epithelial cell growth and differentiation into organoids. First, we describe epithelial cell isolation and organoid growth characterization. Second, we detail a co-culture system that allows the study of stromal-derived paracrine factors on epithelial development. For complete details on the use and execution of this protocol, please refer to Rizo et al.1.

Protocol for quantifying SA-β-gal activity as a measure of senescence in islets of a mouse model of type 1 diabetes

A subpopulation of pancreatic beta cells becomes senescent during type 1 diabetes (T1D) progression, and removal of these populations protects against T1D in mice. Here, we present a protocol to measure senescence in murine pancreatic islet cells through analysis of senescence-associated β-galactosidase activity. We describe steps for staining with the fluorogenic substrate C12FDG and analysis by flow cytometry. Increased cell size is another marker of senescence and can also be concurrently measured in the same experiment. For complete details on the use and execution of this protocol, please refer to Lee et al.1 and Helman et al.2.

Mouse models of spontaneous liver and lung metastasis for colorectal cancer

To investigate underlying mechanisms for cancer metastasis and promising therapies in animal models, spontaneous metastasis models can be used to recreate metastasis development. Here, we present three mouse models of spontaneous lung and/or liver metastasis induction. We describe steps for cancer cell preparation, mouse analgesia, and three injection techniques (subcutaneous, intracecal, and intramucosal). We then detail procedures for evaluating metastasis. Most of these models generate metastasis in a time span of 4 weeks in the majority of injected mice. For complete details on the use and execution of this protocol, please refer to Giannou et al.1.

Brain-wide multi-fiber recording of neuronal activity in freely moving mice

While brain regions function in coordination to mediate diverse behaviors, techniques allowing simultaneous monitoring of many deep brain regions remain limited. Here, we present a multi-fiber recording protocol that enables simultaneous recording of fluorescence signals from multiple brain regions in freely behaving mice. We describe steps for assembling a multi-fiber array and patch cord, implantation, and recording. We then detail procedures for data extraction and visualization. This protocol enables a comprehensive view of the neural activity at the network level. For complete details on the use and execution of this protocol, please refer to Guo et al.1.

Protocol for two models of behavioral transition from action to no-action when facing prolonged uncontrollable experience in mice

Uncontrollability could lead to behavioral adjustment or even giving up when facing repeated failure. Here, we detail a protocol to study the behavioral transition from action to no-action induced by prolonged uncontrollable experiences in mice. We describe the behavioral devices, video analysis, and the exponential learning curve fitting for mathematical assessment. We perform further validation experiments evaluating locomotor, social, and anxiety-/depression-like behaviors. This approach helps study neural mechanisms underlying adaptive decision-making when facing repeated failure. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Protocol for the analysis of hematopoietic lineages in the whole kidney marrow of adult zebrafish

The whole kidney marrow (WKM) is the site for hematopoiesis in the adult zebrafish. Here, we present a protocol for analyzing hematopoietic lineages in the WKM of adult zebrafish. We describe steps for the isolation of hematopoietic cells from the WKM, the downstream analysis of total marrow cellularity, and analysis of cell populations by flow cytometry. We then detail procedures for May-Grünwald-Giemsa staining for analysis of cellular morphology and phenotyping. For complete details on the use and execution of this protocol, please refer to Mahony et al.1.

Ca2+ imaging of synaptic compartments using subcellularly targeted GCaMP8f in Drosophila

GCaMP8f is a sensitive genetically encoded Ca2+ indicator that enables imaging of neuronal activity. Here, we present a protocol to perform Ca2+ imaging of the Drosophila neuromuscular junction using GCaMP8f targeted to pre- or postsynaptic compartments. We describe ratiometric Ca2+ imaging using GCaMP8f fused to mScarlet and synaptotagmin that reveals Ca2+ dynamics at presynaptic terminals. We then detail "quantal" imaging of miniature transmission events using GCaMP8f targeted to postsynaptic compartments by fusion to a PDZ-binding motif. For complete details on the use and execution of this protocol, please refer to Li et al.,1 Han et al.,2 Perry et al.,3 and Han et al.4.

Multiplexed CRISPR-Cas9 protocol for large transgene integration into the Schistosoma mansoni genome

Precise, on-target CRISPR-Cas9 genome editing has been shown in Schistosoma mansoni, involving both non-homology end joining and homology-directed repair pathways. Here, we present a multiplexed CRISPR-Cas9 protocol for large transgene integration into the S. mansoni genome. We describe steps for deploying multiplexed ribonucleoprotein complexes (RNPs) and donor DNA preparation. We then detail procedures for introducing RNPs into schistosome eggs by square-wave electroporation in the presence of a 5' phosphorothioate-modified double-stranded donor transgene. For complete details on the use and execution of this protocol, please refer to Ittiprasert et al. (2023).1.

Protocol for imbibed seed piercing for Agrobacterium-mediated transformation of jute

Here, we present a streamlined Agrobacterium-mediated transformation protocol for jute (Corchorus sp.). We describe steps to pierce and vacuum infiltrate imbibed jute seeds with Agrobacterium suspension. We then detail procedures for selecting transformed seeds by using a hygromycin-B-supplemented medium. This approach can achieve transformation efficiencies of 20.44% ± 1.17% and 15.55% ± 0.58% for tossa (C. olitorius) and white (C. capsularis) jute, respectively. Demanding minimal resources and time, this protocol can elevate genetic engineering research in jute fiber crops. For complete details on the use and execution of this protocol, please refer to Majumder et al. (2020).1.

Manipulating mRNA-binding protein Cth2 function in budding yeast Saccharomyces cerevisiae

Here, we present a protocol for modulating the function of the Cth2 mRNA-binding protein (RBP) in Saccharomyces cerevisiae. We describe steps to amplify and integrate mutations in Cth2 that affect its stability and function. Next, we detail the functional assay to verify the activity of the wild-type and mutant versions of Cth2 in yeast cells. This protocol can be adopted to modify the function of other RBPs with their respective functional mutations. For complete details on the use and execution of this protocol, please refer to Patnaik et al. (2022).1.