Zebrafish genetic mutants have emerged as a valuable model system for studying various aspects of disease and developmental biology. Mutant zebrafish embryos are generally identified based on phenotypic defects at later developmental stages, making it difficult to investigate underlying molecular mechanisms at earlier stages. This protocol presents a PCR-based genotyping method that enables the identification of wild-type, heterozygous, and homozygous zebrafish genetic mutants at any developmental stage, even when they are phenotypically indistinguishable. The approach involves the amplification of specific genomic regions using carefully designed primers, followed by gel electrophoresis. This genotyping method facilitates the investigation of the molecular mechanisms driving phenotypic defects that are observed at later timepoints. This protocol allows researchers to perform analyses such as immunofluorescence, RT-PCR, RNA sequencing, and other molecular experiments on early developmental stages of mutants. The availability of this protocol expands the utility of zebrafish genetic mutants for elucidating the molecular underpinnings of various biological processes throughout development.

Stable-isotope resolved metabolomics (SIRM) is a powerful approach for characterizing metabolic states in cells and organisms. By incorporating isotopes, such as ¹³C, into substrates, researchers can trace reaction rates across specific metabolic pathways. Integrating metabolomics data with gene expression profiles further enriches the analysis, as we demonstrated in our prior study on glioblastoma metabolic symbiosis. However, the bioinformatics tools for analyzing tracer metabolomics data have been limited. In this protocol, we encourage the researchers to use SIRM and transcriptomics data and to perform the downstream analysis using our software tool DIMet. Indeed, DIMet is the first comprehensive tool designed for the differential analysis of tracer metabolomics data, alongside its integration with transcriptomics data. DIMet facilitates the analysis of stable-isotope labeling and metabolic abundances, offering a streamlined approach to infer metabolic changes without requiring complex flux analysis. Its pathway-based "metabologram" visualizations effectively integrate metabolomics and transcriptomics data, offering a versatile platform capable of analyzing corrected tracer datasets across diverse systems, organisms, and isotopes. We provide detailed steps for sample preparation and data analysis using DIMet through its intuitive, web-based Galaxy interface. To showcase DIMet's capabilities, we analyzed LDHA/B knockout glioblastoma cell lines compared to controls. Accessible to all researchers through Galaxy, DIMet is free, user-friendly, and open source, making it a valuable resource for advancing metabolic research.

Nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channels expressed in nervous and non-nervous system tissue important for memory, movement, and sensory processes. The pharmacological targeting of nAChRs, using small molecules or peptides, is a promising approach for the development of compounds for the treatment of various human diseases including inflammatory and neurogenerative disorders such as Alzheimer’s disease. Using the Aplysia californica acetylcholine binding protein (Ac-AChBP) as an established structural surrogate for human homopentameric α7 nAChRs, we describe an innovative protein painting mass spectrometry (MS) method that can be used to identify interaction sites for various ligands at the extracellular nAChR site. We describe how the use of small molecule dyes can be optimized to uncover contact sites for ligand–protein interactions based on MS detection. Protein painting MS has been recently shown to be an effective tool for the identification of residues within Ac-AChBP involved in the binding of know ligands such as α-bungarotoxin. This strategy can be used with computational structural modeling to identify binding regions involved in drug targeting at the nAChR.

Cell cultures play a crucial role in neuroscience research, facilitating the elucidation of the complexities of cellular physiology and pathology. The relative simplicity in producing cultures and the accessibility to cells that the cultures provide, in contrast to in vivo settings, allow users to manipulate and monitor cells more easily at higher throughputs and lower costs. These are ideal for screening purposes and electrophysiological characterizations. Despite the prevalence of methodologies for producing brain cultures from various animal models, rodents in particular, approaches for culturing neurons (and glia) from birds are less established or completely absent as in the case of the Japanese quail model. Here, we present a unique culturing protocol for brain cells (e.g., neurons at different maturation levels, such as progenitor cells, excitatory and inhibitory neurons, microglia, and endothelial cells) from entire forebrains of Japanese quail embryos for high-throughput screening of viral vectors in vitro and other various purposes. Following dissection and digestion methods uniquely suited for avian brains, we tailored the growth media and culturing surface to allow the survival of quail brain cultures for more than three weeks in vitro.

Because of its genetic tractability and amenability for live imaging, larval zebrafish (Danio rerio) have emerged as a model to study the cellular and synaptic properties underlying behavior. The accessibility of Mauthner cells, a pair of escape-organizing neurons located in the brainstem of teleost fish, along with their associated sensory inputs, enables exploration of the correlation between structural and functional synaptic features. This is the case of the endings of auditory afferents on the lateral dendrite of this cell, known as large myelinated club endings, which provide the excitatory drive for the initiation of auditory-evoked escape responses mediated by the Mauthner cell and its spinal network. Here, we describe the procedures that make it possible to expose the molecular composition of these synapses using protein-retention expansion microscopy (proExM). This method allowed us to generate a map of the distribution of synaptic proteins at these identifiable synapses, which could also be applied to examine the organization of other synaptic contacts in this cell.