Neuroscience

Behavioral neuroscience requires precise and unbiased methods for animal behavior assessment to elucidate complex brain–behavior interactions. Traditional manual scoring methods are often labor-intensive and can be prone to error, necessitating advances in automated techniques. Recent innovations in computer vision have led to both marker- and markerless-based tracking systems. In this protocol, we outline the procedures required for utilizing Augmented Reality University of Cordoba (ArUco) markers, a marker-based tracking approach, to automate the assessment and scoring of rodent engagement during an established intracortical microstimulation-based nose-poking go/no-go task. In short, this protocol involves detailed instructions for building a suitable behavioral chamber, installing and configuring all required software packages, constructing and attaching an ArUco marker pattern to a rat, running the behavioral software to track marker positions, and analyzing the engagement data for determining optimal task durations. These methods provide a robust framework for real-time behavioral analysis without the need for extensive training data or high-end computational resources. The main advantages of this protocol include its computational efficiency, ease of implementation, and adaptability to various experimental setups, making it an accessible tool for laboratories with diverse resources. Overall, this approach streamlines the process of behavioral scoring, enhancing both the scalability and reproducibility of behavioral neuroscience research. All resources, including software, 3D models, and example data, are freely available at https://github.com/tomcatsmith19/ArucoDetection.

Long-lasting memories are a core aspect of an animal’s life. Such memories are characterized by unique molecular mechanisms and often unique circuitry, neither of which are completely understood in vivo. The deep knowledge of the identity and connectivity of neurons of the fruit fly Drosophila melanogaster, as well as the sophisticated genetic tools that allow in vivo perturbations and physiology monitoring, make it a remarkably useful organism in which to investigate the molecular mechanisms of long-term memories. In this protocol, we focus on habituation, a non-associative form of learning, and describe a reliable, semi-automated technique to induce and assess long-term olfactory habituation (LTH) in Drosophila using the olfactory arena, thus providing a method aligned with recent technological progress in behavioral measurement. Prior work has shown that LTH is induced by a 4-day exposure to an odorant and is characterized by a long-lasting (> 24 h) reduction in behavioral response to the exposed odorant, measured using a manual and skill-intensive Y-maze assay. Here, we present a semi-automated protocol for obtaining quantifiable measures of LTH, at the level of detail required for other investigators in the field. Unlike previously described methods, the protocol presented here provides quantitative and detailed behavioral measurements obtained by video recording that can be shared with the scientific community and allows sophisticated forms of offline analysis. We suggest that this procedure has the potential to advance our understanding of molecular and circuit mechanisms of olfactory habituation, its control via neuromodulation, and its interactions with other forms of memory.

This paper presents a refined, user-friendly protocol for using boron-dipyrromethene (BODIPY) to assess and quantify foam cells and lipid droplet–accumulating microglia (LDAM) in mouse brain tissue. The protocol aims to enhance existing methodologies by offering precise and efficient evaluation of foam cells and LDAM burden in various neuropathological conditions linked to lipid metabolism and neuroinflammation. A notable challenge in analyzing tissue from mouse models of these neurodegenerative disorders is the interference caused by the autofluorescent molecule lipofuscin. Our protocol addresses this issue with specific steps that effectively distinguish BODIPY fluorescence from lipofuscin autofluorescence, using advanced imaging techniques and filter settings to ensure accurate and reliable analysis. By providing a straightforward and accessible method, this research aims to facilitate the broader adoption of BODIPY-based techniques for detailed foam cell and LDAM analysis in mouse brain tissue, potentially enhancing diagnostic capabilities and deepening our understanding of how these cells contribute to neurodegenerative disease mechanisms.

Neuroscience incorporates manipulating neuronal circuitry to enhance the understanding of intricate brain functions. An effective strategy to attain this objective entails utilizing viral vectors to induce varied gene expression by delivering transgenes into brain cells. Here, we combine the use of transgenic mice, neonatal transduction with adeno-associated viral constructs harboring inhibitory designer receptor exclusively activated by designer drug (DREADD) gene, and the DREADD agonist clozapine N-oxide (CNO). In this way, a chemogenetic approach is employed to suppress neuronal activity in the region of interest during a critical developmental window, with subsequent investigation into its effects on the neuronal circuitry in adulthood.

The neuromuscular junction (NMJ) is an interface between motor neurons and skeletal muscle fibers, facilitating the transmission of signals that initiate muscle contraction. Its pivotal role lies in ensuring efficient communication between the nervous system and muscles, allowing for precise and coordinated movements essential for everyday activities and overall motor function. To provide insights into neuromuscular disease and development, understanding the physiology of NMJ is essential. We target acetylcholine receptors (AChR) by immunofluorescence assay (IFA) with α-bungarotoxin (BTX; snake venom neurotoxins binding to AChR) to visualize and quantify the NMJ. Changes in AChR distribution or structure can indicate alterations in receptor density, which may be associated with neuromuscular disorders or conditions that affect synaptic transmission. This protocol provides the methodology for isolating and longitudinally sectioning gastrocnemius muscle for AChR-targeted IFA for confocal microscopy and performing quantitative analysis of NMJs.

Protein misfolding fuels multiple neurodegenerative diseases, but existing techniques lack the resolution to pinpoint the location and physical properties of aggregates within living cells. Our protocol describes high-resolution confocal and fluorescent lifetime microscopy (Fast 3D FLIM) of an aggregation probing system. This system involves a metastable HaloTag protein (HT-aggr) labeled with P1 solvatochromic fluorophore, which can be targeted to subcellular compartments. This strategy allows to distinguish between aggregated and folded probe species, since P1 fluorophore changes its lifetime depending on the hydrophobicity of its microenvironment. The probe is not fluorescence intensity-dependent, overcoming issues related to intensity-based measurements of labeled proteins, such as control of probe quantity due to differences in expression or photobleaching of a proportion of the fluorophore population. Our approach reports on the performance of the machinery dealing with aggregation-prone substrates and thus opens doors to studying proteostasis and its role in neurodegenerative diseases.

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.

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.

C. elegans is a well-established nematode model organism, with 83% of its genes conserved in humans with translation potential. C. elegans is translucent, with clearly defined cellular organization, and robustly identifiable under a microscope, being an excellent model for studying feeding behavior. Its neuromuscular pharyngeal pump undergoes a pumping motion that can be quantified to study feeding behavior at specific treatment conditions and in genetically modified worms. Understanding the evolutionarily conserved feeding behaviors and regulatory signals is vital, as unhealthy eating habits increase the risk of associated diseases. The current protocol was developed to identify and study evolutionary conserved signals regulating feeding behavior. The protocol described here is very robust in calculating the pumping rate (pumping per minute) as it directly counts the pharyngeal pumping for 30 s. This protocol uses basic laboratory instrumentation, such as a stereomicroscope with an attached camera and a computer with a video program that can be used to count manually. The advantages of studying C. elegans feeding include understanding the genetic basis of feeding regulation, dysregulation of feeding behavior in a disease model, the influence of toxic or environmental substances in feeding behavior, and modulation of feeding behavior by pharmacological agents.

A hexanucleotide GGGGCC repeat expansion in the C9orf72 gene is the most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). C9orf72 repeat expansions are currently identified with long-range PCR or Southern blot for clinical and research purposes, but these methods lack accuracy and sensitivity. The GC-rich and repetitive content of the region cannot be amplified by PCR, which leads traditional sequencing approaches to fail. We turned instead to PacBio single-molecule sequencing to detect and size the C9orf72 repeat expansion without amplification. We isolated high molecular weight genomic DNA from patient-derived iPSCs of varying repeat lengths and then excised the region containing the C9orf72 repeat expansion from naked DNA with a CRISPR/Cas9 system. We added adapters to the cut ends, capturing the target region for sequencing on PacBio’s Sequel, Sequel II, or Sequel IIe. This approach enriches the C9orf72 repeat region without amplification and allows the repeat expansion to be consistently and accurately sized, even for repeats in the thousands.