Neuroscience

A fascinating question in neuroscience is how sensory stimuli evoke calcium dynamics in neurons. Caenorhabditis elegans is one of the most suitable models for optically recording high-throughput calcium spikes at single-cell resolution. However, calcium imaging in C. elegans is challenging due to the difficulties associated with immobilizing the organism. Currently, methods for immobilizing worms include entrapment in a microfluidic channel, anesthesia, or adhesion to a glass slide. We have developed a new method to immobilize worms by trapping them in sodium alginate gel. The sodium alginate solution (5%), polymerized with divalent ions, effectively immobilizes worms in the gel. This technique is especially useful for imaging neuronal calcium dynamics during olfactory stimulation. The highly porous and transparent nature of alginate gel allows the optical recording of cellular calcium oscillations in neurons when briefly exposed to odor stimulation.

Sleep is a conserved biological process in the animal kingdom. Understanding the neural mechanisms underlying sleep state transitions is a fundamental goal of neurobiology, important for the development of new treatments for insomnia and other sleep-related disorders. Yet, brain circuits controlling this process remain poorly understood. A key technique in sleep research is to monitor in vivo neuronal activity in sleep-related brain regions across different sleep states. These sleep-related regions are usually located deeply in the brain. Here, we describe technical details and protocols for in vivo calcium imaging in the brainstem of sleeping mice. In this system, sleep-related neuronal activity in the ventrolateral medulla (VLM) is measured using simultaneous microendoscopic calcium imaging and electroencephalogram (EEG) recording. By aligning calcium and EEG signals, we demonstrate that VLM glutamatergic neurons display increased activity during the transition from wakefulness to non-rapid eye movement (NREM) sleep. The protocol described here can be applied to study neuronal activity in other deep brain regions involved in REM or NREM sleep.

Molecular characterization of different cell types in rodent brains is a widely used and important approach in neuroscience. Fluorescent detection of transcripts using RNAscope (ACDBio) has quickly became a standard in situ hybridization (ISH) approach. Its sensitivity and specificity allow for the simultaneous detection of between three and forty-eight low abundance mRNAs in single cells (i.e., multiplexing or hiplexing), and, in contrast to other ISH techniques, it is performed in a shorter amount of time. Manual quantification of transcripts is a laborious and time-consuming task even for small portions of a larger tissue section. Herein, we present a protocol for creating high-quality images for quantification of RNAscope-labeled neurons in the rat brain. This protocol uses custom-made scripts within the open-source software QuPath to create an automated workflow for the careful optimization and validation of cell detection parameters. Moreover, we describe a method to derive mRNA signal thresholds using negative controls. This protocol and automated workflow may help scientists to reliably and reproducibly prepare and analyze rodent brain tissue for cell type characterization using RNAscope.

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Actin filaments are essential for various biological activities in eukaryotic cellular processes. Available in vitro experimental data on these systems often lack details and information on sample preparation protocols and experimental techniques, leading to unreproducible results. Additionally, different experimental techniques and polymerization buffers provide different, sometimes contradictory results on the properties of these systems, making it substantially difficult to gather meaningful data and conclusive information from them. This article presents a robust, accurate, detailed polymerization protocol to prepare high-quality actin filament samples for light scattering experiments. It has been shown to provide unicity and consistency in preparing stable, dispersed, aggregates-free, homogenous actin filament samples that could benefit many other scientific research groups currently working in the field. To develop the protocol, we used conventional actin buffers in physiological conditions. However, it can easily be adapted to prepare samples using other buffers and biological fluids. This protocol yielded reproducible results on essential actin filament parameters such as the translational diffusion coefficient and electrophoretic mobility. Overall, suitable modifications of the proposed experimental method could generate accurate, reproducible light scattering results on other highly charged anionic filaments commonly found in biological cells (e.g., microtubules, DNAs, RNAs, or filamentous viruses).

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Aging and neuronal deterioration constitute important risk factors for the development of neuronal-related diseases, such as different dementia. The nematode Caenorhabditis elegans has emerged as a popular model system for studying neurodegeneration diseases, due to its complete neuronal connectivity map. DiI is a red fluorescent dye that can fill the worm amphid neurons and enables the visualization of their neurodegeneration over time. This protocol provides an efficient, fast, and safe method to stain worm amphid neurons to highlight the chemosensory structures of live nematodes.

Stimulus-induced narrow-band gamma oscillations (20–70 Hz) are induced in the visual areas of the brain when particular visual stimuli, such as bars, gratings, or full-screen hue, are shown to the subject. Such oscillations are modulated by higher cognitive functions, like attention, and working memory, and have been shown to be abnormal in certain neuropsychiatric disorders, such as schizophrenia, autism, and Alzheimer’s disease. However, although electroencephalogram (EEG) remains one of the most non-invasive, inexpensive, and accessible methods to record brain signals, some studies have failed to observe discernable gamma oscillations in human EEG. In this manuscript, we have described in detail a protocol to elicit robust gamma oscillations in human EEG. We believe that our protocol could help in developing non-invasive gamma-based biomarkers in human EEG, for the early detection of neuropsychiatric disorders.

The pancreas is a heavily innervated organ, but pancreatic innervation can be challenging to comprehensively assess using conventional histological methods. However, recent advances in whole-mount tissue clearing and 3D rendering techniques have allowed detailed reconstructions of pancreatic innervation. Optical clearing is used to enhance tissue transparency and reduce light scattering, thus eliminating the need to section the tissue. Here, we describe a modified version of the optical tissue clearing protocol iDISCO+ (immunolabeling-enabled three-dimensional imaging of solvent-cleared organs) optimized for pancreatic innervation and endocrine markers. The protocol takes 13-19 days, depending on tissue size. In addition, we include protocols for imaging using light sheet and confocal microscopes and for 3D segmentation of pancreatic innervation and endocrine cells using Imaris.

Determining the neuronal circuitry responsible for specific behaviors is a major focus in the field of neurobiology. Activity-dependent immediate early genes (IEGs), transcribed and translated shortly after neurons discharge action potentials, have been used extensively to either identify or gain genetic access to neurons and brain regions involved in such behaviors. By using immunohistochemistry for the protein product of the IEG c-Fos combined with retrograde labeling of specific neuronal populations, precise experimental timing, and identical data acquisition and processing, we present a method to quantitatively identify specific neuronal subpopulations that were active during social encounters. We have previously used this method to show a stronger recruitment of ventral hippocampal neurons that project to the medial prefrontal cortex, compared to those that project to the lateral hypothalamus, following social interactions. After optimization of surgeries for the injection of retrograde tracers, this method will be useful for the identification and mapping of neuronal populations engaged in many different behaviors.

A key component of combating substance use disorders is understanding the neural mechanisms that support drug reward. Tasks such as self-administration assess the reinforcing properties of a drug using a learned behavior but require numerous training sessions and surgery. In comparison, the conditioned place preference (CPP) task assesses reward with little training, without costly surgeries, and confounds that accompany the use of anesthesia or pain-relieving drugs. The CPP task contains three phases: pretest, conditioning, and posttest. During the pretest, mice are allowed to explore a three-compartment apparatus. The two outer compartments contain unique olfactory, tactile, and visual cues whereas the middle compartment is used as an entrance and exit for the mice on test days. During conditioning, mice receive cocaine before being confined to one of the outer compartments. The following day, mice are given saline then confined to the other outer compartment. These pairings are then repeated once. At posttest, mice are permitted to freely explore all compartments in a drug-free state while the time spent in each compartment is recorded. A CPP score is calculated for both the pretest and posttest by comparing the time spent in the cocaine-paired and saline-paired compartments. Enhancements in the CPP score from the pretest to the posttest serve as a measure of the rewarding property of the cocaine. This task offers several notable advantages: 1) the simultaneous recording of locomotor activity and reward, which may utilize different neural mechanisms, 2) the three-compartment CPP setup removes the bias that can be observed in a two-compartment design, and 3) use of multimodal cues support the acquisition of a robust preference in a variety of mouse strains.

Decision-making is a complex cognitive process which consists of choosing one option among several alternatives. In humans, this process is featured in the Iowa gambling task (IGT), a decision-making task that mimics real life situations by reproducing uncertain conditions based on probabilistic rewards or penalties (see Background). Several authors wanted to adapt the IGT in rodents with subtle differences in protocols that match various aspects of the human task. Here we propose, for the first time in mice, a protocol that contains the most important characteristics of the IGT: 4 different options, choices based on 4 ambiguous outcomes with immediate and long term rewards, a total of 100 trials, no learning of the contingency before the task, and presence of both a certain reward and a probable penalty. During this task, mice have to choose between options more or less advantageous in the short and long term by developing a decision-making strategy that differs between individuals. Therefore, the strength of this protocol is that it is one of the first to enable the study of decision-making in a complex situation, and demonstrates inter-individual differences regarding decision-making strategies in mice.