Material below is adapted from the SfN Short Course, Adult Mouse Cortical Cell Taxonomy Revealed by Single-Cell Transcriptomics, by Bosiljka Tasic, PhD. Short Courses are day-long scientific trainings on emerging neuroscience topics and research techniques held just prior to SfN’s annual meeting. Single-cell RNA sequencing (RNA-seq) is a powerful tool that can help researchers look more deeply at individual cells, in order to better understand differences within tissues or groups of cells. One research team used RNA-seq to classify more than 1,600 cells from the cortex of adult male mice.

Functional ultrasound (fUS) imaging is a well-established neuroimaging technology that offers high spatiotemporal resolution and a large field of view. Typical strategies for analyzing fUS data comprise either region-based averaging, typically based on reference atlases, or correlation with experimental events. Nevertheless, these methodologies possess several inherent limitations, including a restricted utilization of the spatial dimension and a pronounced bias influenced by preconceived notions about the recorded activity. In this study, we put forth single-voxel clustering as a third method to address these issues. A comparison was conducted between the three strategies on a typical dataset comprising visually evoked activity in the superior colliculus in awake mice. The application of single-voxel clustering yielded the generation of detailed activity maps, which revealed a consistent layout of activity and a clear separation between hemodynamic responses. This method is best considered as a complement...

For comprehensive anatomical analysis of a mouse brain, accurate and efficient registration of the experimental brain samples to a reference atlas is necessary. Here, we introduce Bell Jar, a semiautomated solution that can align and annotate tissue sections with anatomical structures from a reference atlas as well as detect fluorescent signals with cellular resolution (e.g., cell bodies or nuclei). Bell Jar utilizes Mattes mutual information-directed B-spline transformations to achieve precise alignments, even with damaged sample tissues. While user input remains a requirement for fine-tuning section matches, the platform streamlines the process, aiding rapid analyses in high-throughput neuroanatomy studies. As a standalone desktop application with a user-friendly interface, Bell Jar’s performance, which surpasses traditional manual and existing automated methods, can improve the reproducibility and throughput of histological analyses.

Functional imaging studies indicate that both the assessment of a person as untrustworthy and the assumption that a person has a sexually transmitted infection are associated with activation in regions of the salience network. However, studies are missing that combine these aspects and investigate the perceived trustworthiness of individuals previously assessed with high or low probability of a sexually transmitted infection. During fMRI measurements, 25 participants viewed photographs of people preclassified as having high or low HIV probability and judged their trustworthiness. In a postrating, stimuli were rated for trustworthiness, attractiveness, and HIV probability. Persons preclassified as HIV− in contrast to those preclassified as HIV+ were rated more trustworthy and with lower HIV probability. Activation in medial orbitofrontal cortex was higher for those rated and preclassified as HIV− than HIV+. Based on the individual ratings, but not the preclassification, there was significantly higher activa...

The use of supervised machine learning to approximate poses in video recordings allows for rapid and efficient analysis of complex behavioral profiles. Currently, there are limited protocols for automated analysis of operant self-administration behavior. We provide a methodology to (1) obtain videos of training sessions via Raspberry Pi microcomputers or GoPro cameras, (2) obtain pose estimation data using the supervised machine learning software packages DeepLabCut (DLC) and Simple Behavioral Analysis (SimBA) with a local high-performance computer cluster, (3) compare standard Med-PC lever response versus quadrant time data generated from pose estimation regions of interest, and (4) generate predictive behavioral classifiers. Overall, we demonstrate proof of concept to use pose estimation outputs from DLC to both generate quadrant time results and obtain behavioral classifiers from SimBA during operant training phases.

The role of sleep in memory consolidation is a widely discussed but still debated area of research. In light of the fact that memory consolidation during sleep is an evolutionary adaptive function, investigating the same phenomenon in nonhuman model species is highly relevant for its understanding. One such species, which has acquired human-analog sociocognitive skills through convergent evolution, is the domestic dog. Family dogs have surfaced as an outstanding animal model in sleep research, and their learning skills (in a social context) are subject to sleep-dependent memory consolidation. These results, however, are correlational, and the next challenge is to establish causality. In the present study, we aimed to adapt a TMR (targeted memory reactivation) paradigm in dogs and investigate its effect on sleep parameters. Dogs ( N  = 16) learned new commands associated with different locations and afterward took part in a sleep polysomnography recording when they were re-exposed to one of the previously l...

Observing lip movements of a speaker facilitates speech understanding, especially in challenging listening situations. Converging evidence from neuroscientific studies shows stronger neural responses to audiovisual stimuli compared with audio-only stimuli. However, the interindividual variability of this contribution of lip movement information and its consequences on behavior are unknown. We analyzed source-localized magnetoencephalographic responses from 29 normal-hearing participants (12 females) listening to audiovisual speech, both with and without the speaker wearing a surgical face mask, and in the presence or absence of a distractor speaker. Using temporal response functions to quantify neural speech tracking, we show that neural responses to lip movements are, in general, enhanced when speech is challenging. After controlling for speech acoustics, we show that lip movements contribute to enhanced neural speech tracking, particularly when a distractor speaker is present. However, the extent of this...

The behavioral interactions between adults and newborns are decisive for the fitness and the survival of offspring across the animal kingdom. In laboratory mice, while virgin females display caregiving behaviors, virgin males are rather neglectful or aggressive toward pups. Despite the importance of these behavioral variations, the underlying neural mechanisms remain poorly understood. Brain regions encoding these behaviors may exhibit sex-dependent functional differences at the baseline. Additionally, these structures might undergo sex-specific plasticity after adults interact with the offspring. Emerging evidence suggests sex-based differences in input connectivity, genetics, and receptor expression of the epithalamic lateral habenula (LHb). Moreover, LHb neuronal activity is instrumental for adult–newborn interactions. However, whether LHb neuronal function varies between sexes and/or undergoes adaptations following interactions with pups has not been fully investigated. In this study, we used in vivo a...

Breathing is a complex neuromuscular process vital to sustain life. In preclinical animal models, the study of respiratory motor control is primarily accomplished through neurophysiologic recordings and functional measurements of respiratory output. Neurophysiologic recordings that target neural or muscular output via direct nerve recordings or respiratory muscle electromyography (EMG) are commonly collected during anesthetized conditions. While offering tight control of experimental preparations, the use of anesthesia results in respiratory depression, may impact cardiovascular control, eliminates the potential to record volitional nonventilatory behaviors, and can limit translation. Since the diaphragm is a unique muscle which is rhythmically active and difficult to access, placing diaphragm EMGs to collect chronic recordings in awake animals is technically challenging. Here, we describe methods for fabricating and implanting indwelling diaphragm EMG electrodes to enable recordings from awake rodents for...

The adrenal medulla is packed with chromaffin cells, modified postganglionic sympathetic neurons that secrete the catecholamines, epinephrine and norepinephrine, during the fight-or-flight response. Sometimes overlooked is a population of immune cells that also resides within the gland but whose distribution and function are not clear. Here I examine the location of CD45+ hematopoietic cells in the mouse adrenal medulla and show the majority are F4/80+/Lyz2+ macrophages. These cells are present from early postnatal development and widely distributed. Anatomically they are associated with chromaffin cells, found aligned alongside synapsin-IR neuronal varicosities and juxtaposed to CD31-IR blood vessels. Using Lyz2cre-GCaMP6f mice to quantify calcium signaling in macrophages revealed these cells respond directly and indirectly to a wide variety of neuromodulators, including pre- and postganglionic transmitters and systemic hormones. Purinergic agonists, histamine, acetylcholine, and bradykinin rapidly and re...