Journal of Neuroscience

Contains data and software from the publication: "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse" published in the The Journal of Neuroscience (https://doi.org/10.1523/JNEUROSCI.0363-19.2019). The preprint to this data set has been published on bioRxiv (https://doi.org/10.1101/689653). In this study, we created a helper-dependent adenoviral vector (HdAd) to co-express cytoplasmic EGFP and a genetically encoded peroxidase marker (mito-APEX2) at the calyx of Held, an excellent model for deciphering regulatory mechanisms of presynaptic function. ABSTRACT: The calyx of Held, a large glutamatergic presynaptic terminal in the auditory brainstem undergoes developmental changes to support the high action-potential firing rates required for auditory information encoding. In addition, calyx terminals are morphologically diverse which impacts vesicle release properties and synaptic plasticity. Mitochondria influence synaptic plasticity through calcium buffering and are crucial for providing the energy required for synaptic transmission. Therefore, it has been postulated that mitochondrial levels increase during development and contribute to the morphological-functional diversity in the mature calyx. However, the developmental profile of mitochondrial volumes and subsynaptic distribution at the calyx of Held remains unclear. To provide insight on this, we developed a helper-dependent adenoviral vector (HdAd) that expresses the genetically encoded peroxidase marker for mitochondria, mito-APEX2, at the mouse calyx of Held. We developed protocols to detect labeled mitochondria for use with serial block face scanning electron microscopy to carry out semi-automated segmentation of mitochondria, high-throughput whole terminal reconstruction and presynaptic ultrastructure in mice of either sex. Subsequently, we measured mitochondrial volumes and subsynaptic distributions at the immature postnatal day 7 (P7) and the mature (P21) calyx. We found an increase of mitochondria volumes in terminals and axons from P7 to P21 but did not observe differences between stalk and swelling subcompartments in the mature calyx. Based on these findings, we propose that mitochondrial volumes and synaptic localization developmentally increase to support high firing rates required in the initial stages of auditory information processing. Data are sorted by the figures they appear in. Media (movies and 3D models) and custom-written software are located in separate folders.

statistical analysis

raw data elaborated by author for publication at title

bootstrapped_LFP.mat file contains the raw dataset for the bootstrapped data for LFP. boostrapped euclidean distance - neural trajectories.mat file contains the bootstrapped data for euclidean distance for different subpopulations (positively, negatively or not modulated neurons).

This dataset is related to the study: "The Lactate Receptor HCAR1 Modulates Neuronal Network Activity through the Activation of G(α) and G(βγ) Subunits" by de Castro Abrantes H, Briquet M, Schmuziger C, Restivo L, Puyal J, Rosenberg N, Rocher AB, Offermanns S, Chatton JY. J Neurosci. 2019 Jun 5;39(23):4422-4433. doi: 10.1523/JNEUROSCI.2092-18.2019. Epub 2019 Mar 29. PubMed PMID: 30926749; PubMed Central PMCID: PMC6554634.

This repository contains the EEG and behavioral data described in: Fuglsang, S A, Märcher-Rørsted, J, Dau, T, Hjortkjær, J (2020). Effects of sensorineural hearing loss on cortical synchronization to competing speech during selective attention. Journal of Neuroscience, 40(12):2562–2572, https://doi.org/10.1523/JNEUROSCI.1936-19.2020 Please cite this paper when using the data The data set consists of response data for 22 hearing-impaired and 22 normal-hearing participants. It includes: - EEG data: responses to two-talker and single-talker speech stimuli - Envelopes of the corresponding speech audio - EEG data: responses to 1 kHz tone beeps for ERPs - EEG data: responses to periodic tone sequences for Envelope-following responses (EFRs) - EEG resting-state data recorded with eyes-open and eyes-closed - inEar EEG data for 19 of the 44 subjects (EEG recorded inside the ear canals) - Behavioral data: speech comprehension scores, task difficulty ratings, speech-in-noise scores (SRTs), tone-in-noise scores, digit span working memory scores, SSQ questionnaire ratings - Pure-tone audiograms For more information, see the README and 'dataset_description.json' file. Format ------ The dataset is formatted according to BIDS version 1.3.0 and the BIDS standard extension for EEG (BEP006) that has been merged in the main body of the specification. For more details, see https://bids-specification.readthedocs.io/en/latest/06-extensions.html Behavioural data are stored in the 'participants.tsv' file. Task-difficulty ratings and multiple choice questionnaire data from the selective attention experiment are stored in the events files (see 'task-selectiveattention_events.json'). Code ------ Code for analyzing the data is available at: https://gitlab.com/sfugl/snhl Audio ------ Envelopes of the audio signals are included in the data set. For inquiries regarding the raw audio data, please send an email to jensh@drcmr.dk with the subject line "ds-eeg-snhl audio". Acknowledgments ---------- This work was supported by the EU H2020-ICT grant number 644732 (COCOHA: Cognitive Control of a Hearing Aid) and by the Novo Nordisk Foundation synergy grant NNF17OC0027872 (UHeal). The EarEEG were kindly provided by Eriksholm Research Centre.

Dataset underlying the analysis of dendritic calcium signals evoked by somatic action potentials in MSO neurons during development (postnatal day 10 - 60). The data includes recordings from Mongolian gerbils (Meriones unguiculatus) raised in a normal acoustic environment and in omnidirectional white noise. Linked paper: Franzen DL, Gleiss SA, Kellner CJ, Kladisios N, Felmy F. Activity-Dependent Calcium Signaling in Neurons of the Medial Superior Olive during Late Postnatal Development. J Neurosci. 2020 Feb 19;40(8):1689–700. https://doi.org/10.1523/JNEUROSCI.1545-19.2020. Files included: A folder entitiled data containing: The imaging files (.nix) (1 file per imaged neuron). NIX files contain the kymograph data extracted from a ROI in the raw images along with the metadata. The imaging kymographs and associated .nix files were created with the CaManager: ImageJ Plugin For Ca²⁺ Imaging. An excludes.csv file that contains cells/trials to be excluded (e.g. recording error, movement, difficulty in tracing) A Megatable_C.csv file containing the electrophysiological data corresponding to imaged cells A .nix intermediate analysis file for default parameters A .csv file with the combined electrophysiological and imaging data for default parameters Several .xlsx files with the single cell data in Figures 2C, 2D, 2F. Jupyter notebook: The CaJupyter GitHub repository contains a Jupyter notebook with a step-by-step guide of the analysis. It also allows for further exploration of the data. See also: The original analysis code (without adaptations for the Jupyter notebook and Python 3) can be found at CaAnalysis: Analysis Toolbox for Ca²⁺ Imaging. More information on NIX can be found at this link.

Code and sample data comparable to the analysis of (Reinagel and Reid, 2000) with some improvements and otherwise unpublished extensions. This is not original or replication code. Rather this is new or revised code, based on the code and data used in that paper, as extracted and updated retrospectively on Dec 15, 2020. Material changes are documented in code comments. If this code is useful to you, please cite and attribute this repository.

Code and sample data comparable to the analysis of (Reinagel and Reid, 2000) with some improvements and otherwise unpublished extensions. This is not original or replication code. Rather this is new or revised code, based on the code and data used in that paper, as extracted and updated retrospectively in December 2020. Changes to the code did not materially alter any conclusion of the paper but allow code to generalize more successfully to other data sets.

ABSTRACT Within reflex circuits, specific anatomical projections allow central neurons to relay sensations to effectors that generate movements. A major challenge is to relate anatomical features of central neural populations, such as asymmetric connectivity, to the computations the populations perform. To address this problem, we mapped the anatomy, modeled the function, and discovered a new behavioral role for a genetically defined population of central vestibular neurons in rhombomeres 5–7 of larval zebrafish. First, we found that neurons within this central population project preferentially to motoneurons that move the eyes downward. Concordantly, when the entire population of asymmetrically projecting neurons was stimulated collectively, only downward eye rotations were observed, demonstrating a functional correlate of the anatomical bias. When these neurons are ablated, fish failed to rotate their eyes following either nose-up or nose-down body tilts. This asymmetrically projecting central population thus participates in both upward and downward gaze stabilization. In addition to projecting to motoneurons, central vestibular neurons also receive direct sensory input from peripheral afferents. To infer whether asymmetric projections can facilitate sensory encoding or motor output, we modeled differentially projecting sets of central vestibular neurons. Whereas motor command strength was independent of projection allocation, asymmetric projections enabled more accurate representation of nose-up stimuli. The model shows how asymmetric connectivity could enhance the representation of imbalance during nose-up postures while preserving gaze stabilization performance. Finally, we found that central vestibular neurons were necessary for a vital behavior requiring maintenance of a nose-up posture: swim bladder inflation. These observations suggest that asymmetric connectivity in the vestibular system facilitates representation of ethologically relevant stimuli without compromising reflexive behavior. SIGNIFICANCE STATEMENT Interneuron populations use specific anatomical projections to transform sensations into reflexive actions. Here we examined how the anatomical composition of a genetically defined population of balance interneurons in the larval zebrafish relates to the computations it performs. First, we found that the population of interneurons that stabilize gaze preferentially project to motoneurons that move the eyes downward. Next, we discovered through modeling that such projection patterns can enhance the encoding of nose-up sensations without compromising gaze stabilization. Finally, we found that loss of these interneurons impairs a vital behavior, swim bladder inflation, that relies on maintaining a nose-up posture. These observations suggest that anatomical specialization permits neural circuits to represent relevant features of the environment without compromising behavior.