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1,554 results for “nucleus”
Psychedelic drug effects on reactivity of the paraventricular nucleus of the hypothalamus and threat responding behavior
<p>Psychedelics have experienced renewed interest following studies suggesting potential therapeutic effects in patients with affective disorders. While clinical results look promising, the neurobiological mechanisms underlying acute and prolonged effects of psychedelics remain unclear. Many psychiatric disorders involve hypothalamic-pituitary-adrenal (HPA) axis dysfunction. The paraventricular nucleus of the hypothalamus (PVN) is a midline hypothalamic nucleus that plays an integral role in HPA stress reactivity, autonomic functioning, social behavior, and many other affective processes. We investigated the effect of psilocin, the psychoactive metabolite of psilocybin, on PVN reactivity in Sprague Dawley rats. Psilocin increased stimulus-independent activity as measured by c-Fos expression in the PVN of male and female rats. Psilocin also increased PVN reactivity (ΔF/F) to an aversive air-puff stimulus in males but not females. PVN reactivity was restored at 2- and 7-days post-injection with no group differences. Additionally, we found that prior psilocin injection did not affect PVN reactivity following acute restraint stress. Experimental groups were sub-classified by baseline threat responding and psilocin-induced increases in male PVN reactivity were found to be driven by baseline active threat responders. Overall, these data demonstrate that the PVN is a significant site of psychedelic drug action with implications for threat responding behavior.</p>
◂Fig. 5 Gametogenesis in male and female Veneriserva pygoclava. A–D Semi-thin histological sections of female Veneriserva pygoclava, stained with toluidine blue. A Cross-section of a female Veneriserva. B Close-up of large mature oocytes without discernible nurse cells. C Developing oocytes attached to mesenteries (mes), and oogonia proliferating from the ventral side of the dorsal blood vessel (bv). D Details of vitellogenic oocytes and nurse cells. Arrowheads indicate brownstained yolk platelets and yolk bodies. E Live sperm cells captured in a light micrograph. F–G Cross-sections of male Veneriserva. Note the absence of a gut in the cross-sections. Abbreviations—ac acicula, acr acrosome, bv blood vessel, coe coelomic cavity, mes mesentery, nc nurse cell, nn nurse cell nucleus, nu sperm cell nucleus, Oo oocyte, on oocyte nucleus, sp spermatogonia, vnc ventral nerve cord in Hardly Venus's servant-morphological adaptations of Veneriserva to an endoparasitic lifestyle and its phylogenetic position within Dorvilleidae (Annelida)
◂Fig. 5 Gametogenesis in male and female Veneriserva pygoclava. A–D Semi-thin histological sections of female Veneriserva pygoclava, stained with toluidine blue. A Cross-section of a female Veneriserva. B Close-up of large mature oocytes without discernible nurse cells. C Developing oocytes attached to mesenteries (mes), and oogonia proliferating from the ventral side of the dorsal blood vessel (bv). D Details of vitellogenic oocytes and nurse cells. Arrowheads indicate brownstained yolk platelets and yolk bodies. E Live sperm cells captured in a light micrograph. F–G Cross-sections of male Veneriserva. Note the absence of a gut in the cross-sections. Abbreviations—ac acicula, acr acrosome, bv blood vessel, coe coelomic cavity, mes mesentery, nc nurse cell, nn nurse cell nucleus, nu sperm cell nucleus, Oo oocyte, on oocyte nucleus, sp spermatogonia, vnc ventral nerve cord
The Tangential Nucleus Controls a Gravito-inertial Vestibulo-ocular Reflex
<p>Background</p> <p>Although adult vertebrates sense changes in head position by using two classes of accelerometer, at larval stages zebrafish lack functional semicircular canals and rely exclusively on their otolithic organs to transduce vestibular information.</p> <p>Results</p> <p>Despite this limitation, we find that larval zebrafish perform an effective vestibulo-ocular reflex (VOR) that serves to stabilize gaze in response to pitch and roll tilts. By using single-cell electroporations and targeted laser ablations, we identified a specific class of central vestibular neurons, located in the tangential nucleus, that are essential for the utricle-dependent VOR. Tangential nucleus neurons project contralaterally to extraocular motoneurons and in addition to multiple sites within the reticulospinal complex.</p> <p>Conclusions</p> <p>We propose that tangential neurons function as a broadband inertial accelerometer, processing utricular acceleration signals to control the activity of extraocular and postural neurons, thus completing a fundamental three-neuron circuit responsible for gaze stabilization.</p> <p>Highlights</p> <p>► The utricle and its associated circuitry drive a broadband vestibular-ocular reflex ► Linear summation of bilateral utricular signals mediates compensatory eye rotations ► Central vestibular neurons in the tangential nucleus are necessary for the VOR ► Visual and vestibular signals interact to enhance gaze stabilization</p> <ul> </ul>
Data set for "Dopamine dynamics in nucleus accumbens across reward-based learning of goal-directed whisker-to-lick sensorimotor transformations in mice"
<p>Data set for: Huang J, Crochet S, Sandi C, Petersen CCH (2024) Dopamine dynamics in nucleus accumbens across reward-based learning of goal-directed whisker-to-lick sensorimotor transformations in mice. Heliyon 10: e37831. https://doi.org/10.1016/j.heliyon.2024.e37831<br><br></p> <p>There are 2 files in this upload:</p> <p>1. The file named "2024_Huang_Heliyon.pdf" is the Open Access pdf of the online publication in Heliyon.</p> <p>2. The file named "Huang_data_code.zip" (~6 GB) is a zipped version of a folder "Huang_data_code" (~6 GB), which contains the data analysed in the study along with the Matlab codes used to generate the published figures. To access the data and codes, first unzip the file. You need to install the Matlab 'Signal Processing' and 'Curve Fitting' Toolboxes. In Matlab, add the path of the folder "Huang_data_code" and all subfolders. The main folder unzips into three subfolders: i) "Huang_dLight_data_code", which contains the dLight data; ii) "Huang_muscimol_data_code", which contains the behavioral data for muscimol inactivation experiments; and iii) "Huang_singletrial_example", which contains the data for the single trial example data shown in Figure 1C (note for this to run you first need to load the data file "JH056_190308_WD.mat"). In the folder "Huang_dLight_data_code", you can also find a "DataViewer" to visualise the data trial-by-trial, which you can run by executing "DataViewer.mlapp" directly from the subfolder "Huang_dLight_data_code" after loading the data "Huang_database.mat".</p>
Linked collectors and determiners for: Review of the species of Macrodactylus Dejean (Coleoptera: Scarabaeidae Melolonthinae) from the Central American Nucleus.
Natural history specimen data linked to collectors and determiners held within, "Review of the species of Macrodactylus Dejean (Coleoptera: Scarabaeidae Melolonthinae) from the Central American Nucleus". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8b277405-a91c-4d0c-b77e-8b1d4820c7cd">https://bionomia.net/dataset/8b277405-a91c-4d0c-b77e-8b1d4820c7cd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8b277405-a91c-4d0c-b77e-8b1d4820c7cd">https://gbif.org/dataset/8b277405-a91c-4d0c-b77e-8b1d4820c7cd</a>. Formatted as a Frictionless Data package.
Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus
<p>In eukaryotes, DNA-associated protein complexes co-evolve with genomic sequence to orchestrate chromatin folding. Here, we investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of co-evolution. Using bacterial genomes integrated into S. cerevisiae, which diverged from yeast 1.5 billion years ago, we show that nucleosomes, cohesins and the transcriptional machinery can lead to the formation of two different chromatin archetypes, one transcribed and the other silent, independently of heterochromatin formation. These two archetypes also form on eukaryotic exogenous sequences, depend on sequence composition, and can be predicted using neural networks trained on the native genome. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalization, reminiscent of the organization of vertebrate nuclei. </p> <p> </p>
Distinct population code for movement kinematics and changes of ongoing movements in human subthalamic nucleus
<p>The subthalamic nucleus (STN) is theorized to globally suppress movement through connections with downstream basal ganglia structures. Current theories are supported by increased STN activity when subjects withhold an uninitiated action plan, but a critical test of these theories requires studying STN responses when an ongoing action is replaced with an alternative. We perform this test in subjects with Parkinson's disease using an extended reaching task where the movement trajectory changes mid-action. We show that STN activity decreases during action switches, contrary to prevalent theories. Further, beta oscillations in the STN local field potential, which are associated with movement inhibition, do not show increased power or spiking entrainment during switches. We report an inhomogeneous population neural code in STN, with one sub-population encoding movement kinematics and direction and another encoding unexpected action switches. We suggest an elaborate neural code in STN that contributes to planning actions and changing the plans.</p>
Data for: Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes
<p><span>Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in <em>Drosophila</em> starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022). With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, <em>in situ</em> hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function <em>in vivo</em>.</span></p>
Data from: Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala
<p>This dataset accompanies our publication titled: "Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala."</p> <p><strong>Files Included:</strong></p> <p><strong>1. geno.N26.vcf.gz</strong><br> - Description: Contains genotypes for 26 Heterogeneous Stock rats whose gene expression was predicted.</p> <p><strong>2. pred_expr.Brain.N26.tsv</strong><br> - Description: This tab-delimited table contains predicted relative gene expression in the brain for 26 Heterogeneous Stock rats. <br> - Details: Predictions were made for 8,997 genes from linear models based on cis-eQTLs from whole brain hemisphere tissue downloaded from the <a href="https://ratgtex.org/download/">RatGTEx Portal</a>. A gene is included in the table if it had at least one significant cis-eQTL, and if its predicted expression in these 26 animals had nonzero variance. The values in the table give the predicted log2(relative expression), where log2(2) = 1 is the baseline expression from the two haplotypes of the gene if it had only reference alleles at all its regulatory loci.<br> - Additional Info: Predictions were generated using <strong>gene_expr_pred.py</strong> available at https://github.com/PejLab/gene_expr_pred<br> An explanation of the prediction model is given in https://doi.org/10.1101/2022.01.28.478116</p> <p><strong>3. Behavioral data.xlsx</strong><br> - Description: Contains behavioral data for the Heterogeneous Stock (HS) rats.<br> - Organization: Each sheet in the file corresponds to data for a specific figure.</p> <p><strong>Additional Dataset Locations:</strong></p> <p>The primary datasets generated during this study can be found on the Gene Expression Omnibus under accession number <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212417">GSE212417</a></p> <p><strong>Publicly Available Datasets Utilized:</strong></p> <p>- Rattus norvegicus Ensembl v98 reference genome and genome assembly: <a href="http://useast.ensembl.org/Rattus_norvegicus/Info/Index">Rnor_6.0 </a><br> - JASPAR2022 transcription factor binding profiles for vertebrates: <a href="https://jaspar.genereg.net/">JASPAR</a><br> - ENCODE Honeybadger 2 ChIP-seq: <a href="https://personal.broadinstitute.org/meuleman/reg2map/">Broad Institute</a><br> - Liu et al. 2019106 GWAS for tobacco and nicotine addiction summary statistics: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358542/">PubMed</a><br> - RatGTEx Portal tissue-specific cis-eQTLs: <a href="https://ratgtex.org/download/">RatGTEx Portal </a><br> - 1000 Genomes European reference panel: <a href="https://alkesgroup.broadinstitute.org/LDSCORE/">Alkes Group</a><br> - KEGG pathways: <a href="https://www.kegg.jp/kegg/rest/keggapi.html">KEGG API</a></p>
Distinct population code for movement kinematics and changes of ongoing movements in human subthalamic nucleus
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Psychedelic drug effects on reactivity of the paraventricular nucleus of the hypothalamus and threat responding behavior
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Segmentations of 3D electron microscopy image volume from an albino mouse dorsal lateral geniculate nucleus
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Single nucleus sequencing of mouse hippocampi four days after pilocarpine induced status epilepticus
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Data for: Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes
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Identification of an inhibitory neuron subtype, the L-stellate cells of the cochlear nucleus
<p>Auditory processing depends upon inhibitory signaling by interneurons, even at its earliest stages in the ventral cochlear nucleus (VCN). Remarkably, to date only a single subtype of inhibitory neuron has been documented in the VCN, a projection neuron termed the D-stellate cell. With the use of a transgenic mouse line, optical clearing and imaging techniques, combined with electrophysiological tools, we revealed a population of glycinergic cells in the VCN distinct from the D-stellate cell. These novel multipolar glycinergic cells were smaller in soma size and dendritic area, but over 10-fold more numerous than D-stellate cells. They were activated by auditory nerve fibers and T-stellate cells, and made local inhibitory synaptic contacts on principal cells of the VCN. Given their abundance, combined with their narrow dendritic fields and axonal projections, it is likely that these neurons, here termed L-stellate cells, play a significant role in frequency-specific processing of acoustic signals.</p>
miRNA counts identified by RNA seq in the caudate nucleus of patients neuropathologically diagnosed with late-onset Alzheimer's disease (non-carriers and carriers of intermediate expansions in the HTT gene) and healthy subjects.
<p>These data include the raw miRNA counts identified by RNA-seq in <em>post mortem</em> caudate nucleus samples. Samples with identifier <strong>A</strong> belong to patients with a neuropathological diagnosis of late-onset Alzheimer's disease. Group <strong>B</strong> samples belong to patients with the same neuropathological diagnosis, but carrying CAG expansions in the intermediate range (27-35 CAG) in the <em>HTT</em> gene. Finally, group <strong>C </strong>samples belong to healthy subjects without neuropathological diagnosis. </p> <p> </p>
Data for 'X-ray eruptions every 22 days from the nucleus of a nearby galaxy'
<p>Data used to produce Figure 1 of 'X-ray eruptions every 22 days from the nucleus of a1 nearby galaxy' by Muryel Guolo, Dheeraj R. Pasham, Michal Zajacek, Eric Couglihn, et al. to appear in Nature Astronomy. Units in the files are the same as appear in the Figure 1 of the paper.</p>
Transcription start sites from capped small RNA-seq of rat nucleus accubmens and prefrontal cortex
<p>Small RNAs of ∼15–60 nt were size selected by denaturing gel electrophoresis starting from total RNA extracted from 14 rat brain tissue dissections. For csRNA libraries, cap selection was followed by decapping, adapter ligation, and sequencing. For input libraries, 10% of small RNA input was used for decapping, adapter ligation, and sequencing. After library quality check by gel electrophoresis, the samples were sequenced using the Illumina NextSeq 500 platform using 75 cycles single end. Sequencing reads were aligned to the rat mRatBN7.2 genome assembly using STAR v2.5.3a aligner with default parameters. Transcriptional start regions were defined using HOMER’s findPeaks tool. </p> <p>Duttke, S.H., Montilla-Perez, P., Chang, M.W., Li, H., Chen, H., Carrette, L.L.G., de Guglielmo, G., George, O., Palmer, A.A., Benner, C., et al. (2022). Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction. Front. Neurosci. 16, 858427.</p>
Data from: Diurnal variation of brain activity in the human suprachiasmatic nucleus
<p>The suprachiasmatic nucleus (SCN) is the central clock for circadian rhythms. Animal studies have revealed daily rhythms in the neuronal activity in the SCN. However, the circadian activity of the human SCN has remained elusive. In this study, to reveal the diurnal variation of the SCN activity in humans, the SCN was localized, and its activity was investigated using perfusion imaging. We scanned each participant four times a day, every six hours, and higher activity was observed at noon while lower activity was recorded in the early morning. The SCN activity was then measured every thirty minutes for six hours from midnight to dawn and showed a decreasing trend and was comparable with the rodent SCN activity after switching off the lights. These results suggest that the diurnal variation of the human SCN follows the zeitgeber cycles of mammals and is modulated by physical lights rather than the local time.</p>
A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice
<p>Raw Data for <strong>An atypical phosphoswitch in specific neurons of the suprachiasmatic nucleus gates locomotor activity at the light/dark transition in mice</strong></p> <ol> <li>Multi-electrode array data from PiT2<sup>+/+</sup> and PiT2<sup>-/-</sup> mice</li> <li>Locomotor activity from PiT2<sup>+/+ </sup>and PiT2<sup>-/-</sup> mice in LD 12:12, DD, LD 4:20, LD 20:4 and DD with light pulses</li> <li>Phosphoproteome data</li> </ol>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.