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opencc-by-4.0Aug 2019View details →

Increasing the Expression Level of ChR2 Enhances the Optogenetic Excitability of Cochlear Neurons

This study reveals a dose-response relationship between channelrhodopsin expression and optogenetic excitation. Both single cell and organismal responses depend on the expression level of the heterologous protein.  Expression level of the opsin is thus an important variable in determining the outcome of an optogenetic experiment. These results are key to the implementation of neural prostheses based on optogenetics, such as next generation cochlear implants, which would use light to elicit a neural response to sound.

opencc-by-4.0Aug 2019View details →

Overexpressing HTT in neuronal cells

Overexpressing HTT in neuronal cells.

opencc-by-4.0Nov 2019View details →

Overexpressing HTT in neuronal cells by BacMAM viral transduction

Overexpressing HTT in mammalian cells using protein transfection, protein electroporation and overexpressing HTT in neuronal cells BacMAM viral transduction.

opencc-by-4.0Apr 2024View details →

Dynamics, synchronization and analog circuit implementation of a discrete neuron-like map with pulsating spiral dynamics

These are experimental time series for an electronic model of neural dynamics. They are provided to support the replication of the results reported in the associated publication, as well as any further public-domain academic research in the field of neural dynamics, nonlinear electronic circuits, and related aspects, in compliance with the specified license terms and all applicable legal clauses. The following reference must be cited when using these data: <div> <div> <div>Zhu W, Sun K, Wang H, Fu L, Minati L, Dynamics, synchronization and analog circuit implementation of a discrete neuron-like map with pulsating spiral dynamics, Chaos, Solitons and Fractals 186 (2024) 115281, DOI  10.1016/j.chaos.2024.115281</div> </div> </div> This document is the results of the research project funded by the National Natural Science Foundation of China (Nos. 62071496, 62061008), and the Innovation Project of Graduate of Central South University (Nos. 2024ZZTS0241). L.M. gratefully acknowledges the support of the "Hundred Talents" program of the University of Electronic Science and Technology of China, of the "Outstanding Young Talents Program (Overseas)" program of the National Natural Science Foundation of China, and of the talent programs of the Sichuan province and Chengdu municipality.

opencc-by-4.0Aug 2024View details →

NeuroFly Neuron Reconstruction Dataset

Open the record for dataset details and reuse information.

opencc-by-4.0Sep 2024View details →

Cilia structure and intraflagellar transport differentially regulate sensory response dynamics within and between C. elegans chemosensory neurons

List of data with corresponding files Figure 1 A)    File name: Figure 1A- ASH_IFT_mutants_length_copy.pzfx B)    File names: (Folder) ASH_1Mglycerol_IFT_mutants and (Folder) ASH_10-2IAA_IFT_mutants C)    File names: (Folder) ASH_1Mglycerol_IFT_mutants > Peak_responses and (Folder) ASH_10-2IAA_IFT_mutants > Peak_responses - first pulse D)   File names: Figure 1D – ASH Cher and Marianas Lengths Truncation osm-3(ts) 27 and 30 degree graph and Figure 1D – ASH Cher and Marianas Lengths Truncation osm-3(ts) 27 degrees E)    File name: Figure 1E – ASH IFT Quantification.xlsx F)    File name: (Folder) ASH_1Mglycerol_osm3ts G)   File names: Figure 1 – Glycerol_Assays_Data.pzfx and Figure 1 – Glycerol_Assays_Data.xlsx H)   File name: Figure 1H – ALL ASH Marianas and Cher Lengths che-3(nx159ts) I)     File names: Figure 1- ASH IFT PY12007 v AP457 and Figure 1- ASH IFT PY12007 v AP457.xlsx J)    File name: (Folder) ASH_1Mglycerol_che3ts K)   File names: Figure 1 – Glycerol_Assays_Data.pzfx and Figure 1 – Glycerol_Assays_Data.xlsx Figure 2 B)  File name: (Folder) 10-7Diacetyl_Calcium_IFT_mutants C)  File names: (Folder) 10-6Pyrazine_Calcium_IFT_mutants and (Folder) 10-7Pyrazine_Calcium_IFT_mutants D)  File names: (Folder) Microfluidics > (Folder) 10-6pyrazine and (Folder) 10-7diacetyl E)  File names: (Folder) Microfluidics > Diacetyl_Chemotaxis_index_osm6_osm3kap1.pzfx and Pyrazine_Chemotaxis_index_pyrazine_osm3kap1_osm6.pzfx G)  File name: (Folder) 10-6Pyrazine_Calcium_misexpression Figure 3 A)   File name: Figure 3A- AWA IFT AP303 v AP379.xlsx C)  File names: (Folder) AWA_Calcium_Diacetyl and (Folder) AWA_Calcium_Pyrazine D)  File names: (Folder) AWA_Calcium_Diacetyl and (Folder) AWA_Calcium_Pyrazine E)  File name: Figure 3E- SRX64 and ODR10 within dendritic branches.pzfx Figure 4 A)   File name: (Folder) AWA_Calcium_Diacetyl_grk2 B)   File name: (Folder) AWA_Calcium_Pyrazine_grk2 C)   File name: (Folder) Microfluidics_diacetyl D)   File name: (Folder) Microfluidics_pyrazine E)    File name: Figure 4E- GRK2tRFP_kap1osm3ts.pzfx Figure 5 A)   File names: (Folder) AWA_Diacetyl_Adaptation_osm3ts and (Folder) AWA_Pyrazine_Adaptation_osm3ts B)    File name: Figure 5B and S7B- FRAP.pzfx C)    File names: Figure 5C- SRX64_bbs7jhu590.pzfx and Figure 5C- SRX64_bbs7ok1351.pzfx and Figure 5C- oy158_bbs7jhu590.pzfx and Figure 5C- oy158_bbs7ok1351.pzfx D)   File names: (Folder) AWA_Diacetyl_Adaptation_bbs7 and (Folder) AWA_Pyrazine_Adaptation_bbs7 E)    File name: Figure 5E- Marianas_EV_ODR10_SRX64_osm3tskap1.pzfx Figure S1 A)   File names: (Folder) ASH_IFTmutants_0.5and2Mglycerol > (Folder) 0.5Mglycerol and (Folder) 2Mglycerol B)    File names: (Folder) ASH_IFTmutants_quinine > (Folder) 5mM_quinine and (Folder) 10mM_quinine C)    File name: ASH_IAA_t1/2 D)   File names: (Folder) ASH_IFTmutants_heptanol > (Folder) 10-3_heptanol and (Folder) 10-4_heptanol E)    File names: (Folder) ASH_IFTmutants_2Mglycerol_GABA and (Folder) ASH_IFTmutants_2Mglycerol_bicuculline Figure S2 B)    File name: Figure S2B- Dye-filling_data C)    File name: Figure S2C- ASH_IFT_mutants_length.pzfx D)   File names: Figure S2D- ASH IFT PY6345 v PY12007 and Figure S2D- ASH IFT Quantification Figure S3 A)   File name: (Folder) AWA_10-7Diacetyl_IFTmutants B)    File names: (Folder) AWA_Calcium_heptanone > (Folder) 10-4_heptanone and (Folder) 10-5_heptanone C)    File name: (Folder) AWA_10-5Pyrazine_IFTmutants D)   File names: (Folder) AWA_Calcium_methylpyrazine > (Folder) 10-8_methylpyrazine and (Folder) 10-9_methylpyrazine E)    File name: Figure S3- Chemotaxis IFT_mutants.pzfx Figure S4 A)  File name: Figure S4A – AP419_pyrazine_Chemotaxis.pzfx C)  File name: Figure S4C – srx64SL2gfp_osm5.pzfx Figure S6 A)   File names: Diacetyl_prism_decay_grk2 and Pyrazine_prism_decay_grk2 Figure S7  A)  File name: (Folder) AWA_Calcium_Adaptation_diacetyl_IFT_mutant  B)  File name: Figure 5B and S7B- FRAP  C)  File name: Figure S7C- oy158_grk2_rescue.pzfx  F)  File names: (Folder) AWA_Calcium_Adaptation_diacetyl_grk2 > (Folder) grk2 and (Folder) grk2bbs7double Additional materials             All code is listed under Code from Github > MF.matR-master and Additional Methods

opencc-by-4.0Aug 2024View details →

Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits

Raw data used to generate the figures in the paper "Modelling human brain-wide pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits" published as a bioRxiv preprint doi: https://doi.org/10.1101/2023.08.08.552400; v1 posted August 8, 2023; v2 posted August 14, 2024.

opencc-by-4.0Feb 2024View details →

Dataset for the paper - "Distinct prelimbic cortex neuronal responses to emotional states of others drive emotion recognition in adult mice "

Analysis software for the paper - "Distinct prelimbic cortex neuronal responses to emotional states of others drive emotion recognition in adult mice" <div>Renad Jabarin 1,# , Alok Nath Mohapatra 1,# , Natali Ray 1 , Shai Netser 1 and Shlomo Wagner 1, *</div> <div> </div> <div>1 Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa,</div> <div>Haifa, Israel</div> <div> </div> <div>*Corresponding author: Email: shlomow@research.haifa.ac.il</div> <div> </div> <div>This depository contains the following datasets created from the experiments in the paper:</div> <div> <ul> <li>The folder "Neuropixels_MatlabFile_rawdata.zip" holds the timestamps, video clips tracking results (analyzed using the software TrackRodent), and the spike times data of each session of all the tasks recorded from Neuopixels implanted animals.</li> <li>Further files/folders of the SP, ESPi and ESPs tasks are named with suffix as SP, Isolatn and Restrain respectively.</li> </ul> </div>

opencc-by-4.0Feb 2024View details →

Dataset 2 for paper - Distinct prelimbic cortex neuronal responses drive emotion recognition in male mice during Social Interactions-Behavior - Behavior, Piezo, FP and optogenetics datasets

The uploaded folders contain data for: 1) Analyzed video clips for behavioral testing of C57BL/6J ESP data for both males and females in ESPr, ESPs, ESPi, and ESPi with female subject and male stimuli, and the Three Discrimination Task. Relevant for Figure.1 and Supp.1. 2) Piezo data for ESPs with males, ESPi with males, and ESPi with females. Relevant for Fig.2 Each task folder contains 3 subfolders:     1- Timestamps     2- Piezo-sensors signal     3- Analyzed videos 2) Fiber Photometry data for the SP, ESPs, ESPi, and Food vs. Object tasks. Relevant for Fig.3-4 and Supp.2-8. The data for each task is divided into 3 folders:       1- Timestamps       2- Fiber photometry signal       3- Analyzed videos 3) Optogenetics data for SP, ESPs (excitation and inhibition), and stimulation with Empty Chambers. Relevant for Fig.8 and Supp.16. The SP and ESPs tasks in this experiment have 4 conditions, and the stimulation with empty chambers test has only the first 3 conditions of the following:      1- No stimulation       2- Stimulation with stimulus 1       3- Stimulation with stimulus 2       4- Free stimulation Data folders for conditions 2 and 3 contain two sub-folders:      1- Timestamps for the delivered optic stimulations      2- Analyzed videos

opencc-by-4.0Oct 2024View details →

Source data for Fig. S1F associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

This entry contains source data and statistical test for plots in Fig. S1F associated with: https://doi.org/10.1101/2024.09.24.614704

opencc-by-4.0Sep 2024View details →

Supplementary datasets associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

This entry contains supplementary dataset files associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons".

opencc-zeroJun 2021View details →

Early social deprivation shapes neuronal programming of the social decision-making network in a cooperatively breeding fish

The early social environment an animal experiences may have pervasive effects on its behaviour. The Social Decision-Making network (SDMN), consisting of interconnected brain nuclei from the forebrain and midbrain, is involved in the regulation of behaviours during social interactions. In species with advanced sociality such as cooperative breeders, offspring are exposed to a large number and a great diversity of social interactions every day of their early life, which may have life-long consequences on the development of several neurophysiological systems within the SDMN, although these effects are largely unknown. We studied these life-long effects in a cooperatively breeding fish, Neolamprologus pulcher, focusing on the expression in the SDMN of genes involved in the monoaminergic and stress response systems. N. pulcher fry were raised until an age of two months either with their parents, subordinate helpers and same clutch siblings (+F), or with same clutch siblings only (-F). Analysis of the expression of glucocorticoid receptor (GR), mineralcorticoid receptors (MR), corticotropin releasing factor (CRF), dopamine receptors 1 and 2, serotonin transporter (SERT) and DNA methyltransferase I (DNMT1) genes showed that early social experiences altered the neurogenomic state of the preoptic area (POA) of the hypothalamus. The dopamine receptor 1 gene was up-regulated in the POA of -F fish, compared to +F fish. -F fish also showed up-regulation of GR1 expression in the dorsal medial telencephalon (homologous to the basolateral amygdala). Our results suggest that early social environment has life-long effects on the development of several neurophysiological systems within the SDMN. --

opencc-zeroDec 2017View details →

Data from: Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron

Most neurogenesis in the mammalian brain is completed embryonically, but in certain areas the production of neurons continues throughout postnatal life. The functional properties of mature postnatally-generated neurons often match those of their embryonically-produced counterparts. However, we show here that in the olfactory bulb (OB), embryonic and postnatal neurogenesis produce functionally distinct subpopulations of dopaminergic (DA) neurons. We define two subclasses of OB DA neuron by the presence or absence of a key subcellular specialisation: the axon initial segment (AIS). Large AIS-positive axon-bearing DA neurons are exclusively produced during early embryonic stages, leaving small anaxonic AIS-negative cells as the only DA subtype generated via adult neurogenesis. These populations are functionally distinct: large DA cells are more excitable, yet display weaker and - for certain long-latency or inhibitory events - more broadly-tuned responses to odorant stimuli. Embryonic and postnatal neurogenesis can therefore generate distinct neuronal subclasses, placing important constraints on the functional roles of adult-born neurons in sensory processing.

opencc-zeroApr 2020View details →

Data from: Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent outliers in a moving avian hybrid zone

The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (P. carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent—including glutamate signaling, synaptic transmission, and catabolic processes—but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.

opencc-zeroJul 2021View details →

Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia

An atypical neuronal pacemaker mechanism, based on rhythmic intracellular calcium store release in an identified pair of interneurons (B63) and resulting oscillation of the neurons' membrane potential, acts as an autonomous releaser for the irregular occurrences of the motor program for food-seeking behavior in Aplysia. The rhythmic variations of the membrane potential in B63 neurons were analyzed by Fast Fourier Transform (FFT) analysis in a cycle period bandwidth of 512 s to 8 s. The resulting power spectral density periodograms were used to identify oscillation periods of peak magnitude. The periodograms were computed from the FFT frequency spectrograms by converting the frequency band (in Hz) to its reciprocal, period (in secs). These analysis were performed in isolated buccal ganglia preparations bathed in artifical sea water (ASW), in 'Low Ca+Co' saline to block chemical synapses, or in 'Low Ca+Co' saline and after an intracellular injection of organelle membrane calcium channel blocker heparin into either the bilateral B63 or B31 neurons. The oscillations of B63 membrane potential that were recorded in ASW persisted in 'Low Ca+Co', but were suppressed after heparin injection specifically into B63.

Fig. 4 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)

Fig. 4. Relative expression levels of SzeaSNMP in various tissues of Sitophilus zeamais. mAn = male antennae; fAn = female antennae; H = heads without antennae; T = thoraces without legs and wings; Abd = abdomens; W = wings; L = legs. Error bars represent the standard error, and the different letters above each bar indicate significant differences in relative levels of expression at P <0.05 (Tukey's HSD test).

Fig. 2 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)

Fig. 2. Sequence alignments of Sitophilus zeamais sensory neuron membrane protein with SNMPs from other Coleoptera species. Black triangles represent six conserved cysteine residues that could form three pairs of disulphide bridges in the SNMPs (Rasmussen et al. 1998). Abbreviated species names and GenBank accession numbers of amino acid sequences are described in Fig. 3.

Fig. 3 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)

Fig. 3. Phylogenetic analysis of insect SNMPs. A tree of SNMPs from Sitophilus zeamais and other insects was made by MEGA7 through the Neighbor-joining method with 1,000 bootstrap replications. The insect species and GenBank accession numbers for all the sequences of SNMPs are as follows: Aethina tumida (AtumSNMP2a/XP_019867287.1, AtumSNMP2b/ XP_019867285.1); Anoplophora chinensis (AchiSNMP1a/AUF73093.1, AchiSNMP1b/AUF73091.1); Anoplophora glabripennis (AglaSNMP2a/XP_018566912.1, AglaSNMP2b/XP_018566911.1); Colaphellus bowringi (CbowSNMP1a/ ALR72542.1, CbowSNMP1b/ALR72543.1, CbowSNMP2/ALR72544.1); Dendroctonus ponderosae (DponSNMP1a/ AGI05171.1, DponSNMP1b/XP_019756753.1, DponSNMP2a/XP_019770615.1, DponSNMP2b/AGI05184.1); Holotrichia parallela (HparSNMP1/AVM18969.1); Leptinotarsa decemlineata (LdecSNMP2/XP_023025981.1); Onthophagus taurus (OtauSNMP1/XP_022906339.1); Phyllotreta striolata (PstrSNMP1/ANQ46504.1, PstrSNMP2/ANQ46505.1); Tenebrio molitor (TmolSMMP1/AJO62245.1); Tribolium castaneum (TcasSNMP1/KYB28032.1, TcasSNMP2a/XP_008198962.1, TcasSMMP2b/ XP_970008.1).

Fig. 1 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)

Fig. 1. Nucleotide and deduced amino acid sequences of SzeaSNMPs from Sitophilus zeamais. The stop codons are marked with "-", and the black lines below the amino acid sequences indicate the two transmembrane domains. A) SzeaSNMP1a, B) SzeaSNMP1b, C) SzeaSNMP2a, D) SzeaSNMP2b.