Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
31
datasets available to search
ShareScore release 0.9.0
Dataset results
31 results for “Rhodopsin”
Simulations of bovine rhodopsin
<p>This repository contains the simulations of phosphorylated and unphosphorylated bovine rhodopsin (Uniprot ID: <code>P02699</code>). The simulations and their analysis were published in 'Proteins: Structure, Function, and Bioinformatics'.</p> <p>For any use please cite:</p> <blockquote> <p>Damodaran, K. et al.<br>New simulation insights on the structural transition mechanism of bovine rhodopsin activation.<br>Proteins 91, 771–780 (2023).</p> </blockquote>
Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster
<p>To survive adverse environments, many animals enter a dormant state such as hibernation, dauer, or diapause. Various Drosophila species undergo adult reproductive diapause in response to cool temperatures and/or short day-length. While it is known that flies are less active during diapause, an in-depth understanding of diapause effects on circadian rhythms and sleep is lacking. Here we show that, in diapause-inducing conditions, Drosophila melanogaster exhibit altered circadian activity profiles, including a severely reduced morning activity peak and an advanced evening activity peak. Consequently, the flies have a single activity peak at a time similar to when non-diapausing flies have a siesta. Temperatures ≤15 °C, rather than short day-length, primarily drive the behavior. At cool temperatures, flies also rapidly enter a deep sleep state that lacks the sleep cycles of flies at higher temperatures and requires particularly high levels of stimulation for arousal. Furthermore, we show that at 18–25 °C, flies prefer to siesta in the shade, a preference that is virtually eliminated at 10 °C. Resting in the shade is driven by an aversion to blue light, sensed by rhodopsin 7 (Rh7) outside of the eyes. Flies at 10 ˚C show neuronal markers of elevated sleep pressure, including increased expression of Bruchpilot and elevated Ca2+ in the R5 ellipsoid body neurons. Therefore, sleep pressure might overcome blue light aversion. Thus at temperatures known to cause reproductive arrest, preserve germline stem cells, and extend lifespan, Drosophila melanogaster are prone to deep sleep and exhibit dramatically altered - yet rhythmic - daily activity patterns.</p>
Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster
Open the record for dataset details and reuse information.
Dataset for "Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behaviour"
<p>Dataset files include:</p> <p>- Alignment of rhodopsin (Rh1) sequences formatted for PAML</p> <p>- Corresponding species tree in Newick format for PAML</p> <p>- Ancestral Rh1 amino acid sequences (for Cetacean and Whippomorpha nodes) estimated with PAML (random sites, clade, and amino acid models), Datamonkey, and ProtASR</p>
Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika
<p><span>The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in the virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the achromatic environment with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth-related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability, and 11 sites that may be functionally important on the basis of their </span><span>physicochemical properties. Among the strongest candidate sites for deep-water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is th first compralehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.</span></p>
Datasets relating to characterisation of Jumping Spider Rhodopsin-1 after reconstitution with retinal and retinal analogues
<p>001 - UV-Vis spectra JSR1 reconstituted with all-trans retinal, 9-cis retinal, ATR6.11 and 9CR6.11</p> <p>002 - UV-Vis spectra of JSR1 reconstituted with ATR6.11 and 9CR6.11, before and after acid denaturation</p> <p>003 - UV-Vis spectra of JSR1 reconstituted with ATR6.11, after addition of hydroxylamine</p> <p>004 - UV-Vis spectra of JSR1 reconstituted with 9CR6.11, after addition of hydroxylamine</p> <p>005 - UV-Vis spectra of illuminated JSR/ATR6.11 and JSR/9CR6.11</p> <p>006 - GTPase Glo Assay data measuring catalysis of nucleotide exchange in human G protein heterotrimers by JSR1/ATR6.11, JSR/9CR6.11 and JSR/9-cis retinal, with and without illumination</p> <p>007 - Size exclusion chromatograms JSR1/ATR6.11 after incubations with human Gi or human Gq heterotrimers</p> <p>008 - SDS-PAGE analysis of size exclusion chromatography peaks with JSR/ATR6.11 and human Gi or human Gq heterotrimers</p>
The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy
<p>Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus <em>Catenaria anguillulae</em>, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.</p>
Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika
Open the record for dataset details and reuse information.
The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy
Open the record for dataset details and reuse information.
Optogenetic silencing by combining a rhodopsin cyclase with an engineered cGMP-gated potassium channel
Open the record for dataset details and reuse information.
Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 My. While several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.
Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
Open the record for dataset details and reuse information.
Data from: Evolution of eye morphology and rhodopsin expression in the Drosophila melanogaster species subgroup
A striking diversity of compound eye size and shape has evolved among insects. The number of ommatidia and their size are major determinants of the visual sensitivity and acuity of the compound eye. Each ommatidium is composed of eight photoreceptor cells that facilitate the discrimination of different colours via the expression of various light sensitive Rhodopsin proteins. It follows that variation in eye size, shape, and opsin composition is likely to directly influence vision. We analyzed variation in these three traits in D. melanogaster, D. simulans and D. mauritiana. We show that D. mauritiana generally has larger eyes than its sibling species, which is due to a combination of larger ommatidia and more ommatidia. In addition, intra- and inter-specific differences in eye size among D. simulans and D. melanogaster strains are mainly caused by variation in ommatidia number. By applying a geometric morphometrics approach to assess whether the formation of larger eyes influences other parts of the head capsule, we found that an increase in eye size is associated with a reduction in the adjacent face cuticle. Our shape analysis also demonstrates that D. mauritiana eyes are specifically enlarged in the dorsal region. Intriguingly, this dorsal enlargement is associated with enhanced expression of rhodopsin 3 in D. mauritiana. In summary, our data suggests that the morphology and functional properties of the compound eyes vary considerably within and among these closely related Drosophila species and may be part of coordinated morphological changes affecting the head capsule.
Data from: Creation of photocyclic vertebrate rhodopsin by single amino acid substitution
<p><span>Opsins are universal photoreceptive proteins in animals and can be classified into three types based on their photoreaction properties. Upon light irradiation, vertebrate rhodopsin forms a metastable active state, which cannot revert back to the original dark state via either photoreaction or thermal reaction. By contrast, after photoreception, most opsins form a stable active state which can photo-convert back to the dark state. Moreover, we recently found a novel type of opsins whose activity is regulated by photocycling. However, the molecular mechanism underlying this diversification of opsins remains unknown. In this study, we showed that</span><span> vertebrate rhodopsin acquired the photocyclic and photoreversible properties upon introduction of a single mutation at position 188. This revealed that the residue at position 188 contributes to the diversification of photoreaction properties of opsins by its regulation of the recovery from the active state to the original dark state.</span></p>
Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels - additional data
<p>This repository stores additional data files for the article Rozenberg, Kaczmarczyk, Matzov, Vierock et al (2022) "<a href="https://doi.org/10.1038/s41594-022-00783-x">Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels</a>".</p> <p>The files included are as follows:</p> <ul> <li>Inputs.zip - all input files to <a href="https://github.com/BejaLab/RRB">the workflow</a> (also available there)</li> <li>Species phylogenies: <ul> <li>Chlorophyte_orthogroups.zip, Haptophyte_orthogroups.zip, Dinoflagellate_orthogroups.zip - zip files with the orthogroups used in species phylogeny. Each folder corresponds to an orthogroup (busco orthogroups for chlorophytes and dinoflagellate, proteinortho orthogroups for haptophytes): <ul> <li>mafft.faa - mafft alignment</li> <li>trimal.faa - trimal trimmed alignment</li> <li>iqtree.treefile and iqtree.log - iqtree tree and log file</li> <li>treeshrink.treefile - treeshrink pruned tree</li> </ul> </li> </ul> </li> <li>Structural_alignment.zip includes structural alignments of the bestrhodopsin's rhodopsin and bestrophin domains with reference sequences: <ul> <li>rhodopsins.aln and bestrophins.aln- raw alignments from t_coffee</li> <li>rhodopsins_modified.fasta and bestrophins_modified.fasta - curated alignments</li> <li>rhodopsins.gff and bestrophins.gff - secondary structure features for the sequences</li> </ul> </li> <li>Global phylogeny of bestrophins and rhodopsins: <ul> <li>Bestrophins_global_sequences.zip - sequence data for the bestrophin global phylogeny: <ul> <li>uniref50.txt - uniref50 tabular data matching bestrophins (Pfam PF01062)</li> <li>ur50_long.cdhit, ur50_long.cdhit.clstr - cdhit clustering (50% identity)</li> <li>ur50_trim.faa - filtered and trimmed alignment used as input to iqtree</li> </ul> </li> <li>Bestrophins_global_phylogeny.zip - global bestrophin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick ur50.treefile files.</li> <li>Rhodopsins_global_phylogeny.fasta, Rhodopsins_global_phylogeny.fasta.trimmed - alignment of rhodopsin sequences and its trimmed version as used for rhodopsin bestrophin phylogeny</li> <li>Rhodopsins_global_phylogeny.zip - global rhodopsin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick rhodopsins.treefile files</li> <li>Rhodopsins_global_phylogeny_interproscan.zip - results of interproscan analysis of the rhodopsin sequences used for global phylogeny</li> </ul> </li> </ul>
Data from: Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin
Open the record for dataset details and reuse information.
Data from: Creation of photocyclic vertebrate rhodopsin by single amino acid substitution
Open the record for dataset details and reuse information.
Data from: Evolution of eye morphology and rhodopsin expression in the Drosophila melanogaster species subgroup
Open the record for dataset details and reuse information.
RNA sequencing data after simultaneous transactivation of M-opsin and knockout of rhodopsin upon subretinal injection of mice with the REVeRT dual AAV system
GEO Series GSE198893. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Sex-specific attenuation of photoreceptor degeneration by reserpine in a rhodopsin P23H rat model of autosomal dominant retinitis pigmentosa
GEO Series GSE278306. Rattus norvegicus. 19 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.