Detailed materials and methods are provided in the SI Appendix . This includes information on field work, flow sorting, whole-genome amplification, amplicon library construction and sequencing, data processing, assembly and analysis, including gene predictions, as well as phylogenetic, crystallization and phylogenomic analyses. The final ChoanoV1 genome assembly was assembled from 13,802,665 quality-filtered reads, and viral contigs were differentiated from the cellular assembly by tetranucleotide frequency and GC content. The ChoanoV1 assembly consisted of 11 contigs with average coverage of 215 ± 157×. For eastern North Pacific Ocean gene expression analyses, reads from metatranscriptomes were mapped to ChoanoVirus genomes at >95% nucleotide identity with bbmap. For 18S V4 amplicon sequencing, we had on average 131,385 ± 121,027 amplicons well−1 (the lowest number being 1,037) clustered at 99% and classified via the Protistan Ribosomal Reference database. Rhodopsin functionality of viral VirRDTS was determined via heterologous expression in E. coli. The VirRDTS crystallization samples were produced by a cell-free system, and crystals were grown using the in meso approach. Accession numbers and DOI for alignment and tree files are available in Dataset S2 .
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Rhodopsin
Rhodopsin
Rhodopsin is a light-sensitive G protein-coupled receptor found in the retinal photoreceptor cells of the eye.
It plays a crucial role in the initial steps of vision, converting light energy into electrical signals that are processed by the brain.
Rhodopsin is composed of the protein opsin and the chromophore retinal, which undergoes a conformational change upon absorbing light.
This change activates the G protein transducin, initiating a signaling cascade that ultimately leads to the generation of a neural impulse.
Rhodopsin is essential for both scotopic (low-light) and photopic (daylight) vision, and its dysfunction can result in various vision disorders, such as retinits pigmentosa and Oguchi disease.
Reasearchers studying Rhodopsin can leverage PubCompare.ai, an AI-driven platform that streamlines Rhodopsin research by locating protocols from literature, preprints, and patents, and providing AI-driven comparisons to identify the most effective protocols and products.
This can enhance reproducibity and accuracy in Rhodopsin studies.
It plays a crucial role in the initial steps of vision, converting light energy into electrical signals that are processed by the brain.
Rhodopsin is composed of the protein opsin and the chromophore retinal, which undergoes a conformational change upon absorbing light.
This change activates the G protein transducin, initiating a signaling cascade that ultimately leads to the generation of a neural impulse.
Rhodopsin is essential for both scotopic (low-light) and photopic (daylight) vision, and its dysfunction can result in various vision disorders, such as retinits pigmentosa and Oguchi disease.
Reasearchers studying Rhodopsin can leverage PubCompare.ai, an AI-driven platform that streamlines Rhodopsin research by locating protocols from literature, preprints, and patents, and providing AI-driven comparisons to identify the most effective protocols and products.
This can enhance reproducibity and accuracy in Rhodopsin studies.
Most cited protocols related to «Rhodopsin»
Cell-Free System
Cells
Crystallization
DNA Library
Escherichia coli
Gene Expression Profiling
Genes
Genome
Nucleotides
Rhodopsin
Ribosomes
Trees
Virus Physiological Phenomena
11-cis-Retinal
Biological Assay
Bos taurus
Cells
Chromatography, Affinity
Dithionite
Fatty Acids
Fluorescence
Glycolipids
Homo sapiens
Lipids
Mannose
Membrane Proteins
Monoclonal Antibodies
Phospholipids
proteoliposomes
Rhodopsin
Rod Cell Outer Segment
Rod Opsins
SDS-PAGE
Serum Albumin
Triton X-100
Capsid
Cloning Vectors
Homo sapiens
Rhodopsin
Rod Opsins
Simian virus 40
Transfection
Transgenes
If the LRT indicates that a particular site ( ) is subject to episodic diversifying selection, it may be of interest to explore which branches at that site have undergone diversification. The empirical Bayes (EB) procedure originally used to identify individual sites subject to diversifying selection in random effects models [28] (link), can be readily adapted here. To compute the empirical posterior probability at branch that , we apply Bayes' theorem, using to denote the data at site and to denote all the maximum likelihood parameter estimates from the alternative MEME model fitted to site : To compute the two likelihood terms and , we use and , respectively, for the model assigned to branch in equation 2. The rest of the branches employ the matrices fitted under the alternative model of MEME. Having computed for each branch , we evaluate the empirical Bayes factor for the event of observing positive selection at each branch: When , sequence data increase the prior odds of observing selection at the branch. We do not recommend using this type of inference other than for the purposes of data exploration, even for large values of (e.g. 100). Intuitively, all the information contributing to the estimate of is derived from observing the evolution along a single branch at a single site (i.e. from a sample with size ). To quantify this supposition, we simulated sequence data using the vertebrate rhodopsin phylogeny and branch lengths, applied positive selection of varying strength to five branches in the tree selected a priori (see Text S1 ), and applied the EB procedure to infer the identity of selected branches.
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Biological Evolution
Rhodopsin
Trees
Vertebrates
At 6-8 weeks postinjection, the eyes were harvested and fixed in 4% paraformaldehyde for 1 hour at room temperature. Whole mounts were prepared by making a circular incision around the ora serrata, removing the cornea and gently manipulating the eye cup to remove the neural retina. For retinal cross-sections, whole mounts were embedded in agarose and sectioned transversely using a vibratome (Leica Microsystems) at medium speed, maximum vibration, and 100 μm thickness. Whole mounts and sections were mounted on slides using VECTASHIELD antifade mounting medium (Vector Laboratories) containing DAPI to stain cell nuclei and examined under confocal microscopy to confirm expression of the opsin-YFP fusion proteins. For staining of rhodopsin, mounted sections were permeabilised with 0.2% Triton-X-100 PBS for 20 minutes at room temperature then blocked with 10% donkey serum (D9663, Sigma UK) in 0.2% Triton-X-100 PBS for one hour at room temperature. Primary antibody solution was then applied for 3 hours at room temperature (1 : 200 rabbit anti-human rhodopsin, Abcam ab112576 in blocking buffer). Sections were rinsed with 0.05% Tween20 PBS four times for 10 minutes each then incubated with secondary antibody solution for 2 hours at room temperature (1 : 200 AlexaFluor donkey anti-rabbit 488 in 2.5% donkey serum, 0.2% Triton-X-100 PBS). Slides were rinsed four times in 0.05% Tween20 PBS then once with water before being DAPI mounted as described above.
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Buffers
Cardiac Arrest
Cell Nucleus
Cloning Vectors
Cornea
DAPI
Equus asinus
Homo sapiens
Immunoglobulins
Microscopy, Confocal
Nervousness
Ora Serrata
paraform
Proteins
Rabbits
Retina
Rhodopsin
Rod Opsins
Sepharose
Serum
Stains
Triton X-100
Tween 20
Vibration
Most recents protocols related to «Rhodopsin»
The AON-treated ROs were fixed in 2% paraformaldehyde (Thermo Fisher Scientific) and 5% sucrose (Thermo Fisher Scientific) for 15 min at 4°C, followed by a 30-min incubation in 7.5% sucrose, 30 min in 15% sucrose, and 2 h incubation in 30% sucrose. The organoids were transferred to a cryomold and embedded in 7.5% gelatin (porcine skin; Merck KGaA) and 10% sucrose. The sample blocks were then frozen at −80°C. Sections of 10 μm thickness were sliced on a Cryotome FSE (Thermo Fisher Scientific), rehydrated in PBS, and stained following the protocol described by Cowan et al.46 (link) ABCA4 was detected using the anti-ABCA4 3F4 clone (1:100; Abcam, Cambridge, UK), rhodopsin was stained using the anti-rhodopsin 4D2 clone (1:300, Invitrogen), mitochondria were detected with an anti-MTCO2 antibody (1:150; Abcam), and nuclei were stained with Hoechst 33,342 (1:1000; Thermo Fisher Scientific). Images were collected on an LSM 800 confocal microscope (Carl Zeiss, Oberkochen, Germany) using a 60× objective and analyzed with ZEN Blue edition (Carl Zeiss) using the maximum intensity projection.
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Antibodies, Anti-Idiotypic
Cell Nucleus
Clone Cells
Freezing
Gelatins
Microscopy, Confocal
Mitochondria
Organoids
paraform
Pigs
Rhodopsin
Skin
Sucrose
Mouse eyes were enucleated in darkness under dim red light. Each eye was flash-frozen on dry ice immediately after enucleation. Rhodopsin was extracted with 20 mm HEPES, pH 7.4, containing 10 mm n-dodecyl-β-maltoside and 5 mm freshly neutralized NH2OH·HCl, as described previously (Palczewska et al., 2018 (link)). Briefly, the tissue was homogenized with 0.9 ml of buffer in a 2-ml Dounce tissue homogenizer (Kontes Glass Co) and shaken for 5 min at 4°C. The sample was then centrifuged at 17,200 × g for 5 min at 4°C. The supernatant was collected, the pellet was extracted a second time with 0.9 ml of buffer, and the combined supernatants were filtered through a 0.22-μm polyethersulfone membrane. Absorbance spectra were recorded using a Varian Cary 50-Scan UV-Vis spectrophotometer (Varian Australian Pty Ltd.); the sample was used as blank, then it was bleached for 5 min with a white-light, 875-Lumens bulb, and finally the difference absorbance spectrum was recorded immediately following a bleach. The concentration of rhodopsin was determined by the decrease in absorbance at 500 nm using the molar extinction coefficient ε500nm = 42,000 M−1 ·cm−1.
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Buffers
Darkness
dodecyl maltoside
Dry Ice
Extinction, Psychological
Freezing
HEPES
Light
Mice, House
Molar
Plant Bulb
polyether sulfone
Radionuclide Imaging
Rhodopsin
Tissue, Membrane
Tissues
Protocol full text hidden due to copyright restrictions
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Alexa594
alexa fluor 488
Antibodies
Arrestin
Clone Cells
Cryoultramicrotomy
DAPI
Eye
Goat
Mice, House
Microscopy, Confocal
paraform
Rabbits
Retinal Cone
Rhodopsin
Serum
Sucrose
Triton X-100
Our study followed the NIH Guide for the Care and Use of Laboratory Animals and the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research. The Institutional Animal Care and Use Committee (IACUC) at the University of Oklahoma Health Sciences Center approved all protocols. The floxed LDHA (Stock No: 030112), Chx10-EGFP/Cre (Stock No: 005105), transgenic glial high-affinity glutamate transporter (GLAST-CreER), Rax-CreER (Stock No: 025521), tdTomato reporter (Stock No: 007909), and RiboTag (Stock No: 011029) mice were purchased from the Jackson Laboratory (Bar Harbor, ME). The rhodopsin-Cre (i75-Cre) mice have been described earlier (47 (link)) and were provided by Dr. Ching-Kang Jason Chen (Baylor College of Medicine, Houston, TX). Tetracycline-inducible RPE-specific VMD2-Cre mice and cone opsin-Cre (human red/green pigment gene promoter) mice were provided by Dr. Yun Le (University of Oklahoma). All mice were screened for rd1 and rd8 mutations and were negative for these mutations. The eyes or retinas were harvested after CO2 asphyxiation. For metabolic experiments, mouse retinas were harvested under deep anesthesia, or retinas were removed after decapitation. These tissues were subjected to biochemistry or immunohistochemistry. To eliminate bias, mice of the same sex, age, and genetic strain were randomly assigned to each experimental group. Litters were mixed to prevent litter bias. Once mice were genotyped and provided with unique ear tag identifiers, cohorts were selected randomly by the principal investigator (Dr. Rajala), such that research personnel doing experiments were blinded and only knew the ear tag number.
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Anesthesia
Animals
Animals, Laboratory
Animals, Transgenic
Asphyxia
Cone Opsins
Decapitation
Eye
Glutamate Transporter
Homo sapiens
Immunohistochemistry
Institutional Animal Care and Use Committees
LDH 5
Mice, Laboratory
Mutation
Neuroglia
Patient Holding Stretchers
Pharmaceutical Preparations
Pigmentation
Promoter, Genetic
Reproduction
Retina
Rhodopsin
Strains
tdTomato
Tetracycline
Tissues
Vision
Vitelliform Macular Dystrophy
Immunohistochemistry and immunoblot analysis were performed as previously described (48 (link)). In the current study, blots were incubated with LDHA (1:1,000), LDHB (1:1,000), hexokinase 1 (1:1,000), hexokinase 2 (1:1,000), Aldolase C (1:1,000), cone arrestin (1:1,000), pPKM2 (1:1,000), PKM2 (1:1,000), PKM1 (1:1,000), Pde6β (1:1,000), rhodopsin (1:1,000), rod arrestin (1:1,000), M-opsin (1:1,000), PDH (1:1,000) and actin (1:1,000) antibodies (Table S5 ) overnight at 4° C. The blots were then washed and incubated with HRP-coupled anti-mouse or anti-rabbit secondary antibodies (as appropriate) for 60 min at room temperature. After washing, blots were developed with enhanced SuperSignal West Dura Extended Duration Substrate (Thermo Fisher Scientific, Waltham, MA) and visualized using a Kodak Imager with chemiluminescence capability.
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Actins
Aldolase C
Anti-Antibodies
Antibodies
Arrestin
Chemiluminescence
Dura Mater
Hexokinase
Hexokinase II
Immunoblotting
Immunohistochemistry
LDH 5
Mus
Rabbits
Retinal Cone
Rhodopsin
Rod Opsins
Top products related to «Rhodopsin»
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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
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Alexa Fluor 488 is a fluorescent dye used in various biotechnological applications. It has an excitation maximum at 495 nm and an emission maximum at 519 nm, producing a green fluorescent signal. Alexa Fluor 488 is known for its brightness, photostability, and pH-insensitivity, making it a popular choice for labeling biomolecules in biological research.
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MAB5356 is a laboratory instrument manufactured by Merck Group. It is designed for the detection and quantification of specific biomolecules in research and diagnostic applications. The core function of this product is to provide accurate and reliable analytical results.
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Ab5417 is a laboratory antibody product. It is a polyclonal antibody developed in rabbit. The core function of this product is to detect the target protein.
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Rhodopsin is a photoreceptor protein found in the retinal cells of the eye. It is responsible for initiating the visual transduction process, which converts light energy into electrical signals that the brain can interpret. Rhodopsin is a member of the G protein-coupled receptor family and is essential for the detection of light in low-light conditions.
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Rhodopsin is a light-sensitive G-protein-coupled receptor found in the retinal photoreceptor cells of the eye. It plays a central role in the visual transduction process, converting light energy into electrical signals that are transmitted to the brain.
Sourced in United States, Germany
AB15282 is a laboratory equipment product. It is a device used for scientific analysis and experimentation. The core function of this equipment is to facilitate the measurement and investigation of various samples and materials in a controlled laboratory environment.
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Anti-rhodopsin is a laboratory reagent used for the detection and analysis of rhodopsin, a light-sensitive protein found in the retinal cells of the eye. It provides a specific and sensitive tool for researchers studying visual perception and related biological processes.
Sourced in United States
The AB5405 is a laboratory instrument designed for performing various analytical and research tasks. It is a versatile piece of equipment that can be utilized in a wide range of scientific applications. The core function of the AB5405 is to facilitate precise measurements and data collection, but a detailed description of its intended use is not available.
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DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.
More about "Rhodopsin"
Rhodopsin, a light-sensitive G protein-coupled receptor, plays a crucial role in the initial stages of vision.
Located in the retinal photoreceptor cells, rhodopsin converts light energy into electrical signals that are processed by the brain.
This essential visual protein is composed of the opsin protein and the chromophore retinal, which undergoes a conformational change when exposed to light.
This light-induced activation of rhodopsin triggers a signaling cascade that ultimately leads to the generation of a neural impulse.
Rhodopsin is vital for both scotopic (low-light) and photopic (daylight) vision, and its dysfunction can result in various vision disorders, such as retinitis pigmentosa and Oguchi disease.
Researchers studying rhodopsin can leverage PubCompare.ai, an AI-driven platform that streamlines the research process.
PubCompare.ai helps locate protocols from literature, preprints, and patents, and provides AI-driven comparisons to identify the most effective protocols and products.
This can enhance reproducibility and accuracy in rhodopsin studies.
When exploring rhodopsin, researchers may also encounter related terms and techniques, such as DAPI (4',6-diamidino-2-phenylindole), Alexa Fluor 488, MAB5356, Ab5417, AB15282, Anti-rhodopsin, and AB5405.
These tools and reagents can be utilized to visualize, detect, and analyze rhodopsin in various experimental settings.
By utilizing the insights gained from PubCompare.ai and incorporating relevant terms and techniques, researchers can enhance their understanding and investigation of this crucial visual protein, ultimately advancing the field of vision research and addressing related health concerns.
Located in the retinal photoreceptor cells, rhodopsin converts light energy into electrical signals that are processed by the brain.
This essential visual protein is composed of the opsin protein and the chromophore retinal, which undergoes a conformational change when exposed to light.
This light-induced activation of rhodopsin triggers a signaling cascade that ultimately leads to the generation of a neural impulse.
Rhodopsin is vital for both scotopic (low-light) and photopic (daylight) vision, and its dysfunction can result in various vision disorders, such as retinitis pigmentosa and Oguchi disease.
Researchers studying rhodopsin can leverage PubCompare.ai, an AI-driven platform that streamlines the research process.
PubCompare.ai helps locate protocols from literature, preprints, and patents, and provides AI-driven comparisons to identify the most effective protocols and products.
This can enhance reproducibility and accuracy in rhodopsin studies.
When exploring rhodopsin, researchers may also encounter related terms and techniques, such as DAPI (4',6-diamidino-2-phenylindole), Alexa Fluor 488, MAB5356, Ab5417, AB15282, Anti-rhodopsin, and AB5405.
These tools and reagents can be utilized to visualize, detect, and analyze rhodopsin in various experimental settings.
By utilizing the insights gained from PubCompare.ai and incorporating relevant terms and techniques, researchers can enhance their understanding and investigation of this crucial visual protein, ultimately advancing the field of vision research and addressing related health concerns.