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.
6,467
datasets available to search
ShareScore release 0.9.0
Dataset results
6,467 results for “process”
Fig. 56 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 56. The oxidation of glycolate catalyzed by glycolate oxidase. Glycolate, the shortest substrate of the family of 2-hydroxy acid oxidases, is oxidized to glyoxylate in the peroxisomes. The members of the family feature different chain-length specificities (see text for further details). The reduced FMN is reoxidized by dioxygen yielding hydrogen peroxide.
Fig. 58 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 58. Flavoenzymes involved in the generation of ROS in A. thaliana. A total of 68 flavin-dependent enzymes were found to be involved in the formation of ROS in A. thaliana, either as hydrogen peroxide or superoxide radical (dark blue, taken from Table 1). Out of these 68, 48 enzymes were predicted to be present in a single cellular compartment, 19 were in at least two and one enzyme was predicted in at least three cellular compartments. The enzymes are ubiquitously distributed across the different cellular compartments (AP, apoplast = 19; PX, peroxisome = 15; PM, plasma membrane = 12; M, mitochondria = 11; Cyto, cytosol = 12; CP, chloroplast = 10; N, nucleus = 4; G, Golgi and EX, extracellular region = 2 and ER, endoplasmic reticulum = 1 enzyme). The predicted ROS producing flavoproteins from Table 5 are shown in light blue. Out of 18, 13 enzymes were predicted to be present in a single cellular compartment and 5 were predicted to be present at least in two. (PM = 2; M = 1; Cyto = 2; CP = 10; N = 3; EX = 2, EMS, endomembrane system = 1 and ER = 2). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 53 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 53. Mechanism of action of quiescin sulfhydryl oxidase. The enzyme possesses two pairs of cysteines (see text) of which only the proximal pair is shown in the figure. In the resting state, the two proximal cysteines form an intramolecular disulfide that is reduced via interaction with the reduced dithiol of the thioredoxin domain. The reduced proximal dithiol then reduces the FAD, which is reoxidized by dioxygen.
Fig. 54 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 54. Mechanism of Erv and Ero as partners for protein disulfide isomerase. In contrast to quiescin sulfhydryl oxidase, Erv and Ero do not interact directly with client proteins but serve to keep protein disulfide isomerase in an active oxidized state in order to allow for the proper generation of disulfide bonds in client proteins. Reduced Erv and Ero are reoxidized by dioxygen giving rise to the production of hydrogen peroxide.
Fig. 52 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 52. Reaction of glutathione reductase with its cognate substrate glutathione. Glutathione reductase is primed by reduction at the expense of NADPH generating the reduced FAD, which subsequently reduces the internal disulfide bond. Next, oxidized glutathione (GSSG) is cleaved to two molecules of (reduced) glutathione (GSH) by a dithiol-disulfide exchange reaction. For a detailed mechanistic discussion see Miller (2013).
Fig. 51 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 51. Proposed reaction mechanism of lysine-specific histone demethylase. The oxidation of a methylated lysine residue (typically in position 4 of histone 3) is shown. Initially, oxidation of the substrate generates reduced FAD, which is re-oxidized by dioxygen leading to the production of hydrogen peroxide. The intermediate imine is hydrolyzed by water to produce the final products, the demethylated lysine side chain and formaldehyde (see also reaction of sarcosine oxidase).
Fig. 50 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 50. Reaction catalyzed by TYW1. N1-methylguanosine (m1G) in position 37 of the tRNA is converted to 4-demethylwyosine (imG-14). The two carbon atoms required to set up the tricyclic system are derived from pyruvate (Lombard and Hamdane, 2017).
Fig. 45 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 45. Reaction catalalyzed by quinone reductases. As an example, the reduction of benzoquinone is shown. However, quinone reductases generally have a broad substrate spectrum with regard to modifications at the aromatic ring. The source of electrons is typically NAD(P)H.
Fig. 41 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 41. Reaction catalyzed by cellodextrin oxidase (AtBBE22/CELLOX). This enzyme oxidizes the reducing end of oligosaccharides with a preference to chains with n = 1–4 (Locci et al., 2019). Based on the analysis of the oxygen reactivity motif, all reduced cellodextrin oxidases are predicted to react with dioxygen to yield hydrogen peroxide (Zafred et al., 2015) (see also discussion below).
Fig. 49 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 49. Reactions catalyzed by tRNA-dihydrouridine synthase (DUS) and the MnmE/MnmG (GidA) complex. (Top) Reduction of tRNA-uridine by tRNA-dihydrouridine synthase. The reduced FMN is generated at the expense of NADH. (Bottom) The modification of tRNA-uridine by the MmnEG complex requires GTP and methylenetetrahydrofolate (MTHF). The latter provides the carbon atom that is directly transferred to the 5′-position of the pryrimidine ring. Depending on whether ammonia or glycine is used as a co-substrate either nm5U or cmnm5U are generated. For more details on the reaction mechanism see text and Moukadiri et al. (2009).
Fig. 46 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 46). The ten genes encoding RBOHs in A. thaliana exhibit distinct expression patterns and exert special roles in various processes ranging from immune responses to plant development (for a review see Smirnoff and Arnaud, 2019). For example, RBOHD was shown to participate in wound response and systemic signaling (Miller et al., 2009) and RBOHD/F is involved in stomatal function and pathogen defense
Fig. 40 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 40. Reaction catalyzed by oligogalacturonide oxidase (AtBBE20). This enzyme specifically oxidizes oligogalacturonides with similar activities found for a chain length of n = 2 to n = 12 (Benedetti et al., 2018). Based on the analysis of the oxygen reactivity motif, all reduced oligogalacturonide oxidases are predicted to react with dioxygen to yield hydrogen peroxide (Zafred et al., 2015).
Fig. 36 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 36. Putative mechanism of isomerization followed by reduction. Isomerization is initiated by hydride transfer resulting in the removal of a deuteride from the (25)-carbon. This deuteride may be accepted by the flavin cofactor in exchange to the hydride provided in the initial step. Since the hydrogens of the reduced FAD cofactor are prone to exchange with solvent-borne hydrogens the reduction of the double bond will occur by transfer of a hydride
Fig. 38 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 38. Reduction of (9S,13S)-12-oxophytodienoic acid by 12-oxophytodienoic acid reductase 3. The preferred electron donor for this reaction is NADH, which is also the case for most old yellow enzyme homologs characterized thus far. Although the exact role of the other homologs in plant biochemistry is currently unknown, we hypothesize that they carry out similar C– –C-bond reductions in as yet unidentified substrates.
Fig. 32 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 32. Last step in abscisic acid biosynthesis catalyzed by abscisic aldehyde oxidase. Note that substrate oxidation occurs at the Moco and electrons are transferred to the FAD cofactor via two iron-sulfur-clusters, i.e. the same reaction mechanism as found in xanthine dehydrogenase. Reoxidation of reduced FAD occurs by dioxygen generating hydrogen peroxide.
Fig. 31 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 31. Reaction of zeaxanthin epoxidase. The enzyme catalyzes the consecutive epoxidation (monooxygenation) of both β-ionone rings in all-trans- zeaxanthin at the expense of reduced NAD(P)H. Dioxygen is cleaved during the reaction with one oxygen atom introduced into the substrate and the other one being released as water.
Fig. 26 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 26. Reaction catalyzed by protoporphyrinogen IX oxidase. The conversion of protoporphyrinogen IX to protoporphyrin IX, the last common step in heme and chlorophyll biosynthesis, requires three consecutive two-electron oxidations. Regeneration of the reduced FAD cofactor occurs by reoxidation with dioxygen leading to the production of hydrogen peroxide.
Fig. 21 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 21. Oxidation of L-aspartate to iminoaspartate initiates NADþ biosynthesis. The reduced FAD cofactor is reoxidized by dioxygen or fumarate leading to the production of either hydrogen peroxide or succinate (not shown).
Fig. 19 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 19. Reaction catalyzed by squalene epoxidase. The reducing equivalents are delivered by NADPH, and therefore, the enzyme was assigned to subclass A of flavin-dependent monooxygenases (Paul et al., 2021). Similar to zeaxanthine epoxidase the enzyme forms an unusual epoxide (see Fig. 31).
Fig. 18 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 18. Reaction catalyzed by dihydrooroate dehydrogenase. In the pyrimidine-half reaction the FMN cofactor is reduced by transfer of a hydride to the N(5)-position of the isoalloxazine ring (highlighted in red) followed by proton abstraction from the 5-position of dihydroorotate. A. thaliana dihydrooroate dehydrogenase belongs to the class 2 enzymes that are localized in the inter membrane space and associated with the inner mitochondrial membrane. Thus, reoxidation occurs by two successive one-electron transfer steps from the reduced FMN to CoQ (shown here as a single step). For a detailed discussion on the reaction mechanism see Palfey (2013). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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.