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904 results for “Biosynthesis”
Fig. 2 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)
Fig. 2. Expression analysis of genes involved in melatonin biosynthesis. A: Heat map showing tissue-specific expression profiles of melatonin biosynthetic genes in M. notabilis, including MnTDC, MnT5Hs, MnSNATs, MnASMT genes and MnCOMTs. Sample names are shown above the heat maps. The color scale indicates the degree of expression: "green" indicates low expression; "red" indicates high expression. B: Tissue-specific expression levels of MnTDC, MnT5H2, MnSNAT5, MnASMT12 and MnCOMT1 as determined by qRT-PCR. Data was analyzed using 2 ΔCt method and MnACTIN3 was used as an internal control. Data are means ±SDs (n = 3), significant differences (P <0.05) are indicated by different letters above the bars. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)
Fig. 1. Phylogenetic tree of amino acid sequences of genes involved in melatonin biosynthesis in M. notabilis and other plants. The phylogenetic trees were generated with the neighbor-joining method using MEGA 5.0 software. All IDs of gene in other plant species involved in melatonin biosynthesis are provided in Supplementary Table S1. Red circles: M. notabilis genes. A, TDC; B, T5H; C, SNAT; D, ASMT. ASMT proteins were separated into three classes: I (black), II (red), III (blue); E, COMT. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 3. Size exclusion chromatography (SEC) and indication of relative 21MaT activity investigation pools III (A) and IV (B) of the ammonium sulfate precipitation.
Fig. 4 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 4. Docking of modeled AtPMaT1 (ribbon diagram) with an overlay of the potential pregnane substrates (Sub) (shown in grey). The catalytic histidine (His) and the cosubstrate (CoS) are also shown.
Fig. 1 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 1. Postulated biosynthetic pathway of cardenolide formation in Digitalis. The malonylation step [8] is marked by a rectangle. 1 Putative side chain cleaving enzyme (SCCE), 2 NAD:3β-hydroxysteroid dehydrogenase (3βHSD), 3 Δ4,5-3-ketosteroid-isomerase (3KSI), 4 progesterone-5β-reductase (P5βR), 5 NAD:3β-hydroxysteroid dehydrogenase (3βHSD), 6 putative pregnane 14β-hydroxylase, 7 putative pregnane 21β-hydroxylase, 8 malonyl coenzyme A:21- hydroxypregnane 21-O-malonyltransferase (21MaT).
Fig. 6 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 6. Docking of homology modeled malonyltransferases with 3-O-acetylketol (displayed in grey) showing the distances between the catalytic histidine (His), the hydroxy group to be malonylated (Sub) and the malonyl residue presented by the co-substrate (CoA). A AtPMaT1 B AtPMaT2 C DlMaT1.
Fig. 5 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 5. Expression of Dlmat1, Dlmat2, Dlmat3, and Dlmat4 in different plant tissues measured by real-time quantitative PCR (qPCR). Expression rates are standardized to the values of the actin transcript in each tissue and were displayed in relation to the expression in young leaves (set to equal 1) for each Dlmat gene.
Fig. 6 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 6. Heatmap representing organ specific significantly enriched genes corresponding to (A) Isosteroidal alkaloid biosynthesis, (B) Sucrose and starch metabolism, (C) UGTs and CYPs, (D) aquaporins, (E) ABC transporters, (F) Transcription factor and Transposable elements. The red-blue scale represents positive enrichment (red) and negative enrichment (Blue) of transcripts. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 5. Significantly enriched transcripts (nodes) in predicted interactome network. (A) Steroidal alkaloid biosynthesis pathways (B) Isopentenyl diphosphate biosynthesis pathway, (C) Sucrose and starch metabolic pathways and (D) Aquaporins. The nodes encircled in red color represents higher enrichment in the bulb while the nodes encircled in grey and blue represents higher enrichment in arial organs (leaf and stem). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 7. qRT-PCR expression-based validation of RNA-seq data using potential 20 genes involved in isosteroidal alkaloid biosynthetic pathway. (A) Bulb vs. Leaf, (B) Leaf vs. Stem and (C) Bulb vs. Stem.
Fig. 3 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 3. Significant KEGG pathway enrichment analysis in tissues from aerial organs (leaf & Stem) and bulb. The green colour enrichment indicates higher expression in aerial tissue while pink represents higher enrichment in bulb. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 4. Transcriptional protein-protein interactome (PPIN) prediction in F. roylei along the network statistics. (A) Overall prediction of PPI network based on significantly differential expressed transcripts. Spatial PPI network prediction of significantly enriched transcripts in (B) Bulb, (C) Leaf and (D) Stem.
Fig. 1 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 1. Summary of organ specific spatial transcriptome sequencing in F. roylei. (A): Overall quality filtering of sequenced reads; (B): Tissue specific high quality filtered reads obtained after removing low quality/adaptor contaminated sequences; (C): Assembly statistics details; (D): Venn diagram representing functional annotation with six different public protein databases.
Fig. 8 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 8. Representation of isosteroidal alkaloid biosynthesis pathway in F. roylei and heat map representing expression of genes in Stem, Leaf and Bulb tissue using red-blue scale (red: positive enrichment and Blue: negative enrichment of transcripts). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 2. Clustering of 2488 significant differentially expressed transcripts in leaf, stem and bulb in F. roylei (A) sub-cluster 1 represent transcripts with significant higher expression in bulb; (B): Sub-cluster 2 in Stem and (C): Sub-cluster 3 in leaf; (D): Pearson's correlation of organ specific significant differentially expressed clustered transcripts in leaf, stem and bulb tissues.
Fig. 4 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 4. The stress-related increase of the concentration of natural products. In principle, two major effects are responsible for the stress-related increase, i. e., the decrease of the reference value (e.g. dry weight), and an enhancement of biosynthetic activity. The latter one is due either to stress-related up-regulation ("active increase" of enzymatic activity) or a "passive shift" cause by the stress-related overreduction due to stomatal closure. Decreases of factors are displayed in red, the related enhancements in blue. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 3. Dry weight, alkaloid concentration, and alkaloid content in leaves of Catharanthus roseus plants under salt stress. (a): Dry weight of the entire leaves; (b): Concentration of alkaloids in old leaves; (c): Concentration of alkaloids in young leaves; (d): Total alkaloids content in all aerial plant parts. Differentiation between young and old leaves is mentioned in the Materials and methods section. Different lower-case letters on top of the columns for each period of time (10 and 20 days) indicate significant differences (P ≤ 0.05) as calculated using the least significant difference (LSD) test; n = 8. Every period has 5 bars, and these bars from left to right are control, 100 mM, 200 mM, 300 mM, 400 mM NaCl solution, respectively. The bars display the standard deviation.
Fig. 1 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 1. Evapotranspiration rate of drought-stressed Catharanthus roseus plants. The evapotranspiration rates for mild (20% watering) and severe drought stress (40% watering) were obtained by calculating the amount of water lost. Control plant results were used as a reference to normalize the rate. Arrows indicate the days of sampling.
Fig. 4 in Anthocyanin 5,3 -aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin
Fig. 4. Superimposed structures between Gt5,3′ acyltransferase and vinorine synthase. Superposition was performed for four amino acids around the binding pocket (Ser45, Ala179, Phe182, and Gly402 in Gt5,3′ acyltransferase). The backbone structures are shown in cyan (caffeoyl-CoA-bound Gt5,3′AT) and green (vinorine synthase), respectively. The caffeoyl-CoA molecule is shown as a stick model. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Anthocyanin 5,3 -aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin
Fig. 5. Summary of key amino acids for acyl-CoA specificity. The acyl-CoA binding pocket is illustrated with gray elongated semicircles. The upper and lower parts are binding pockets for malonyl/acetyl-CoA and caffeoyl/ coumaroyl-CoA, respectively. Four critical positions for acyl-CoA selectivity are indicated by blue ellipse. In the vicinity of these amino acid positions, the enzymes which have corresponding amino acid(s) are listed. The malonyl-CoA selective enzymes possess either Arg at the position 45/182, Val at the position 179, or Asp/Trp at the position 401 (upper part). In contrast, the caffeoyl/ coumaroyl-CoA selective enzymes have Ala/Gly at the position 179 and Gly/ Ser at the position 401 and include Arg neither at the position 45 nor 182 (lower part). PDB-ID is indicated in parentheses for enzymes with known structure. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
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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.