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Fig. 2 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

Fig. 2. KEGG classifications of the sweetpotato unigenes. The y-axis shows the KEGG metabolic pathway names, and the x-axis shows the number and proportion of genes associated with the pathways. The genes were divided into five branches according to involvement in the following KEGG pathways: Cellular Processes (A), Environmental Information Processing (B), Genetic Information Processing (C), Metabolism (D), and Organismal Systems (E).

Fig. 1. Sweetpotato cultivars Zhengshu 20 and Luoxushu 8 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

Fig. 1. Sweetpotato cultivars Zhengshu 20 and Luoxushu 8. The tuberous roots were transected, and the carotene content of Zhengshu 20 and Luoxushu 8 is shown.

Fig. 5 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

Fig. 5. KEGG pathway enrichment scatter plot of the up-regulated genes between Zhengshu 20 and Luoxushu 8. The y-axis shows the pathway name, and the x-axis shows the richness factor of the pathway. The colors indicate the q-values; the smaller the q-value, the redder the color and the sizes of the point represent differences in the expression of the gene number in each pathway.

Fig. 3 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

Fig. 3. Gene ontology (GO) classification of the assembled in vitro tissue transcripts. The results of the following three main GO categories are summarized: biological process, cellular component, and molecular function. The y-axis shows the total number of genes in each category.

opencc-by-4.0Dec 2022View details →

Data for "Coordination of bacterial cell wall and outer membrane biosynthesis"

Raw data used in the paper "Coordination of bacterial cell wall and outer membrane biosynthesis" by Katherine R. Hummels, Samuel P. Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K. Min, Suzanne Walker, Debora S. Marks, and Thomas G. Bernhardt. These data were collected with the aim of understanding how the lipopolysaccharide biosynthetic enzyme LpxC is regulated in diverse gram-negative bacteria, particularly Pseudomonas aeruginosa. The dataset contains the following tarred directories: Experimental data <ul> <li>Microscopy (microscopy.tar.gz)</li> <li>LC-MS/MS (lc-ms_ms.tar.gz)</li> </ul> Covariation analysis <ul> <li>Multiple sequence alignments (alignments.tar.gz)</li> <li>AlphaFold structures (alphafold.tar.gz)</li> <li>EVcomplex models and couplings (evcomplex.tar.gz)</li> <li>Phylogenetic trees (trees.tar.gz)</li> </ul> For more detailed methods and file descriptions, please see README.md. Associated code for analysis can be found at https://github.com/samberry19/evcomplex-interaction-scoring.

opencc-by-4.0Nov 2022View details →

Raw data for: Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

This repository contains data related to "Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides" by Pandi et al. Included are molecular dynamics parameter files, initial structures after system equilibration and production trajectories. For simulations of AMPs with membranes, trajectories are subsampled with 1 frame every 5 ns and final structures after 1 μs of production simulation are included. Contact information: Name: Stefan L. Schaefer Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: stefan.schaefer@biophys.mpg.de

Fig. 5 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 5. Extracted-ion chromatograms (EIC; m/z 124, 127) obtained by HS-SPME–GCxGC-ToF-MS-analysis after feeding [2H]- -leucine to several fruit tissues of 10 Lunripe bell peppers (Capsicum annuum cv. Allrounder).

Fig. 6 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 6. Extracted-ion chromatograms (EIC; m/z 124, 127) obtained by HS-SPME–GCxGC-ToF-MS-analysis after feeding [2H]- -leucine to several organs of bell 10 Lpepper plants (Capsicum annuum cv. Allrounder).

Fig. 3 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 3. IBMP-content (means ± standard deviations (n = 5–8) expressed as ng/g FW (fresh weight)) in the various parts of unripe (A) and ripe (B) bell pepper fruits (Capsicum annuum cv. Allrounder). Ripening stages of bell pepper fruits: unripe (fully green), breaking point (green and yellow) and ripe (fully yellow) (C). (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 Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 4. Structure (A) and electron ionization (EI) mass spectra (B) of the biosynthetic product ([2H]-IBMP) after incorporation of stable-isotope labelled [2H]- 9 10 L-leucine.

Fig. 2 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 2. EI-MS spectra and fragmentation pattern of IBMP (A) and EI-MS spectra and fragmentation pattern of [2H]-IBMP (B).

Fig. 1 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants

Fig. 1. Total ion chromatogram (TIC) (A) and extracted ion chromatogram (EIC) (B) of ripe bell pepper pericarp (Capsicum annuum cv. Allrounder) analyzed by HSSPME–GC-ToF-MS.

Fig. 5 in Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 5. DF11 effect on the accumulation of tanshinones and salvianolic acid in aseptic seedling roots of S. miltiorrhiza. Compared with the control group, *p <0.05, **p <0.01, ***p <0.001.

Fig. 3 in Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 3. Root phenotypes of S. miltiorrhiza seedlings 8 weeks after strain DF11 inocculation. (a)the control group inoculated with PDA liquid, (b) the treatment group inoculated with DF11 fungal suspension, (c) and (d) Red boxed areas of (a) and (b) are enlarged in (c) and (d) respectively. Scale bar = 1.0 cm. (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 Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 2. Morphological characteristics and phylogenetic analysis of strain DF11. (a)and(b) Frontal and backside morphology of DF11 colony respectively (Scale bar = 1.0 cm); (c)and(d) Microscopic morphology of spores and mycelium of DF11 respectively (40 × 10, Scale bar = 20 μm); (e)and(g) mycelium structure of DF11 showed by scanning electron microscopy (SEM); (e) Mycelium and conidiophore; (f) Conidiophore; (g) Conidium; (h) Neighbor-joining tree of DF11 based on the ITS gene sequences.

Fig. 1 in Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 1. The tanshinone biosynthesis pathway in S. miltiorrhiza. AACT: acetyl-CoA C-acetyltransferase, HMGS: 3-hydroxy-3- methylglutaryl-CoA synthase, HMGR: 3-hydroxy-3-methylglutaryl-CoA reductase, MK: mevalonate kinase, PMK: 5-phosphomevalonate kinase, MDC: mevalonate 5-diphosphate decarboxylase, DXS: 1-deoxy-Dxylulose-5- phosphate synthase, DXR: 1- deoxy-D-xylulose-5- phosphatereductoisomerase, MCT: 2-C-methyl-D- erythritol- 4-phosphate cytidylyltransferase, CMK: 4- (cytidine 5-diphospho) -2-C-methyl- Derythritolkinase, MECPS: 2-C-methyl- erythritol 2,4-cyclodiphosphatesynthase, HDS: 1-hydroxy-2- methyl-2-(E)- butenyl-4-diphosphate synthase, HDR: 1-hydroxy-2-methyl-2- (E)- butenyl-4- diphosphate reductase), IDI: isopentenyl diphosphate isomerase, GGPPS: geranylgeranyl diphosphate synthase, CPS: copalyl diphosphate synthase, KSL: kaurene synthase-like, CYP76AH1: cytochrome P450 enzyme (CYP) 76AH1.

Fig. 6 in Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 6. The effects of DF11 on the expression of genes encoding for key enzymes of tanshinone biosynthesis pathway in S. miltiorrhiza roots. HMGR,3-hydroxy-3- methylglutaryl-CoA reductase, GGPPS, geranylgeranyl diphosphate synthase, CPS,copalyl diphosphate synthase, DXR,1-deoxy-D-xylulose5- phosphate reductoisomerase, DXS,1-deoxy-D- xylulose5-phosphate synthase, CYP76AH1,cytochrome P450 enzyme (CYP) 76AH1. Compared with the control group, *p <0.05, **p <0.01, ***p <0.001. ACTIN was the internal reference gene.

Fig. 4 in Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Fig. 4. The colonization of DF11 in the root of aseptic seedling of S. miltiorrhiza after immunofluorescence staining (8 weeks). Magnify 400x; Green: ConA-FITC; Blue: DAPI. Control: PDA sterile liquid medium. Red arrow: DF11 is located within the root cell; Red triangle: DF11 is located in the root cell space. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedJul 2022View details →

Fig. 7. A in MAPKK2/4/5/7-MAPK3-JAZs modulate phenolic acid biosynthesis in Salvia miltiorrhiza

Fig. 7. A proposed model for the roles of SmMAPK3 in S. miltiorrhiza phenolic acid biosynthesis. Model illustrating the roles of SmMAPK3 in S. miltiorrhiza phenolic acid biosynthesis.