Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Pateto charts for the article "Biomass composition of Nephroselmis sp. under different ex-perimental conditions of nitrogen, salinity, and light: optimiza-tion of lipids accumulation (including EPA)"

Pareto charts for the statistical significance of the nitrogen concentration, salinity level and illuminance, regarding the derived equations for (a) proteins, (b) carbohydrates, (c) pigments, (d)fatty acids and (e) EPA production.

opencc-by-4.0Jun 2023View details →

Rapid shoaling of Aragonite Saturation Horizon (ASH) in the Indian Ocean: Influence of accumulation of anthropogenic CO2 and atmospheric pollutants

This data set contains the various cruise data of Aragonite saturation depth in the Northern Indian Ocean.  The shallowest aragonite saturation horizon (ASH) was observed in the Bay of Bengal (BoB; 219±10 m) within the tropical Indian Ocean. The ASH shoaled at the rate of 6.3±5 and 4.4±3 m y-1 in the past two and half decades in the BoB and Arabian Sea respectively. As a result, an increase in total alkalinity (TA) was observed at the rate of 0.5±0.3 and 0.25±0.2 mmol kg-1 y-1 at the depth of ASH in the BoB, and Arabian Sea respectively. The rapid shoaling of ASH in the BoB than the Arabian Sea may result from the higher accumulation of anthropogenic CO2 due to the freshening of the upper ocean associated with an increase in river discharge/ precipitation and deposition of atmospheric pollutants leading to corrosion of the aragonite skeletal material. Under a business-as-usual scenario, aragonite-secreting organisms may not survive by the middle of this century in the BoB.

Fig. 3 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 3. Two-dimensional gel electrophoresis and immunoblotting of asparaginase in developing leaves. Arrows indicate the polypeptide precursor and α-subunit. The experimental pI of the α subunit was measured as 4.87.

Fig. 2 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 2. Diurnal accumulation of asparaginase and related metabolites in developing leaves. (A) Immunoblot and corresponding SDS-PAGE. The top band corresponds to the polypeptide precursor and lower band to the α-subunit. Position of molecular wt markers is indicated on the left; (B) asparaginase activity. Average ± s.d.; n = 3. (C) Concentration of asparagine (Asn), aspartate (Asp) and NH+ in leaf tissue. Average ± s.d.; n = 3.

Fig. 4 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 4. Analysis of circadian regulation of asparaginase protein. Plants were exposed to a 16 h light and 8 h dark cycle followed by exposure to continuous light. Leaves were sampled at the indicated times and asparaginase detected by immunoblotting.

Fig. 1 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 1. RNA-Seq expression profile of PvASPG1 and PvASPG2. Expression value is given as Z-score (Severin et al., 2010). Samples are grouped by tissue. Data are from O'Rourke et al. (2014) (see Supplementary Table S1).

opennotspecifiedFeb 2023View details →

Fig. 1 in Isoavenaciol and 7-hydroxy-isoavenaciol: Zn-chelating metallophores produced by root-endophytic Pezicula ericae in a Zn-accumulating plant, Aucuba japonica

Fig. 1. Zn-chelating activity of each sample solution. The activities were shown as means ± standard errors (n = 3). (+) indicates that a clear zone only inside the steel cup or paper disk. The different letters indicate a statistically significant difference was observed in one-way ANOVA and post-hoc Scheffe´at P <0.05.

Fig. 2 in Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 2. Phylogenetic relationships between ACTs and other BAHD members. The amino acid sequences of the BAHD family were aligned using CLUSTALW. The neighbor-joining tree was generated with MEGA X (https://www. megasoftware.net/). Bootstrap values from 1000 replicates are indicated at each node. Bar = 0.1 amino acid substitutions per site. The ACTs in barley, wheat, and H. murinum are shaded in grey. The following BAHD acyltransferases are shown: AtACT (A. thaliana, NP_200924), Dm3MAT1 (Dendranthema x morifolium, AAQ63615), Dv3MAT (Dahlia variabilis, AAO12206), MpAAT1 (Malus pumila, AAU14879), Glossy2 (Zea mays, CAA61258), CER2 (A. thaliana, AAM64817), CmAAT4 (Cucumis melo, AAW51126), SAAT (Fragaria x ananassa, AAG13130), CbBEAT (Clarkia breweri, AAC18062), HvACT1-1 (H. vulgare, BAF97626), HvACT1-2 (H. vulgare, BAF97627), TaACT2 (T. aestivum, AMY96376), HvACT2 (H. vulgare, BAK00935), OsAHT1 (O. sativa, ANQ47369), Os09g0544000 (O. sativa, XP_015651357), BdACT2a (Brachypodium distachyon, XP_003578560), OsTHT1 (O. sativa, ANQ47373), OsTHT2 (O. sativa, ANQ47374), OsTBT1 (O. sativa, ANQ47375), OsTBT2 (O. sativa, ANQ47376), SbHCT (S. bicolor, XP_002452435), AtHCT (A. thaliana, NP_199704), and PsHCT (Plectranthus scutellarioides, CBI83579).

Fig. 1 in Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 1. Biosynthetic pathway of hydroxycinnamoylagmatines in plants. ADC, arginine decarboxylase; PAL, phenylalanine ammonia-lyase; C3H, 4-coumarate 3-hydroxylase; C4H, cinnamate 4-hydroxylase; COMT; caffeic acid 3-O- methyltransferase.

Fig. 5 in Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 5. Comparison of the entrance architectures of TaACT2 and HvACT1-1, and structure-based sequence alignment. (A) Surface diagram of TaACT2 viewed from the acyl acceptor entrance side. The loops of HvACT1-1 (K206–E222 and A350–D364) are shown as ribbon (light brown), as the corresponding regions in TaACT2 were not determined, except for 358LVTTA362. Note that the structure of 211AHDV214 in HvACT1-1 is also missing (Yamane et al., 2020). To improve visibility, 358LVTTA362 of TaACT2 is shown as ribbon and transparent surface diagrams. The cavity for substrate binding, Phe39, and His153 in TaACT2, are indicated in deep blue, pink, and orange, respectively. To clarify the possible substrate binding site, SbHCT, complexed with p-coumaroylshikimate (PDB ID 4KEC), was superimposed on TaACT2, and the structure of the ligand is shown as stick (p-coumaroyl moiety) and wire (shikimate moiety) in magenta. (B) Structures of the entrance for the acyl acceptor. The loops located near the entrance are shown in ribbon diagram, and Phe39 and the catalytic center His are shown as sticks (TaACT2: cyan; HvACT1-1: light brown). The His residues in TaACT2 and HvACT1-1 are indicated in white and green, respectively. The structure of the loop in TaACT2 (363DAAE366) was not determined and the corresponding region in HvACT1-1 is indicated in yellow. The blue in stick format indicates nitrogen atoms. (C) Multiple sequence alignment based on the tertiary structures of TaACT2, HvACT1-1, SbHCT, and AtHCT. Regions, structures of which were not determined, are indicated by grey characters. The residues that are estimated to constitute the substrate binding pockets are shaded in cyan. Closed orange circle indicates Phe39. HXXXD and DFGWG motifs are indicated by closed red triangles. The catalytic center His residues are surrounded by a red frame. Clade IV-specific motif of the BAHD superfamily, the EVDSWL and VLWAFP motifs, are indicated by open green triangles. The Arg residues that interact with the carboxy group of shikimate in SbHCT and AtHCT were indicated by an orange diamond. The molecular graphics were produced using UCSF Chimera (A) and PyMOL (Schrodinger) (B), and structure-based alignment (C) was performed using UCSF Chimera. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 4. The global structure of apo-TaACT2. (A) Superposition of TaACT2 (cyan) on HvACT (PDB ID 7CYS; light brown) and SbHCT (PDB ID 4KEC; pink). (B) Surface diagram of apo-TaACT2. Domains I, II, and the crossover part are colored in blue, light grey, and yellow, respectively. The black triangle indicates the solvent tunnel. The catalytic center, His153, is shown in red. The molecular graphics were produced by UCSF Chimera (https://www.rbvi.ucsf.edu/ch imera). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. The structure around clade-IV in Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 6. The structure around clade-IV-specific EVDSWL motif. The Glu, Asp, and Trp in the motif of HvACT1-1 (yellow) and TaACT1-1 (cyan) and their corresponding residues in SbHCT (pink; PDB 4KEC), and AtHCT (light grey; PDB 5KJU) are shown with sticks. The catalytic His and the Arg that interact with the carboxy group of shikimate in SbHCT and AtHCT are also shown. Ala360 and 362 of barley and wheat ACTs, respectively, correspond to the Arg in HCTs. p-Coumaroylshikimate molecules bounded to the crystals of SbHCT and AtHCT are presented. Note that the structures of HCTs were those of holoenzymes complexed with a natural product, p-coumaroylshikimate. (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 Molecular and structural characterization of agmatine coumaroyltransferase in Triticeae, the key regulator of hydroxycinnamic acid amide accumulation

Fig. 3. Relative transcription levels of ACTs in barley, wheat, and rice shoots. The absolute quantity of transcripts of HvACT1 (A), HvACT2 (B), TaACT1 (C), TaACT2 (D), OsAHT1 (E), and HmACT (F) was quantified using real-time PCR and normalized to actin level. The relative transcription levels were described as the percentage ratio to HvACT1 at 48 h. The data are shown as means ± standard deviation (n = 6). Different characters of the bars indicate significant differences (p <0.05, Tukey–Kramer test).

Fig. 9 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 9. Dynamic emission and distribution of the two predominant sesquiterpene volatiles EβF and GD in T. cinerariifolium flower. EβF and GD concentrations peak at the S2 flower stage. Their microdistribution patterns strongly differ though: the peduncle is dominated by EβF but the corolla and stigma by GD. This uneven distribution leads to a dominant EβF emission at the S2 flower stage which attracts ladybird beetles and repels aphids. Presumably the later dominance of GD released from the stigma and corollas when disc florets open up is promoting the pollination process. In peduncle, relatively pure EβF was largely produced in the parenchyma cells and further transported and stored in the secretory ducts. Lines at the S2 and S4 flower stages show the EβF/GD oil ducts. Pyrethrins were increasingly accumulated in the pericarp of the developed ovary.

Fig. 7 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 7. NADI and aniline blue staining of cross sections of young T. cinerariifolium flower peduncles. (A and B) NADI staining of two cross sections of S0 and S1 upper flower peduncles. The positive NADI stained oil droplets are pointed out by white arrows. (C) Cross section of S2 flower peduncle stained by NADI reagent coupled with aniline blue staining observed under the bright light. (D) Cross section of the same S2 flower peduncles as in C observed under the UV light, callose in the sieve elements was stained by aniline blue and indicated by white arrowhead. The white arrows point to NADI stained oil droplets in C that appear to be outside the cell wall as indicated by red arrows in D. Ph, phloem; Xy, xylem; Co, cortex; Pi, pith; Se, sieve element.. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 6. Chromatogram profiles of hexane extract of T. cinerariifolium stigma and corolla analyzed by GC–MS. For analysis conditions see text. GC-MS chromatogram of volatiles extracted from stigma and corolla are presented as total extracted ion current (EIC, m/z 93). Methyl laurate was used as an internal standard (IS). The concentration of EβF and GD were showed in the figure and presented as ng/mg fresh tissue. Localization of terpene oils in the closed and open disk floret was shown in the inset drawing pictures with purple (EβF and GD) and blue (pyrethrins) color.. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 4. EβF and GD accumulations in different parts of flower head at different developmental stages. Quantitated EβF and GD accumulations in different parts (upper disk floret, lower disk floret, receptacle, bract) of field flower following flower development. Fresh flower tissues were extracted by hexane and analyzed by GC-MS. GD concentration was evaluated by compared with EβF. Error bars indicate ± SD of three biological replicates.

Fig. 5 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 5. NADI staining for longitudinal sections of flower of T. cinerariifolium. (A) NADI staining for disk floret of S1 flower. (B) NADI staining of the upper section of a disk floret of S1 flower. (C) NADI staining of the upper section of a disk floret of an S2 flower showing the bilobed stained stigma on top of a short style. (D) NADI staining of longitudinal sections of S3 flower. (E) NADI staining of the upper sections of disk florets of S4 flower. Df, disk floret; Rec, receptacle; Sty, style; An, anther; Ac, anther cylinder; Sti, stigma; Co, corolla; GT, glandular trichome. Pure GD, EβF and pyrethrins were individually stained by NADI reagent and shown in A. The white arrows point to the positive NADI stained oils. The inset picture in D represents the top view of the flower.

Fig. 1 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 1. Morphological and anatomical structures of stage 2 (S2) Tanacetum cinerariifolium flowers. (A) Longitudinal section of an S2 flower with peduncle attached. The arrow points to a cavity in the center of the pith that will become larger when the flower matures. The inset pictures show cross sections of the upper and lower peduncle (4 cm individually). (B) A closed disk flower. (C–G) SEM images of the T. cinerariifolium S2 flower organs and tissues. (C) The corollas of closed disk flowers. (D and E) Different magnifications of bract tissue, with an arrow pointing to the longitudinal serpentine vascular system located in the joining site with receptacle. (F and G) Cross sections of the flower peduncle and a detailed view of the disintegrating pith tissue.

Fig. 2 in Tissue specificity of (E)-β-farnesene and germacrene D accumulation in pyrethrum flowers

Fig. 2. Analysis of terpene volatiles in flower head and peduncle (upper and lower) at early flowering stages (S0–S2). (A) Chromatogram profiles of T. cinerariifolium S1 flower head and upper peduncle hexane extracts analyzed by GC–MS and presented as total extracted ion current (EIC, m/z 93). Chromatogram profile of lower peduncle hexane extraction was not shown here due to the same peak patterns with the upper peduncle. For analysis conditions see text. List of the main terpene components, see Table 1 (B) Quantification of EβF and GD content in flower head and lower and upper peduncle at early flowering stages (S0–S2). Fresh flower tissues were extracted with hexane and analyzed by GC-MS. The GD and EβF concentrations were both estimated using an EβF standard reference curve. Error bars indicate ± SE of three biological replicates.