The visualization of the spatial distribution of Cocculus orbiculatus based on air flow-assisted desorption electrospray ionization mass spectrometry imaging.

Cocculus orbiculatus (C. orbiculatus), the root of plants belonging to the Menispermaceae family, has been extensively used to treat various diseases, including malaria and rheumatism. The main chemicals in these plants are alkaloids; however, the spatial distribution of these compounds within the plant roots remains undefined. This study aimed to visualize the spatial distribution of C. orbiculatus using air flow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI). In total, the spatial distribution of four aporphine alkaloids, five benzyltetrahydroisoquinoline alkaloids, six bisbenzylisoquinoline alkaloids, and one morphinane alkaloid in the cork layer, xylem, and ray of the root of C. orbiculatus was observed; the distribution characteristics of the different compounds in C. orbiculatus were significantly different. This study provides a visualized spatial distribution analysis method for the characterization of metabolites in the root tissue of C. orbiculatus and also provides valuable information for the specificity of the root of C. orbiculatus, which is beneficial for understanding its chemical separation, biosynthesis, and pharmacological activities.

Rapid characterization of the potential active metabolites of diacerein in rat plasma based on UHPLC-Q-exactive orbitrap mass spectrometry and molecular docking.

Diacerein, a competently semisynthetic diacetyl derivative of anthraquinone, is a nonsteroidal anti-inflammatory drug, which has been used for treating osteoarthritis and preventing vascular diseases. However, previous investigation indicated that diacerein metabolites and its metabolic pathway in vivo was still unclear. In this research, an effective method was established based on ultra-high-performance liquid chromatography coupled with Q-Exactive-Orbitrap mass spectrometer and molecular docking to screen and detect the potential active metabolites of diacerein in rat plasma after oral administration. The data acquisition and processing methods including Full MS-ddMS2 combined with parallel reaction monitoring mode, extracted ion chromatogram and diagnostic fragment ions were adopted to detect and identify more infinitesimal and unknown diacerein metabolites in vivo. As a result, a total of 32 metabolites were detected and identified in rat plasma according to retention times, accurate mass, diagnostic fragment ions, and relevant drug biotransformation knowledge, among 31 metabolites were firstly reported in this study. Then, the relevant reactions in vivo such as deacetylation, hydroxylation, methylation, sulfate conjugation, glucuronidation, and their composite reactions, were all detected. Ultimately, the results of molecular docking showed that the metabolites of diacerein might have good affinity with IL-1 receptor in vivo. Among them, the metabolites M21 and M1 have the strongest binding affinity with IL-1 receptors, and could be considered as potential active metabolites of diacerein, which have an efficient effect on exerting pharmacological effects of diacerein in vivo. In conclusion, the study of diacerein metabolites in rat plasma expanded our understanding about the metabolism of diacerein in vivo and provided the significant foundation for further drug efficacy studies.

Systemic chemical characterization of Lemna minor by UHPLC-Q-Exactive Orbitrap MS coupled with parallel reaction monitoring.

Lemna minor L. (LM) has been used for measles opacity, rubella itching, edema, and oliguria, and the main active ingredients were flavonoids, namely, apigenin, apigenin-7-O-glucoside, and luteolin-7-O-glucoside. However, few systematic analyses of their constituents have been performed; thus, it was necessary to establish a fast and efficient method to identify the chemical composition of LM. In this study, the UHPLC-Q-Exactive Orbitrap mass spectrometry coupled with parallel reaction monitoring was established. Finally, a total of 112 constituents, including 30 dipeptides, 28 nucleosides, 11 amino acids, 10 organic acids, 10 flavonoids, and 23 other compounds, were identified by MS, diagnostic fragment ions, and retention time. One hundred one of those chemicals were first found in LM, which was very beneficial for the further development and utilization of nutriments and the medicinal use of LM.

Comprehensive characterization of multiple components of Ziziphus jujuba Mill using UHPLC-Q-Exactive Orbitrap Mass Spectrometers.

Ziziphus jujuba Mill is the dried ripe fruit of the Rhamnaceae family; it is widely distributed in Shandong, Henan, Liaoning, and other places in China. In folk medicine, it was used to restore vital energy, as a blood tonic, and for the treatment of spleen deficiency. To date, a complete investigation of the compounds of Z. jujuba has rarely been performed. Therefore, a reliable strategy based on UHPLC-Q-Exactive Orbitrap MS, combined with trace data acquisition mode (parallel reaction monitoring scanning, PRM) and multiple data processing methods, is necessary for the characterization of compounds in the Z. jujuba. Ultimately, 295 compounds, including 69 flavonoids, 60 alkaloids, 82 phenylpropanoids, 52 organic acids, and 32 other components, were identified in the Z. jujuba; of these, 270 have been reported in Z. jujuba for the first time. This study provides deep insights into the chemistry of Z. jujuba and could be useful for further studies aimed at identifying the factors contributing to the health benefits attributed to this fruit.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

Rapid Identification of Constituents in Cephalanthus tetrandrus (Roxb.) Ridsd. et Badh. F. Using UHPLC-Q-Exactive Orbitrap Mass Spectrometry.

Cephalanthus tetrandrus (Roxb.) Ridsd. et Badh. F. (CT) belongs to the Rubiaceae family. Its dried leaves are widely used in traditional Chinese medicine to treat enteritis, dysentery, toothache, furuncles, swelling, traumatic injury, fracture, bleeding, and scalding. In order to further clarify the unknown chemical composition of CT, a rapid strategy based on UHPLC-Q-exactive orbitrap was established for this analysis using a Thermo Scientific Hypersil GOLDTM aQ (100 mm × 2.1 mm, 1.9 µm) chromatographic column. The mobile phase was 0.1% formic acid water-acetonitrile, with a flow rate of 0.3 mL/min and injection volume of 2 µL; for mass spectrometry, an ESI ion source in positive and negative ion monitoring modes was adopted. A total of 135 chemicals comprising 67 chlorogenic acid derivatives, 48 flavonoids, and 20 anthocyanin derivatives were identified by comparing the mass spectrum information with standard substances, public databases, and the literature, which were all discovered for the first time in this plant. This result broadly expands the chemical composition of CT, which will contribute to understanding of its effectiveness and enable quality control.

Rapid Characterization and Action Mechanism of the Antidiabetic Effect of Diospyros lotus L Using UHPLC-Q-Exactive Orbitrap MS and Network Pharmacology.

Diospyros lotus L, F. Ebenaceae, is an edible fruit that is widely distributed in China and other Asian countries. Presently, Diospyros lotus L can be used to treat patients with diabetes; however, its chemical composition and pharmacological profiles remain to be elucidated. This study investigated the potential bioactive compounds of Diospyros lotus L and their mechanisms of action using LC-MS and network pharmacology analysis. First, the components of Diospyros lotus L were identify using a reliable strategy for UHPLC-Q-Exactive Orbitrap mass spectrometry combined with parallel reaction monitoring (PRM) in the negative ion mode. Second, a network pharmacology study, including target gene prediction and functional enrichment, was applied to screen the main quality markers of Diospyros lotus L and explore its potential mechanism for the treatment of diabetes. The results showed that a total of 159 compounds were identified from Diospyros lotus L, among which, 140 were reported for the first time. Furthermore, 40 active components, such as quercetin, luteolin, and kaempferol, were proposed as active components of Diospyros lotus L for the treatment of diabetes based on network pharmacology analysis. In addition, 92 relevant antidiabetic targets were mainly related to positive regulation of transcription from the RNA polymerase II promoter, extracellular space, and protein binding, suggesting the involvement of TNF, PI3K-Akt, and HIF-1 signaling pathways in the antidiabetic effect of Diospyros lotus L. Our results may provide a useful approach to identify potential active components and molecular mechanisms of Diospyros lotus L for the treatment of diabetes.

Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits.

An F6 : 8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.