Combination of ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry and network pharmacology to reveal the key effective compounds and mechanism of Shengxian decoction for ameliorating doxorubicin cardiotoxicity.

Shengxian decoction, a traditional Chinese medicinal prescription, has been shown to alleviate doxorubicin-induced chronic heart failure. This study established an ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry method to separate and characterize the complex chemical compositions of Shengxian decoction, and the absorbed compounds in the bio-samples of the cardiotoxicity rats with chronic heart failure after its oral delivery. Note that 116 chemical compounds were identified from Shengxian decoction in vitro, 81 more than previously detected. Based on the three-dimensional data of these compounds, 28 absorbed compounds were confirmed in vivo. Network pharmacology and molecular docking experiments indicated that timosaponin B-II, timosaponin A-III, gitogenin, and 7,8-didehydrocimigenol were recognized as the key effective compounds to exert effects against doxorubicin cardiotoxicity by acting on targets such as caspase 3, cyclin-dependent kinase 1, cyclin-dependent kinase 4, receptor tyrosine-protein kinase erbB-2, and mitogen-activated protein kinase 1 in p53 and phosphatidylinositol 3-kinase-Akt signaling pathways. This study developed the understanding of the composition of Shengxian decoction for the treatment of doxorubicin cardiotoxicity, as well as a feasible strategy to elucidate the effective constituents in traditional Chinese medicines.

The role of hydrodynamics for the spatial distribution of high-temperature hydrothermal vent-endemic fauna in the deep ocean environment.

Active hydrothermal vents provide the surrounding submarine environment with substantial amounts of matter and energy, thus serving as important habitats for diverse megabenthic communities in the deep ocean and constituting a unique, highly productive chemosynthetic ecosystem on Earth. Vent-endemic biological communities gather near the venting site and are usually not found beyond a distance of the order of 100 m from the vent. This is surprising because one would actually expect matter ejected from high-temperature vents, which generate highly turbulent buoyancy plumes, to be suspended and carried far away by the plume flows and deep-sea currents. Here, we study this problem from a fluid dynamics perspective by simulating the vent hydrodynamics using a numerical model that couples the plume flow with induced matter and energy transport. We find that both low- and high-temperature vents deposit most vent matter relatively close to the plume. In particular, the tendency of turbulent buoyancy plumes to carry matter far away is strongly counteracted by generated entrainment flows back into the plume stem. The deposition ranges of organic and inorganic hydrothermal particles obtained from the simulations for various natural high-temperature vents are consistent with the observed maximum spatial extent of biological communities, evidencing that plume hydrodynamics exercises strong control over the spatial distribution of vent-endemic fauna. While other factors affecting the spatial distribution of vent-endemic fauna, such as geology and geochemistry, are site-specific, the main physical features of plume hydrodynamics unraveled in this study are largely site-unspecific and therefore universal across vent sites on Earth.

Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field.

The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1 T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13C VPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.

Dissection of the Active Ingredients and Potential Mechanism of Han-Shi-Yu-Fei-Decoction in Treating COVID-19 Based on In Vivo Substances Profiling and Clinical Symptom-Guided Network Pharmacology.

This work was aimed to elucidate the mechanism of action of Han-Shi-Yu-Fei-decoction (HSYFD) for treating patients with mild coronavirus disease 2019 (COVID-19) based on clinical symptom-guided network pharmacology. Experimentally, an ultra-high performance liquid chromatography technique coupled with quadrupole time-of-flight mass spectrometry method was used to profile the chemical components and the absorbed prototype constituents in rat serum after its oral administration, and 11 out of 108 compounds were identified. Calculatingly, the disease targets of Han-Shi-Yu-Fei symptoms of COVID-19 were constructed through the TCMIP V2.0 database. The subsequent network pharmacology and molecular docking analysis explored the molecular mechanism of the absorbed prototype constituents in the treatment of COVID-19. A total of 42 HSYFD targets oriented by COVID-19 clinical symptom were obtained, with EGFR, TP53, TNF, JAK2, NR3C1, TH, COMT, and DRD2 as the core targets. Enriched pathway analysis yielded multiple COVID-19-related signaling pathways, such as the PI3K/AKT signaling pathway and JAK-STAT pathway. Molecular docking showed that the key compounds, such as 6-gingerol, 10-gingerol, and scopoletin, had high binding activity to the core targets like COMT, JAK2, and NR3C1. Our work also verified the feasibility of clinical symptom-guided network pharmacology analysis of chemical compounds, and provided a possible agreement between the points of views of traditional Chinese medicine and western medicine on the disease.

The ideal harvest time for seed production in maize (Zea mays L.) varieties of different maturity groups.

BACKGROUND: The correct time for harvesting is a key factor contributing to the production of high-quality maize seeds. We conducted field experiments to harvest seeds at 11 developmental stages for 3 years, to investigate seed vigor traits in three early maturity maize varieties and two late maturity varieties in one location. RESULTS: Significant correlations (r = 0.72 ~ 0.89) were found among six seed-related traits: standard germination (SG), accelerated aging germination (AAG), cold test germination (CTG), hundred-seed weight (HSW), seed moisture content (SMC), and ≥ 10 °C accumulated temperature from pollination to harvest (AT10). Analysis of variance showed that harvest stage, year, and variety had significant effects on all traits, and harvest stage displayed the greatest effect. The responses of SG, AAG, CTG, HSW and SMC to harvest stage fitted quadratic models, and AT10 fitted a linear model. From the quadratic models, an ideal harvest time (IHT, the final date to reach maximum SG, AAG, and CTG) could be calculated for each variety. The three early maturity varieties reached their IHT at 54.94-58.44 days after pollination (DAP); the two later maturity varieties reached IHT several days later (at 59.87-59.90 DAP). The early maturity varieties consistently required less AT10 to reach the IHT than the later maturity varieties. However, all of the varieties reached the IHT at similar SMC levels of about 35%. CONCLUSION: The later maturity varieties reached the IHT at later DAPs when they acquired more AT10 than the early maturity varieties but both reached it at similar SMC levels. © 2022 Society of Chemical Industry.

Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean.

A novel mesophilic, hydrogen-, and sulfur-oxidizing bacterium, designated strain ST-419T, was isolated from a deep-sea hydrothermal vent plume on the Carlsberg Ridge of the Northwestern Indian Ocean. The isolate was a Gram-staining-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 4-50 °C (optimum 37 °C), pH 5.0-8.6 (optimum pH 6.0) and 1.0-5.0 % (w/v) NaCl (optimum 3.0 %). ST-419T could grow chemlithoautotrophically with molecular hydrogen, sulfide, elemental sulfur and thiosulfate as energy sources. Molecular oxygen, nitrate and elemental sulfur could be used as electron acceptors. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 42.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that ST-419T represented a member of genus Sulfurovum and was most closely related to Sulfurovum riftiae 1812ET, with 97.6 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between ST-419T and S. riftiae 1812ET were 74.6 and 19.6 %, respectively. The combined genotypic and phenotypic data indicate that ST-419T represents a novel species within the genus Sulfurovum, for which the name Sulfurovum indicum sp. nov. is proposed. The type strain is ST-419T (=MCCC 1A17954T=KCTC 25164T).

Elucidation of miRNAs-mediated responses to low nitrogen stress by deep sequencing of two soybean genotypes.

Nitrogen (N) is a major limiting factor in crop production, and plant adaptive responses to low N are involved in many post-transcriptional regulation. Recent studies indicate that miRNAs play important roles in adaptive responses. However, miRNAs in soybean adaptive responses to N limitation have been not reported. We constructed sixteen libraries to identify low N-responsive miRNAs on a genome-wide scale using samples from 2 different genotypes (low N sensitive and low N tolerant) subjected to various periods of low nitrogen stress. Using high-throughput sequencing technology (Illumina-Solexa), we identified 362 known miRNAs variants belonging to 158 families and 90 new miRNAs belonging to 55 families. Among these known miRNAs variants, almost 50% were not different from annotated miRNAs in miRBase. Analyses of their expression patterns showed 150 known miRNAs variants as well as 2 novel miRNAs with differential expressions. These differentially expressed miRNAs between the two soybean genotypes were compared and classified into three groups based on their expression patterns. Predicted targets of these miRNAs were involved in various metabolic and regulatory pathways such as protein degradation, carbohydrate metabolism, hormone signaling pathway, and cellular transport. These findings suggest that miRNAs play important roles in soybean response to low N and contribute to the understanding of the genetic basis of differences in adaptive responses to N limitation between the two soybean genotypes. Our study provides basis for expounding the complex gene regulatory network of these miRNAs.