MODMS: a multi-omics database for facilitating biological studies on alfalfa (Medicago sativa L.).

Alfalfa (Medicago sativa L.) is a globally important forage crop. It also serves as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Multi-omics data on alfalfa continue to accumulate owing to recent advances in high-throughput techniques, and integrating this information holds great potential for expediting genetic research and facilitating advances in alfalfa agronomic traits. Therefore, we developed a comprehensive database named MODMS (multi-omics database of M. sativa) that incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genomic variants, proteomics, and metabolomics. This report describes our continuously evolving database, which provides researchers with several convenient tools and extensive omics data resources, facilitating the expansion of alfalfa research. Further details regarding the MODMS database are available at https://modms.lzu.edu.cn/.

Anthraquinone metabolites isolated from the rhizosphere soil Streptomyces of Panax notoginseng (Burk.) F. H. Chen target MMP2 to inhibit cancer cell migration.

ETHNOPHARMACOLOGICAL RELEVANCE: Panax notoginseng (Burk.) F. H. Chen belongs to the Araliaceae family. It has been used by traditional Chinese people in Northeast Asia for centuries as an antidiabetic, antioxidant, antitumor agent, etc. Endophytic or rhizospheric microorganisms play key roles in plant defense mechanisms, and they are essential in the discovery of pharmaceuticals and valuable new secondary metabolites. In particular, endophytic or rhizospheric microorganisms of traditional medicinal plants. AIM OF THE STUDY: To discover valuable new secondary metabolites from rhizosphere soil Streptomyces sp. SYP-A7185 of P. notoginseng, and to explore potential bioactivities and targets of metabolites protrusive function. MATERIALS AND METHODS: The metabolites were obtained via column chromatography and identified by multiple spectroscopic analyses. The antitumor, antioxidant, antibacterial, and antiglycosidases effects of isolated metabolites were tested using 3-[4,5-dimethythiazol-2-yl]-2,5-diphenyltetazolium bromide (MTT), 2,2-diphenyl-1-picrylhydrazyl (DPPH), 96-well turbidimetric, and α-glucosidase inhibitory assays. The potential antitumor targets were predicted through network pharmacological approaches. The interactions between metabolites and target were verified by molecular docking and biolayer interferometry (BLI) assay. The effects of cancer cells migration were detected through wound healing assays in A549 and MCF-7. Other cellular validation experiments including reverse transcription-quantitative PCR (RT‒qPCR) and western blotting (WB) were used to confirm the hypothesis of network pharmacology. RESULTS: Five different chemotypes of anthraquinone derivatives (1-10), including six new compounds (3, 6-10), were identified from Streptomyces sp. SYP-A7185. Compounds 1-6 and 9 displayed moderate to strong cytotoxicity on five human cancer cell lines (A549, HepG2, MCF-7, MDA-MD-231, and MGC-803). Moreover, matrix metalloproteinase-2 (MMP2) were predicted as a potential antitumor target of metabolites 1-6 and 9 by comprehensive network pharmacology analysis. Later, BLI assays revealed strong intermolecular interactions between MMP2 and antitumor metabolites, and molecular docking results showed the interaction of metabolites 1-6 and 9 with MMP2 was dependent on the crucial amino acid residues of LEU-83, ALA-84, LEU-117, HIS-131, PRO-135, GLY-136, ALA-140, PRO-141, TYR-143, and THR-144. These results implied that metabolites (1-6 and 9) might inhibit cancer cell migration besides cancer cell proliferation. After that, the cell wound healing assay showed that the cell migration processes were also inhibited after the treatments of compounds 1 and 3 in A549 and MCF-7 cells. In addition, the RT‒qPCR and WB results demonstrated that the gene expression levels of MMP2 were decreased after the treatment with compounds 1 and 3 in A549 and MCF-7 cells. Besides, compound 2 displayed moderate antioxidant activity (EC50, 27.43 µM), compounds 3 and 6 exhibited moderate antibacterial activity, and compound 3 inhibited α-glucosidase with an IC50 value of 13.10 µM. CONCLUSIONS: Anthraquinone metabolites, from rhizosphere soil Streptomyces sp. of P. notoginseng, possess antitumor, antioxidant, antibacterial, and antiglycosidase activities. Moreover, metabolites 1 and 3 inhibit cancer cells migration through downregulating MMP2.

Identification of SARS-CoV-2 inhibitors using lung and colonic organoids.

There is an urgent need to create novel models using human disease-relevant cells to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biology and to facilitate drug screening. Here, as SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs (particularly alveolar type-II-like cells) are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines following SARS-CoV-2 infection, similar to what is seen in patients with COVID-19. Nearly 25% of these patients also have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes1. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high-throughput screen of drugs approved by the FDA (US Food and Drug Administration) and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid and quinacrine dihydrochloride. Treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics.

Understanding the thermal degradation patterns of hopane biomarker compounds present in crude oil.

In-situ burning (ISB) is a common oil spill response technique used for managing marine oil spills. The burnt residues generated from ISB can have several toxic compounds and therefore their impacts on aquatic ecosystem are of major environmental concern. When quantifying the fate of the toxic compounds in ISB residues, C30-αß hopane is routinely used as a conservative biomarker since it has shown to be resistant to most natural weathering processes. However, a recent laboratory study has shown that C30-αß and other hopane compounds have the potential to degrade when crude oil was physically burnt under controlled conditions. When crude oil is burnt, the temperature of the oil can raise up to 350-500 °C; however, so far, no one has studied the fate of hopanes when crude oil is simply heated to very high temperatures. In this study, we hypothesize that heating crude oil to very high temperatures would result in the degradation of hopane compounds. Results of our study show that C30-αß hopane in crude oil will start to degrade at around 160 °C and the degradation pattern follows first order kinetics. Other types of hopanes and their diagnostic ratios can also change when the oil is exposed to severe heating conditions. We conclude that removal of hopane biomarkers via thermal degradation is a possible depletion pathway during ISB. Therefore, caution should be exercised when using hopanes as conservative biomarker compounds for characterizing ISB residues.

Fate of hopane biomarkers during in-situ burning of crude oil - A laboratory-scale study.

In-situ burning (ISB) is a remediation strategy that is used for managing oil spills. ISB generates heavy residues that can submerge and negatively impact benthic environments. To track the fate of toxic contaminants in ISB residues, a conservative hopane biomarker, such as C30-αß hopane, is often used. Furthermore, diagnostic ratios of various hopanes are used for source oil identification. Use of these biomarkers assume that during ISB the quantity of C30-αß hopane will be conserved, and the diagnostic ratios of various hopanes will be stable. The objective of this study is to test the validity of these two assumptions. We conducted laboratory-scale ISB experiments using a model oil prepared from commercial C30-αß hopane standard, and a reference crude oil. Laboratory data collected under controlled burning conditions show that C30-αß hopane will not be conserved; however, the diagnostic ratios of hopanes will still remain fairly stable.

Environmental impacts of the Chennai oil spill accident - A case study.

Chennai, a coastal city in India with a population of over 7 million people, was impacted by a major oil spill on January 28th 2017. The spill occurred when two cargo ships collided about two miles away from the Chennai shoreline. The accident released about 75 metric tons of heavy fuel oil into the Bay of Bengal. This case study provides field observations and laboratory characterization data for this oil spill accident. Our field observations show that the seawalls and groins, which were installed along the Chennai shoreline to manage coastal erosion problems, played a significant role in controlling the oil deposition patterns. A large amount of oil was trapped within the relatively stagnant zone near the seawall-groin intersection region. The initial cleanup efforts used manual methods to skim the trapped oil and these efforts indeed helped recover large amount of oil. Our laboratory data show that the Chennai oil spill residues have unique fingerprints of hopanes and steranes which can be used to track the spill. Our weathering experiments show that volatilization processes should have played a significant role in degrading the oil during initial hours. The characterization data show that the source oil contained about 503,000 mg/kg of total petroleum hydrocarbons (TPH) and 17,586 mg/kg of total polycyclic aromatic hydrocarbons (PAHs). The field samples collected 6 and 62 days after the spill contained about 71,000 and 28,000 mg/kg of TPH and 4854 and 4016 mg/kg of total PAHs, respectively. The field samples had a relatively large percentage of heavy PAHs, and most of these PAHs are highly toxic compounds that are difficult to weather and their long-term effects on coastal ecosystems are largely unknown. Therefore, more detailed studies are needed to monitor and track the long term environmental impacts of the Chennai oil spill residues on the Bay of Bengal coastal ecosystem.