Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau

IntroductionThe increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied.MethodCulture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against “ESKAPE” pathogens by paper-disk diffusion method and the double fluorescent protein reporter “pDualrep2” system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively.ResultsA total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the “pDualrep2” system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics.DiscussionAssisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau

Dataset of the complete genome of Streptomyces cavourensis strain 2BA6PGT isolated from sediment from the bottom of the salt lake Verkhnee Beloe (Buryatia, Russia)

The Streptomyces cavourensis strain 2BA6PGT was isolated from sediment from the bottom of the salt lake Verkhnee Beloe (Buryatia, Russia). This strain’s 7,651,223 bp complete genome has a high G + C content of 72.1% and consists of 7,069 coding sequences and 315 subsystems. The 16S ribosomal RNA of isolate 2BA6PGT was most closely related to Streptomyces cavourensis strain NBRC 13026T (98.91% identity), followed by Streptomyces bacillaris strain ATCC 15855T (95.36%), Streptomyces rhizosphaericola strain 1AS2cT (94.68%), and Streptomyces pluricolorescens strain JCM 4602T (86.75%). These comparisons were supported by pairwise comparisons using average nucleotide identity (ANI) and DNA-DNA hybridization analysis. This is the first complete genome reported on Streptomyces cavourensis isolated from sediment from the bottom of the salt lake Verkhnee Beloe

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

Circulating tumor cells (CTCs) enter peripheral blood from primary tumors and seed metastases. The genome sequencing of CTCs could offer noninvasive prognosis or even diagnosis, but has been hampered by low single-cell genome coverage of scarce CTCs. Here, we report the use of the recently developed multiple annealing and looping-based amplification cycles for whole-genome amplification of single CTCs from lung cancer patients. We observed characteristic cancer-associated single-nucleotide variations and insertions/deletions in exomes of CTCs. These mutations provided information needed for individualized therapy, such as drug resistance and phenotypic transition, but were heterogeneous from cell to cell. In contrast, every CTC from an individual patient, regardless of the cancer subtypes, exhibited reproducible copy number variation (CNV) patterns, similar to those of the metastatic tumor of the same patient. Interestingly, different patients with the same lung cancer adenocarcinoma (ADC) shared similar CNV patterns in their CTCs. Even more interestingly, patients of small-cell lung cancer have CNV patterns distinctly different from those of ADC patients. Our finding suggests that CNVs at certain genomic loci are selected for the metastasis of cancer. The reproducibility of cancer-specific CNVs offers potential for CTC-based cancer diagnostics.Chemistry and Chemical Biolog

Research on the Capacity of Underground Reservoirs in Coal Mines to Protect the Groundwater Resources: A Case of Zhangshuanglou Coal Mine in Xuzhou, China

This study analyzes the ability of coal mine underground reservoirs to protect groundwater resources. As the demand for coal mining continues to increase, the potential impact on groundwater resources around mines has become a growing problem. Underground water reservoirs, also known as coal mine underground reservoirs, have been constructed as a solution to protect water wastage in mining operations. However, there is a lack of awareness related to the ability of underground water reservoirs in mines to protect groundwater resources. In this study, we used FLAC3D software to analyze the formation process, water storage volume, and central storage location of the underground water reservoir in Zhangshuanglou Coal Mine. The results show that the damaged volume is 3.39 × 106 m3, and the groundwater resources that can be protected by coal mine underground reservoirs in the study area amount to 1.98 × 105 m3. We found that the storage capacity of underground reservoirs is more significantly affected by the extent of mining, which can be expressed as y = 49,056.44 + 255.75x + 1.46x2 (R2 = 0.995) (x ≠ 0). Additionally, the water storage location obtained through simulation can provide a reference for the construction of underground reservoir regulation and water storage projects. The results of the water quality analysis indicate that the concentrations of SO42− decreased by 42% with the closure of the mining area, and the pH also gradually converged to neutral. This highlights the significant role of underground water reservoirs in coal mines in promoting green production and protecting water resources and the environment

Polyphenolics extracts from Ascophyllum nodosum protect against ultraviolet B-induced oxidative damage in mouse retinal Müller cells

Long-term exposure to sunlight, especially ultraviolet (UV), induces eye injury in people. We investigated the protective potential of Polyphenolic extract from Ascophyllum nodosum (PEAn) against UV-B-induced oxidative damage in retinal Müller cells (RMCs). In the UV-B-induced damage model of RMCs, PEAn demonstrated a potent photoprotective effect that reduced oxidative damage and apoptosis. PEAn significantly regulated the concentrations of ROS, Caspase-3, and Calcium ions (Ca2+) in RMCs generated by UV-B. The mitochondrial membrane potential (ΔΨm) and activities of various antioxidant enzymes (SOD, CAT, and GSH-Px) were significantly increased, whereas the MDA was reduced. Lipidomic research in RMCs also revealed that UV-B irradiation significantly altered the lipid compounds in the cells, while PEAn therapy gradually restored normal cells. Both the accumulation of triacylglycerides and the toxicity of the lipids in RMCs were simultaneously reduced by PEAn. The findings indicated that PEAn could be a potential natural photochemical protectant against UV-B-induced oxidative damage

Metabolomic Approach for Characterization of Polyphenolic Compounds in Laminaria japonica, Undaria pinnatifida, Sargassum fusiforme and Ascophyllum nodosum

Profiling of polyphenolics in four types of brown macroalgae, namely Laminaria japonica (L. japonica), Undaria pinnatifida (U. pinnatifida), Sargassum fusiforme (S. fusiforme), and Ascophyllum nodosum (A. nodosum), and their effect on oxidation resistance were investigated for the first time. Polyphenolic extracts from marine brown macroalgae were shown to effectively remove oxidants from cells and cellular systems. A. nodosum showed the highest antioxidant activity among evaluated brown macroalgae, showing a better scavenging effect on 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical and alleviating oxidative damage caused by hydrogen peroxide to human keratinocytes (HaCaT) cells. Through Q-Exactive HF-X mass spectrometry analysis, 12 polyphenolic compounds were preliminarily identified, including phlorotannins, phenolic acids, and flavonoids. Significant differences in content and variety of polyphenolics were found in evaluated brown macroalgae, which could be related to differences in antioxidant activity in vivo and in vitro. Moreover, the antioxidant activity might be related to the total phenolic content and the types of polyphenolics, especially phlorotannins. The findings presented in this study indicate that A. nodosum could be used as an important substitute for functional ingredients in foods and pharmaceutical preparations, as well as a raw material for phlorotannins research.This article is published as Shen, Ping, Yue Gu, Chunxu Zhang, Chenghang Sun, Lei Qin, Chenxu Yu, and Hang Qi. "Metabolomic approach for characterization of polyphenolic compounds in Laminaria japonica, Undaria pinnatifida, Sargassum fusiforme and Ascophyllum nodosum." Foods 10, no. 1 (2021): 192. DOI: 10.3390/foods10010192. Copyright 2021 by the authors. Attribution 4.0 International (CC BY 4.0). Posted with permission

PLIF diagnostics of NO oxidization and OH consumption in pulsed corona discharge

Pulsed corona discharge is an efficient method on NO oxidization, and the investigation of the oxidization process is significant both for model validation and industrial application. In-situ visualization of NO and OH in pulsed corona discharge was performed by planar laser-induced fluorescence (PLIF) in this work. Two dimensional NO oxidization and OH consumption were studied under different conditions. Some significant results were obtained for mixing behaviors of NO oxidization process. The NO oxidization rate and OH consumption increased by 22% and 40%, respectively, as the Re number of additional gas flow increased from 1379 to 4138. The OH utilization ratio was defined to describe the effect of OH radicals on NO oxidization process. It is demonstrated that OH plays an important role on NO oxidization. The NO reaction and OH consumption zone has a good consistent. (C) 2012 Elsevier Ltd. All rights reserved

Phlorotannin Extracts from Ascophyllum nodosum Inhibited Proteases Activities and Structural Changes from Apostichopus japonicus

Fresh Apostichopus japonicas (A. japonicas) are easy to autolyze through the actions of endogenous proteases under certain circumstances, further inducing a decline in A. japonicas product quality and business value. To solve this serious problem in the A. japonicas industry, we investigated the inhibition of phlorotannin extracts (PhTE) on the activities and structural changes of crude endogenous proteinase (CEP) from A. japonicas. The results of enzyme activity and SDS-PAGE indicated that PhTE could inhibit enzyme activity in a dose dependent manner. Analysis of multiple spectroscopic methods, scanning electron microscopy, and differential scanning calorimetry indicated that PhTE promoted the cross-linking and aggregation of CEP and increased the particle size of the enzyme, thus changing the structure of the enzyme protein and decreasing the thermostability of protease. In conclusion, PhTE might be an effective inhibitor on endogenous proteinase in A. japonicas, which opened up a new way to prevent the A. japonicas autolysis