Pyrimidine Metabolism Pathways Research Articles

Integrative metabolomic and microbiomic profiling: Unveiling the therapeutic mechanisms of Yangyinqingfei Decoction in acute lung injury

Acute lung injury (ALI) is a severe inflammatory condition characterized by disruption of the alveolar-capillary barrier, leading to impaired gas exchange and respiratory failure. The gut-lung axis has emerged as a crucial player in the pathogenesis of ALI, highlighting the potential therapeutic value of modulating gut microbiota and associated metabolic pathways. This study aimed to investigate the mechanisms underlying the protective effects of Yangyinqingfei Decoction (YYQFD) in treating ALI from the perspective of the gut-lung axis using an integrative multi-omics approach. Eight key gut microbiota genera were identified and associated with YYQFD treatment, including Lachnospiraceae, Prevotellaceae_NK3B31_group, Lachnospiraceae_NK4A136_group, and unclassified_Eubacterium_coprostanoligenes_group, etc. Metabolomic analysis revealed significant regulation of purine metabolism and pyrimidine metabolism pathways by YYQFD, involving metabolites such as xanthine, inosine, hypoxanthine, guanine, deoxyadenosine, thymine, and thymidine. Correlation analysis demonstrated significant associations between specific gut microbiota and metabolites, suggesting their potential as diagnostic or therapeutic targets. Furthermore, the mediation analysis revealed that YYQFD might regulate deoxyadenosine and L-isoleucine levels via the unclassified_Eubacterium_Coprostanoligenes_group and unclassified_Clostridia_vadinBB60_group, contributing to its therapeutic effects in ALI. This finding highlights the importance of the gut-lung axis in the therapeutic mechanisms of YYQFD and provides insights for future research and development of targeted interventions.

Sputum Metabolomic Signature and Dynamic Change of Cough Variant Asthma.

Cough variant asthma (CVA), a common reason for chronic cough, is a globally prevalent and burdensome condition. The heterogeneity of CVA and a lack of knowledge concerning the exact molecular pathogenesis has hampered its clinical management. This study presented the first sputum metabolome of CVA patients, revealed the dynamic change during treatment, and explored biomarkers related to the occurrence and treatment response of CVA. We found arginine biosynthesis, purine metabolism, and pyrimidine metabolism pathways were enriched in CVA compared to healthy controls. Part of metabolic disturbances could be reversed by anti-asthmatic medication. The levels of dipeptides/tripeptides (alanyltyrosine, Gly-Tyr-Ala, Ala-Leu, and Thr-Leu) were significantly associated with sputum Neu% or Eos% of CVA patients. Differential metabolites pre-treatment between effective and ineffective groups enriched in purine metabolism, thiamine metabolism, and arginine metabolism. 2-isopropylmalate was down-regulated in CVA patients and increased after treatment, and effective group had a lower 2-isopropylmalate level pre-treatment. Random forest and logistic regression models identified glutathione, thiamine phosphate, alanyltyrosine, and 2'-deoxyadenosine as markers for distinguishing CVA from healthy controls (all AUC > 0.8). Thiamine phosphate might also be promising for predicting therapy responsiveness (AUC = 0.684). These findings implied that disturbed mitochondrial energy metabolism and imbalanced oxidation-reduction homeostasis probably underlay the metabolic pathogenesis of CVA.

Network pharmacology combined with molecular docking and molecular dynamics to verify the therapeutic potential of mung beans (Vigna radiata) against prostate cancer

BackgroundProstate cancer is the most common oncological disease in men and one of leading causes of death worldwide. Growing evidence has demonstrated the effectiveness of mung bean bioactive compounds in suppressing various cancer cells. However, their effects and underlying mechanisms on prostate cancer have not been verified. The present study aimed to investigate the therapeutical effects and underlying mechanisms of mung bean compounds against prostate cancer.ResultsThe results revealed that 56 proteins related to prostate cancer could be modulated by mung bean, including several vital proteins of SRC (Sarcoma), Mitogen-Activated Protein Kinase 8 (MAPK8), Heat shock protein 90 kDa alpha member A1 (HSP90AA1), and Harvey Rat sarcoma virus (HRAS). It was also found that the potential pathways associated with prostate cancer pathogenesis comprising pyrimidine metabolism, nitrogen metabolism, and prolactin signaling pathways. Of 19 mung bean compounds docked to four key proteins reveal three promising compound (dulcinoside, peonidin-3-glucoside, and chlorogenic acid) with lower binding affinity score of − 7.7, − 12.2, − 9.0, and − 6.5 kcal/mol against SRC, MAPK8, HSP90AA1, and HRAS, respectively in their site of action. Dynamic simulation results also showed values of − 36.52 ± 2.93, − 35.93 ± 1.67, and − 35.77 ± 1.17 kJ/mol for Dulcinoside-SRC, Dulcinoside-MAPK8, and P3G-HSP90AA1 complexes, respectively. The binding of the compound occur in stable and flexible with the proteins. Moreover, all mung bean compounds predicted to have good ADMET properties.ConclusionsThe study concluded that dulcinoside, peonidin-3-glucoside, and chlorogenic acid potentially exhibited anticancer activity against prostate cancer in silico. Nevertheless, further studies such as in vitro and in vivo are needed to optimize and prove the efficacy of the mung brand and its compounds against prostate cancer.Graphical abstract

PSIII-7 Effects of Saccharomyces cerevisiae fermentation product on total tract digestibility, ruminal fermentation, and plasma metabolome of beef steers fed a finishing diet

Abstract Saccharomyces cerevisiae fermentation product (SCFP) has been widely studied; however, its mode of action on high-concentrate diets has not been fully elucidated. This study evaluated the impact of SCFP on total tract digestibility, fecal excretions of N, P, Zn, and Cu, rumen fermentation, and plasma metabolome of finishing beef steers. Ruminally cannulated Holstein steers [n = 8; body weight (BW) = 580 ± 29.2 kg] were enrolled in a crossover design study with 25-d treatment periods and a 24-d washout period. Steers were fed ad libitum a finishing diet consisting of 20% corn silage and 80% concentrate (on DM basis). Steers were blocked based on initial BW and randomly assigned to two treatments in period 1 and switched to the other treatment in period 2. The treatments were CON (Control, basal diet only) and SCFP (basal diet top-dressed with 12 gּ steer-1ּ ּ d-1 SCFP, NaturSafe, Diamond V, Cedar Rapids, IA). Feed and fecal samples were collected during d 22 to 24 for determination of digestibility. Blood was collected before morning feeding on d 25. Plasma samples were analyzed for metabolome with liquid chromatography-mass spectrometry (LC-MS). Rumen fluid was collected via the rumen cannula at 0, 4, 8, and 12 h post-morning feeding on d 25 and analyzed for pH, volatile fatty acids (VFA), and NH3-N. Performance and ruminal fermentation characteristics data were analyzed using the GLIMMIX procedure of SAS 9.4. Metabolomic data analysis was conducted with Metaboanalyst 6.0. Supplementing steers with SCFP reduced DMI (10.6 vs. 11.4 kg/d, P = 0.05) without affecting (P > 0.05) average daily gain, feed efficiency, and digestibility of organic matter, crude protein, and neutral detergent fiber. Treatment did not affect (P > 0.10) fecal excretions of N, P, Cu, and Zn. Feeding SCFP increased ruminal pH (6.29 vs. 6.01, P = 0.01), numerically reduced concentrations of NH3-N (5.01 vs 6.25 mM, P = 0.16), and total VFA (96.8 vs. 102.5 mM, P = 0.15). SCFP also reduced the ruminal molar proportion of butyrate (11.2 vs. 12.8 molar %, P = 0.01) and tended to increase those of isobutyrate (1.03 vs. 0.90, molar %, P = 0.06) and isovalerate (2.62 vs. 2.29, molar %, P = 0.10). Supplementation of SCFP enriched (P ≤ 0.05) purine metabolism, amino sugar and nucleotide sugar metabolism, and lysine degradation pathways in the plasma. Additionally, tryptophan metabolism and pyrimidine metabolism pathways tended to be enriched (0.05 < P ≤ 0.10) by SCFP. Our findings indicate that feeding SCFP improved the ruminal pH of finishing cattle, which may be beneficial for preventing subacute ruminal acidosis in feedlot cattle. Additionally, SCFP enriched several important plasma nitrogen metabolism pathways, potentially associated with microbial nitrogen metabolism in the rumen, warranting further research.

The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen

Ethnopharmacological relevanceThe prevalence of allergic airway inflammation (AAI) worldwide is high. Artemisia annua L. pollen is spread worldwide, and allergic diseases caused by its plant polysaccharides, which are closely related to the intestinal microbiota, have anti-inflammatory effects. Further isolation and purification of Lycium barbarum L. yielded its most effective component Lycium barbarum L. glycopeptide (LbGP), which can inhibit inflammation in animal models. However, its therapeutic effect on AAI and its mechanism of regulating the intestinal flora have not been fully investigated. Aim of the studyTo explore LbGP in APE-induced immunological mechanisms of AAI and the interaction mechanism of the intestinal flora and metabolites. MethodsA mouse model of AAI generated from Artemisia annua pollen was constructed, and immunological indices related to the disease were examined. A combination of macrogenomic and metabolomic analyses was used to investigate the effects of LbGP on the gut microbial and metabolite profiles of mice with airway inflammation. ResultsLbGP effectively alleviated Artemisia. annua pollen extract (APE)-induced AAI, corrected Th1/Th2 immune dysregulation, decreased Th17 cells, increased Treg cells, and altered the composition and function of the intestinal microbiota. LbGP treatment increased the number of OdoribacterandDuncaniella in the intestines of the mice, but the numble of Alistipes and Ruminococcus decreased. Metabolite pathway enrichment analysis were used to determine the effects of taurine and hypotaurine metabolism, bile acid secretion, and pyrimidine metabolism pathways on disease. ConclusionOur results revealed significant changes in the macrogenome and metabolome following APE and LbGP intervention, revealed potential correlations between gut microbial species and metabolites, and highlighted the beneficial effects of LbGP on AAI through the modulation of the gut microbiome and host metabolism.

Studying temperature’s impact on Brassica napus resistance to identify key regulatory mechanisms using comparative metabolomics

To investigate the effects of temperature on Brassica napus (canola) resistance to Leptosphaeria maculans (LM), the causal agent of blackleg disease, metabolic profiles of LM infected resistant (R) and susceptible (S) canola cultivars at 21 °C and 28 °C were analyzed. Metabolites were detected in cotyledons of R and S plants at 48- and 120-h post-inoculation with LM using UPLC-QTOF/MS. The mock-inoculated plants were used as controls. Some of the resistance-related specific pathways, including lipid metabolism, amino acid metabolism, carbohydrate metabolism, and aminoacyl-tRNA biosynthesis, were down-regulated in S plants but up-regulated in R plants at 21 °C. However, some of these pathways were down-regulated in R plants at 28 °C. Amino acid metabolism, lipid metabolism, alkaloid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis were the pathways linked to combined heat and pathogen stresses. By using network analysis and enrichment analysis, these pathways were identified as important. The pathways of carotenoid biosynthesis, pyrimidine metabolism, and lysine biosynthesis were identified as unique mechanisms related to heat stress and may be associated with the breakdown of resistance against the pathogen. The increased susceptibility of R plants at 28 °C resulted in the down-regulation of signal transduction pathway components and compromised signaling, particularly during the later stages of infection. Deactivating LM-specific signaling networks in R plants under heat stress may result in compatible responses and deduction in signaling metabolites, highlighting global warming challenges in crop disease control.

Immunomodulatory effect of tibetan medicine compound extracts against ORFV in vitro by metabolomics

Ovine contagious pustular dermatitis (ORF) is one of the main diseases of sheep and is a zoonotic disease caused by Ovine contagious pustular dermatitis virus (ORFV) infection, posing a significant constraint on sheep breeding industry and human health. The Tibetan medical formulation composed of Polygonum leucoides, Polygonum xanthoxylum and Acanthophora rotunda significantly regulated lymphocyte immune function following ORFV stimulation, although the mechanism remains unclear. In order to study the immunomodulatory effects and mechanism of three Tibetan medicinal extracts (Polygonum leucoides, Polygonum xanthoxylum, and Acanthophora rotunda) against ORFV in vitro, sheep peripheral blood lymphocytes were isolated in vitro and treated with different concentrations of Tibetan medicine compound extract solution after ORFV infection. The cytokine expression levels in lymphocytes were measured at 4 h, 8 h and 12 h. Additionally endogenous metabolites in lymphocytes at 0 h, 4 h, 8 h and 12 h were quantified by untargeted metabolomics method. The results showed that, the extracts could regulate the lymphocyte immune factors altered by ORFV, and regulate the lymphocyte immune function through cysteine and methionine metabolic pathways as well as the pyrimidine metabolic pathways, potentially alleviating the immune evasion induced by ORFV.

Interventional Effect of Donkey Bone Collagen Peptide Iron Chelate on Cyclophosphamide Induced Immunosuppressive Mice.

Immunodeficiency can disrupt normal physiological activity and function. In this study, donkey bone collagen peptide (DP) and its iron chelate (DPI) were evaluated their potential as immunomodulators in cyclophosphamide (Cytoxan®, CTX)-induced Balb/c mice. The femoral tissue, lymphocytes, and serum from groups of mice were subjected to hematoxylin and eosin (H&E) staining, methylthiazolyldiphenyl-tetrazolium bromide (MTT) cell proliferation assays, and enzyme-linked immunosorbent assay (ELISA), respectively. Furthermore, a non-targeted metabolomics analysis based on UPLC-MS/MS and a reverse transcription polymerase chain reaction (RT-qPCR) technology were used to explore the specific metabolic pathways of DPI regulating immunocompromise. The results showed that CTX was able to significantly reduce the proliferative activity of mouse splenic lymphocytes and led to abnormal cytokine expression. After DP and DPI interventions, bone marrow tissue damage was significantly improved. In particular, DPI showed the ability to regulate the levels of immune factors more effectively than Fe2+ and DP. Furthermore, metabolomic analysis in both positive and negative ion modes showed that DPI and DP jointly regulated the levels of 20 plasma differential metabolites, while DPI and Fe2+ jointly regulated 14, and all 3 jointly regulated 10. Fe2+ and DP regulated energy metabolism and pyrimidine metabolism pathways, respectively. In contrast, DPI mainly modulated the purine salvage pathway and the JAK/STAT signaling pathway, which are the key to immune function. Therefore, DPI shows more effective immune regulation than Fe2+ and DP alone, and has good application potential in improving immunosuppression.

Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database.

Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 485 351 transcripts, 35 336 were recorded as reference transcripts (genes), while 450 015 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) (http://pepper-database.cn/) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.

Efficacy and mechanism of the Ermiao San series of formulas for rheumatoid arthritis based on Chinmedomics strategy

BackgroundThe Ermiao San Series of Formulas (ESSF) refers to Ermiao San (TS), Sanmiao Wan (TW), and Simiao Wan (FW), which are widely used traditional Chinese medicine (TCM) formulas for treating rheumatoid arthritis (RA). However, the therapeutic advantages and underlying mechanisms of ESSF treatment are unclear, especially regarding the improper selection of these three formulas when treating RA. PurposeTo explore the efficacy and mechanisms of ESSF treatment for RA. MethodsComplete Freund's adjuvant was used to induce RA in rats. Chinmedomics strategy, which included metabolomics, serum pharmacochemistry of TCM, molecular docking, western blotting and qPCR, was applied to reveal the therapeutic advantages, pathways, and targets of ESSF. ResultsIn the early stages of treatment, TS quickly reduced joint swelling and the arthritis score index and regulated pathways such as arachidonic acid metabolism and purine metabolism. TW increases the regulation of tryptophan metabolism and pyrimidine metabolism pathways, promoting the recovery of the thymus and spleen. FW increases the regulation of linoleic acid metabolism and has the greatest effect on immune organ and bone recovery. In addition, 54, 67, and 86 bioactive compounds were detected in the serum from TS, TW, and FW, respectively. Berberine, phellodendrine, atractylolide III, limonin, 25R-inokosterone, coixol, and stigmasterol were found to act on the key enzymes COX-2, mPGES-1, ALOX5, and XDH in arachidonic acid metabolism and purine metabolism pathways. Western blot and qPCR results showed that ESSF can reduce the activity of these targets, thereby inhibiting the expression of the inflammatory factors IL-1β, IL-6, IL-17, and TNF-α; the tissue injury factors MMP-3 and CRP; and the rheumatoid factors CCP Ab and RF, thereby achieving anti-RA efficacy. ConclusionESSF has a good therapeutic effect on RA. TS focus on rapid swelling reduction in the early stages of RA, TW focus on the recovery of immune organ function, and FW can be used for bone recovery in the later stage of RA treatment. The key mechanism of treating RA is that ESSF reduces the activity of COX-2, mPGES-1, ALOX5, and XDH. These findings provide valuable guidance for targeted therapy for RA and for the clinical application of ESSF.

The role of cytidine 5'-triphosphate synthetase 1 in metabolic rewiring during epithelial-to-mesenchymal transition in non-small-cell lung cancer.

Epithelial-to-mesenchymal transition (EMT) contributes to the poor prognosis of patients with cancer by promoting distant metastasis and anti-cancer drug resistance. Several distinct metabolic alterations have been identified as key EMT phenotypes. In the present study, we further characterize the role of transforming growth factor-β (TGF-β)-induced EMT in non-small-cell lung cancer. Our study revealed that TGF-β plays a role in EMT functions by upregulation of cytidine 5'-triphosphate synthetase 1 (CTPS), a vital enzyme for CTP biosynthesis in the pyrimidine metabolic pathway. Both knockdown and enzymatic inhibition of CTPS reduced TGF-β-induced changes in EMT marker expression, chemoresistance and migration in vitro. Moreover, CTPS knockdown counteracted the TGF-β-mediated downregulation of UDP-glucuronate, glutarate, creatine, taurine and nicotinamide. These findings indicate that CTPS plays a multifaceted role in EMT metabolism, which is crucial for the malignant transformation of cancer through EMT, and underline its potential as a promising therapeutic target for preventing drug resistance and metastasis in non-small-cell lung cancer.

Investigation on the molecular mechanism of SPA interference with osteogenic differentiation of bone marrow mesenchymal stem cells

Binding of Staphylococcus aureus protein A (SPA) to osteoblasts induces apoptosis and inhibits bone formation. Bone marrow-derived mesenchymal stem cells (BMSCs) have the ability to differentiate into bone, fat and cartilage. Therefore, it was important to analyze the molecular mechanism of SPA on osteogenic differentiation. We introduced transcript sequence data to screen out differentially expressed genes (DEGs) related to SPA-interfered BMSC. Protein–protein interaction (PPI) network of DEGs was established to screen biomarkers associated with SPA-interfered BMSC. Receiver operating characteristic (ROC) curve was plotted to evaluate the ability of biomarkers to discriminate between two groups of samples. Finally, we performed GSEA and regulatory analysis based on biomarkers. We identified 321 DEGs. Subsequently, 6 biomarkers (Cenpf, Kntc1, Nek2, Asf1b, Troap and Kif14) were identified by hubba algorithm in PPI. ROC analysis showed that six biomarkers could clearly discriminate between normal differentiated and SPA-interfered BMSC. Moreover, we found that these biomarkers were mainly enriched in the pyrimidine metabolism pathway. We also constructed '71 circRNAs-14 miRNAs-5 mRNAs' and '10 lncRNAs-5 miRNAs-2 mRNAs' networks. Kntc1 and Asf1b genes were associated with rno-miR-3571. Nek2 and Asf1b genes were associated with rno-miR-497-5p. Finally, we found significantly lower expression of six biomarkers in the SPA-interfered group compared to the normal group by RT-qPCR. Overall, we obtained 6 biomarkers (Cenpf, Kntc1, Nek2, Asf1b, Troap, and Kif14) related to SPA-interfered BMSC, which provided a theoretical basis to explore the key factors of SPA affecting osteogenic differentiation.

Anti-hyperuricemia effect of Clerodendranthus spicatus: a molecular biology study combined with metabolomics

Hyperuricemia (HUA), a metabolic disease caused by excessive production or decreased excretion of uric acid (UA), has been reported to be closely associated with a variety of UA transporters. Clerodendranthus spicatus (C. spicatus) is an herbal widely used in China for the treatment of HUA. However, the mechanism has not been clarified. Here, the rat model of HUA was induced via 10% fructose. The levels of biochemical indicators, including UA, xanthine oxidase (XOD), adenosine deaminase (ADA), blood urea nitrogen (BUN), and creatinine (Cre), were measured. Western blotting was applied to explore its effect on renal UA transporters, such as urate transporter1 (URAT1), glucose transporter 9 (GLUT9), and ATP-binding cassette super-family G member 2 (ABCG2). Furthermore, the effect of C. spicatus on plasma metabolites was identified by metabolomics. Our results showed that C. spicatus could significantly reduce the serum levels of UA, XOD, ADA and Cre, and improve the renal pathological changes in HUA rats. Meanwhile, C. spicatus significantly inhibited the expression of URAT1 and GLUT9, while increased the expression of ABCG2 in a dose-dependent manner. Metabolomics showed that 13 components, including 1-Palmitoyl-2-Arachidonoyl-sn-glycero-3-PE, Tyr-Leu and N-cis-15-Tetracosenoyl-C18-sphingosine, were identified as potential biomarkers for the UA-lowering effect of C. spicatus. In addition, pathway enrichment analysis revealed that arginine biosynthesis, biosynthesis of amino acids, pyrimidine metabolism and other metabolic pathways might be involved in the protection of C. spicatus against HUA. This study is the first to explore the mechanism of anti-HUA of C. spicatus through molecular biology and metabolomics analysis, which provides new ideas for the treatment of HUA.

OsPPG encodes a pseudouridine-5′-phosphate glycosidase and regulates rice spikelet development

Florets are the basic structural units of spikelets, and their morphogenesis determines the yield and quality of rice grains. However, whether and how pseudouridine-5′-phosphate glycosidase participates in rice spikelet development remains an open question. In this study, we identified a novel gene, OsPPG, which encodes a peroxisome-localized pseudouridine-5′-phosphate glycosidase and regulates the development of rice spikelets. osppg mutants exhibited abnormal sterile lemma, lemma, palea, lodicule, stamens, and pistils; male sterility; shorter panicles; and reduced plant height. OsPPG was found to regulate several OsMADS genes, thereby affecting the morphogenesis of rice spikelets. Furthermore, metabolomics revealed that the OsPPG gene was involved in the decomposition of pseudouridine via the pyrimidine metabolism pathway and may affect the jasmonic acid signaling pathway. These results suggest that OsPPG is a key regulator of rice spikelet development.

The energy metabolism and transcriptomic responses of the Manila clam (Ruditapes philippinarum) under the low-temperature stress

Low temperature in winter poses a threat to the Manila clam Ruditapes philippinarum in North China. However, a number of low-temperature-tolerant clams could survive such condition. It is therefore of interest to explore the survival mechanisms underlying the cold tolerance of R. philippinarum. The Zebra II population of R. philippinarum (Zebra II) from North China and the native Putian population from South China were used as experimental materials. Both populations were stressed with low-temperature and the differences in their survival rates, energy metabolism and transcriptional responses were compared. The results shown that after cold treatment at −1.9 °C, survival rate of Zebra II was higher than that of the Putian group. For both groups, the respiration, ammonia excretion, and ingestion rates continuously decreased till 0 with reductions temperature. In addition, RNA-seq revealed that as compared with the Putian group, there were 3682 up-regulated differentially expressed genes (DEGs) and 3361 down-regulated DEGs in Zebra II group. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGs were mostly enriched in the purine, pyrimidine, and pyruvate metabolism pathways in Zebra II under low-temperature stress. Furthermore, qRT–PCR analysis further confirmed that Zebra II responded to low-temperature stress through upregulating genes involved in purine, pyrimidine, and pyruvate metabolism pathways. Taken together, all these results indicated that Zebra II has higher cold tolerance than the Putian group. Therefore, Zebra II is capable for overwintering in the intertidal zone of North China.

Investigating the effects of rare ginsenosides on hyperuricemia and associated sperm damage via nontargeted metabolomics and gut microbiota

Ethnopharmacological relevanceIn ancient times, ginseng was used for hyperuricemia treatment as described in the classic traditional Chinese medical text Shang Han Lun. Recent studies have shown that common ginsenosides and rare ginsenosides (RGS) are the main active compounds in ginseng. RGS have higher activity and are less studied in the treatment of hyperuricemia. Aim of the studyTo determine whether RGS prevents and ameliorates potassium oxonate(PO)-induced hyperuricemia and concomitant spermatozoa damage in mice and the possible underlying mechanisms. Materials and methodsPotassium oxonate (PO, 300 mg/kg) induced hyperuricemia in mice via the oral administration of RGS (50, 100, or 200 mg/kg) or allopurinol (ALL, 5 mg/kg) for 35 days. Uric acid (UA) and xanthine oxidase (XO) levels were measured to assess the degree of histopathological damage in the liver, kidney, and testis, and renal creatinine (CRE), urea nitrogen (BUN), malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), and inflammatory factor (IL-1β) levels were measured to calculate the sperm density. Mechanisms were also explored based on blood and urine metabolomics and the gut microbiota. ResultsIn this study, we demonstrated that RGS containing Rg3, Rk1, Rg6, and Rg5 could reduce serum UA levels, inhibit serum and hepatic XO activity, reduce renal CRE and BUN levels, further restore renal SOD and GSH activities, reduce the accumulation of MDA in the kidneys, and attenuate the production of renal IL-1β. RGS was able to restore sperm density. Metabolomic analysis revealed that RGS improved sphingolipid metabolism, pyrimidine metabolism, and other metabolic pathways. 16S rDNA sequencing revealed that RGS could increase gut microbial diversity, restore the Firmicutes/Bacteroidetes (F/B) ratio, and adjust the intestinal microbial balance. Spearman's correlation analysis revealed a correlation between differentially metabolites and the gut microbiota. Lactobacillus and Akkermansia are the core genera. ConclusionRGS can be a candidate for the prevention and amelioration of hyperuricemia and concomitant sperm damage. Its mechanism of action is closely related to sphingolipid metabolism, pyrimidine metabolism, and the modulation of gut microbiota, such as Lactobacillus and Akkermansia.

Transcriptome analysis reveals key genes and pathways associated with heat stress in Pleurotus pulmonarius.

Pleurotus pulmonarius is a medium temperature edible mushroom, and its yield and quality are severely affected by high temperature. However, the molecular mechanism of Pleurotus pulmonarius response to heat stress remains unknown. In this study, transcriptome sequencing and analysis of Pleurotus pulmonarius mycelia under heat stress were performed, related differentially expressed genes (DEGs) were verified by fluorescence quantitative PCR (qPCR) and the reduced glutathione content was detected. 5906 DEGs, including 1086 upregulated and 4820 downregulated, were identified by RNA-Seq. GO analysis revealed that DEGs were mainly enriched in the pathways of Aminoacyl-tRNA biosynthesis, pyrimidine metabolism, arginine and proline metabolism, fructose and mannose metabolism, and glutathione metabolism. qPCR analysis showed that the expression of ggt decreased after heat stress treatment, while gst2 and gst3 increased. The glutathione content in mycelia after heat stress was significantly higher than that in the control group. These results suggest that glutathione metabolism may play an important role in the response to heat stress. Our study will provide a molecular-level perspective on fungal response to heat stress and a basis for research on fungal environmental response and molecular breeding.

Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.

Microbiome profiling and Co-metabolism pathway analysis in cervical cancer patients with acute radiation enteritis

BackgroundIntestinal bacteria significantly contribute to the metabolism of intestinal epithelial tissues. As the occurrence and development of radiation enteritis (RE) depend on the “co-metabolism” microenvironment formed by the host and intestinal microbiota, which involves complex influencing factors and strong correlations, ordinary techniques struggle to fully explain the underlying mechanisms. However, given that it is based on systems biology, metabolomics analysis is well-suited to address these issues. This study aimed to analyze the metabolomic changes in urine, serum, and fecal samples during volumetric modulated arc therapy (VMAT) for cervical cancer and screen for characteristic metabolites of severe acute radiation enteritis (SARE) and RE. MethodsWe enrolled 50 patients who received radiotherapy for cervical cancer. Urine, serum, and fecal samples of patients were collected at one day before radiotherapy and the second week, fourth week, and sixth week after the start of radiotherapy. Control group samples were collected during the baseline period. Differential metabolites were identified by metabolomics analysis; co-metabolic pathways were clarified. We used the mini-SOM library for incorporating characteristic metabolites, and established metabolite classification models for predicting SARE and RE. ResultsUrine and serum sample data showed remarkable clustering effect; metabolomics data of the fecal supernatant were evidently disturbed. Patient sample analyses during VMAT revealed the following. Urine samples: Downregulation of the pyrimidine and riboflavin metabolism pathways as well as initial upregulation followed by downregulation of arginine and proline metabolism pathways and the arginine biosynthesis pathway. Fecal samples: Upregulation of linoleic acid and phenylalanine metabolic pathways and initial downregulation followed by upregulation of arachidonic acid (AA) metabolic pathways. Serum samples: Initial upregulation followed by downregulation of the arginine biosynthesis pathway and downregulation of glutathione, AA, and arginine and proline metabolic pathways. ConclusionPatients with cervical cancer exhibited characteristic metabolic pathways and characteristic metabolites predicting RE and SARE were screened out. An effective RE mini-SOM classification model was successfully established.

Postharvest quality and metabolism changes of daylily flower buds treated with hydrogen sulfide during storage

Daylily flower buds are a good source of nutrients and contain lots of bioactive compounds, but they are subject to deterioration after harvest, which limits the taste and consumer satisfaction. Hydrogen sulfide (H2S) has been regarded as an important gaseous signaling molecule, which could prolong postharvest freshness of fruits and vegetables. The present study aims to investigate the effects of H2S on postharvest quality and metabolism changes of daylily flower buds during storage. The results showed that 3.2 mM NaHS (H2S donor) effectively inhibited weight loss, blooming and decay of daylily during storage. H2S application markedly reduced the accumulation of malondialdehyde and H2O2. H2S treatment also delayed the loss of total protein and antioxidant glutathione, and maintained the activities of antioxidant enzymes superoxide dismutase and catalase at higher level compared to control group. Widely targeted metabolomics identified various differentially accumulated metabolites (DAMs) during storage and with H2S treatment of daylily. These DAMs largely distributed in the classes of amino acids, organic acids, sugars and alcohols, terpenoids. A special focus was given to 303 common DAMs between the comparison of CK0 vs. CK6 and CK6 vs. T6, of which the DAMs were mainly enriched in the KEGG pathways of monobactam biosynthesis, pyrimidine metabolism, glycine, serine and threonine metabolism, arginine biosynthesis, pentose and glucuronate interconversions. Four DAMs including Cytidine 5′-Monophosphate, Fumaric Acid, Hydroxypyruvic Acid, 2′-Deoxycytidine-5′-Monophosphoric Acid exhibited great downregulation during storage, and H2S treatment dramatically recovered their relative contents. This study indicated that H2S treatment offers the potential to preserve the quality of daylily flower buds and extend their postharvest life.