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Disasters caused by mine water inflows significantly threaten the safety of coal mining operations. Deep mining complicates the acquisition of hydrogeological parameters, the mechanics of water inrush, and the prediction of sudden changes in mine water inflow. Traditional models and singular machine learning approaches often fail to accurately forecast abrupt shifts in mine water inflows. This study introduces a novel coupled decomposition-optimization-deep learning model that integrates Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN), Northern Goshawk Optimization (NGO), and Long Short-Term Memory (LSTM) networks. We evaluate three types of mine water inflow forecasting methods: a singular time series prediction model, a decomposition-prediction coupled model, and a decomposition-optimization-prediction coupled model, assessing their ability to capture sudden changes in data trends and their prediction accuracy. Results show that the singular prediction model is optimal with a sliding input step of 3 and a maximum of 400 epochs. Compared to the CEEMDAN-LSTM model, the CEEMDAN-NGO-LSTM model demonstrates superior performance in predicting local extreme shifts in mine water inflow volumes. Specifically, the CEEMDAN-NGO-LSTM model achieves scores of 96.578 in MAE, 1.471% in MAPE, 122.143 in RMSE, and 0.958 in NSE, representing average performance improvements of 44.950% and 19.400% over the LSTM model and CEEMDAN-LSTM model, respectively. Additionally, this model provides the most accurate predictions of mine water inflow volumes over the next five days. Therefore, the decomposition-optimization-prediction coupled model presents a novel technical solution for the safety monitoring of smart mines, offering significant theoretical and practical value for ensuring safe mining operations.
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Metastasis is a major contributing factor that affects the prognosis of melanoma patients. Nevertheless, the underlying molecular mechanisms involved in melanoma metastasis are not yet entirely understood. Here, we identified ubiquitin-specific protease 22 (USP22) as a pro-oncogenic protein in melanoma through screening the survival profiles of 52 ubiquitin-specific proteases (USPs). USP22 demonstrates a strong association with poor clinical outcomes and is significantly overexpressed in melanoma. Ablation of USP22 expression remarkably attenuates melanoma migration, invasion, and epithelial-mesenchymal transition in vitro and suppresses melanoma metastasis in vivo. Mechanistically, USP22 controls melanoma metastasis through the SIRT1/PTEN/PI3K pathway. In addition, we conducted an United States Food and Drug Administration-approved drug library screening and identified topotecan as a clinically applicable USP22-targeting molecule by promoting proteasomal degradation of USP22. Finally, we found that both pharmacological and genetic silence of USP22 sensitize RSL3-induced ferroptosis through suppressing the PI3K/Akt/mTOR pathway and its downstream SCD, and ferroptosis inhibitor could partly rescued the decreased lung metastasis by topotecan in vivo. Overall, our findings reveal a prometastatic role of USP22 and identify topotecan as a potent USP22-targeting drug to limit melanoma metastasis.
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BACKGROUND: According to the studies, more than 80% of pediatric patients with cancer can achieve a survival rate greater than 5 years; however, long-term chemotherapy and/or radiation therapy may seriously affect their reproductive ability. Fertility preservation in adolescents with cancer in China was initiated late, and related research is lacking. Analyze data to understand the current situation and implement measures to improve current practices. METHODS: From 2011 to 2020, data on 275 male adolescents with cancer whose age ranged from 0 to 19 years old were collected from 16 human sperm banks for this retrospective study. Methods include comparing the basic situation of male adolescents with cancer, the distribution of cancer types, and semen quality to analyze the status of fertility preservation. RESULTS: The mean age was 17.39 ± 1.46 years, with 13 cases (4.7%) aged 13-14 years and 262 cases (95.3%) aged 15-19 years. Basic diagnoses included leukemia (55 patients), lymphomas (76), germ cell and gonadal tumors (65), epithelial tumors (37), soft tissue sarcomas (14), osteosarcoma (7), brain tumors (5), and other cancers (16). There are differences in tumor types in different age stages and regions. The tumor type often affects semen quality, while age affects semen volume. Significant differences were found in sperm concentration and progressive motility before and after treatment (p < 0.001). Moreover, 90.5% of patients had sperm in their semen and sperm were frozen successfully in 244 patients (88.7%). CONCLUSIONS: The aim of this study is to raise awareness of fertility preservation in male adolescents with cancer, to advocate for fertility preservation prior to gonadotoxic therapy or other procedures that may impair future fertility, and to improve the fertility status of future patients.
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Preservación de la Fertilidad , Neoplasias , Análisis de Semen , Humanos , Masculino , Adolescente , Preservación de la Fertilidad/métodos , Estudios Retrospectivos , Neoplasias/radioterapia , China/epidemiología , Adulto Joven , Infertilidad Masculina/etiología , Infertilidad Masculina/prevención & control , Criopreservación/métodos , NiñoRESUMEN
Significant advancements have been made in catalytic asymmetric α-C-H bond functionalization of ethers via carbenoid insertion over the past decade. Effective asymmetric catalytic systems, featuring a range of chiral metal catalysts, have been established for the enantioselective synthesis of diverse ether substrates. This has led to the generation of various enantioenriched, highly functionalized oxygen-containing structural motifs, facilitating their application in the asymmetric synthesis of bioactive natural products.
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PURPOSE: Male cancer survivors experience confusion about fertility following cancer treatment. The aims of this study were to evaluate survivors' semen quality in different tumor type groups in China and to analyze the current situation and challenges of male cancer patients with sperm cryopreservation. METHODS: This was a multicenter retrospective study of male patients with cancer who underwent sperm cryopreservation in 16 regions of the national sperm banks over an 11-year period from 2010 to 2020. RESULTS: The number of male cancer patients with sperm cryopreservation showed an overall upward trend. The development of male cancer fertility preservation (FP) in the eastern, central, and western regions of Chinese displayed imbalance. There are seven tumor types for sperm preservation in the top incidence ten tumor types, including lymphoma, leukemia, nasopharyngeal carcinoma, sarcoma, thyroid cancer, and brain tumor. Moreover, nasopharyngeal carcinoma is a high incidence rate in China, which is related to high sperm preservation rate, different from other countries. The most percentage of males receiving sperm cryopreservation in the testicular cancers (15-39 years old) of China in 2020 was 5.55%, 1.29% in the lymphoma, and 0.39% in the leukemia. According to the type of cancer, a statistically significant lower pre-sperm density, total sperm output, and post-sperm density was observed in testicular cancers. It is worth noting that the prevalence of azoospermia 22.2% in leukemia patients attribute to urgent treatment before sperm cryopreservation. Disposition of cryopreserved sperm categories included continued storage (47.2%), discarded (9%), death (0.9%), and use (3.7%). CONCLUSION: This study provides the first comprehensive national statistical census and review of fertility preservation in male cancer patients with respect to trends, prevalence, and cancer types. The development of male cancer fertility preservation in China is imbalanced and percentage of males receiving sperm cryopreservation in the adolescent and young adult cancers was low. Sixteen human sperm banks from China analyze current problems and challenges, and then prioritize steps toward the achievement of the FP strategy framework for Healthy China 2030.
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Criopreservación , Preservación de la Fertilidad , Neoplasias , Preservación de Semen , Bancos de Esperma , Humanos , Masculino , Preservación de la Fertilidad/métodos , China/epidemiología , Criopreservación/métodos , Adulto , Preservación de Semen/métodos , Neoplasias/epidemiología , Neoplasias/patología , Adolescente , Espermatozoides , Estudios Retrospectivos , Análisis de Semen , Infertilidad Masculina/epidemiología , Adulto Joven , Pueblos del Este de AsiaRESUMEN
Targeting angiotensin-converting enzyme 2 (ACE2) represents a promising and effective approach to combat not only the COVID-19 pandemic but also potential future pandemics arising from coronaviruses that depend on ACE2 for infection. Here, we report ubiquitin specific peptidase 2 (USP2) as a host-directed antiviral target; we further describe the development of MS102, an orally available USP2 inhibitor with viable antiviral activity against ACE2-dependent coronaviruses. Mechanistically, USP2 serves as a physiological deubiquitinase of ACE2, and targeted inhibition with specific small-molecule inhibitor ML364 leads to a marked and reversible reduction in ACE2 protein abundance, thereby blocking various ACE2-dependent coronaviruses tested. Using human ACE2 transgenic mouse models, we further demonstrate that ML364 efficiently controls disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as evidenced by reduced viral loads and ameliorated lung inflammation. Furthermore, we improved the in vivo performance of ML364 in terms of both pharmacokinetics and antiviral activity. The resulting lead compound, MS102, holds promise as an oral therapeutic option for treating infections with coronaviruses that are reliant on ACE2.
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COVID-19 , SARS-CoV-2 , Animales , Humanos , Ratones , Enzima Convertidora de Angiotensina 2 , Antivirales/farmacología , Antivirales/uso terapéutico , Ratones Transgénicos , Pandemias , Peptidil-Dipeptidasa A/metabolismo , Ubiquitina TiolesterasaRESUMEN
Bt (Bacillus thuringiensis) maize is expected to be commercial cultivated widely in China. When Bt maize is planted near mulberry trees, it renders silkworms (Bombyx mori) vulnerable, as they belong to the same class as the Lepidoptera insects targeted by Bt maize. Cry1F has been found to be highly toxic to silkworms, particularly in their early larval stages. In this study, we aimed to assess the effects of non-lethal Cry1F exposure on the growth, immune response, and intestinal microbiota in silkworms. The results showed that feeding silkworms with mulberry leaves soaked in 100 µg/mL Cry1F for 96 h had an impact on larval body weight acquisition, leading to a decrease in cocoon and pupae weight. Cry1F exposure disrupted the intestinal integrity of silkworms by affecting the columnar cells of the midgut. The activity of detoxification enzymes (CarE, AChE, and GST) as well as antioxidant enzymes (SOD, CAT, and POD) were also affected by Cry1F. After 96 h Cry1F exposure, the evenness of the bacterial community was disrupted, resulting in alterations in the structure of the intestinal microbiota. Additionally, Cry1F exposure affected the relative expression levels of the peritrophic membrane (PM) protein and the corresponding immune pathways genes of silkworms. Most of the immune-related gene expressions were inhibited after exposure to Cry1F toxin but increased with prolonged treatment. This study demonstrates that non-lethal Cry1F exposure can affect the growth, immune response, and intestinal microbiota of silkworm.
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Bombyx , Microbioma Gastrointestinal , Lepidópteros , Morus , Animales , Bombyx/genética , Antioxidantes , Larva , Proteínas de la Membrana , InmunidadRESUMEN
Background: Indoleamine-2,3-dioxygenase 1 (IDO1) is responsible for tumor immune escape by regulating T cell-associated immune responses and promoting the activation of immunosuppressive. Given the vital role of IDO1 in immune response, further investigation on the regulation of IDO1 in tumors is needed. Methods: Herein, we used ELISA kit to detect the interferon-gamma (IFN-γ), Tryptophan (Trp), and kynurenic acid (Kyn) levels; western blot, Flow cytometry, and immunofluorescence assays detected the expression of the proteins; Molecular docking assay, SPR assay and Cellular Thermal Shift Assay (CETSA) were used to detect the interaction between IDO1 and Abrine; nano live label-free system was used to detect the phagocytosis activity; tumor xenografts animal experiments were used to explore the anti-tumor effect of Abrine; flow cytometry detected the immune cells changes. Results: The important immune and inflammatory response cytokine interferon-gamma (IFN-γ) up-regulated the IDO1 expression in cancer cells through the methylation of 6-methyladenosine (m6A) m6A modification of RNA, metabolism of Trp into Kyn, and JAK1/STAT1 signaling pathway, which could be inhibited by IDO1 inhibitor Abrine. CD47 is IFN-γ-stimulated genes (ISGs) and prevents the phagocytosis of macrophages, leading to the cancer immune escape, and this effect could be inhibited by Abrine both in vivo and in vitro. The PD-1/PD-L1 axis is an important immune checkpoint in regulating immune response, overexpression of PD-1 or PD-L1 promotes immune suppression, while in this study Abrine could inhibit the expression of PD-L1 in cancer cells or tumor tissue. The combination treatment of Abrine and anti-PD-1 antibody has a synergistic effect on suppressing the tumor growth through up-regulating CD4+ or CD8+ T cells, down-regulating the Foxp3+ Treg cells, and inhibiting the expression of IDO1, CD47, and PD-L1. Conclusion: Overall, this study reveals that Abrine as an IDO1 inhibitor has an inhibition effect on immune escape and has a synergistic effect with the anti-PD-1 antibody on the treatment of HCC.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , Animales , Humanos , Antígeno B7-H1/metabolismo , Carcinoma Hepatocelular/tratamiento farmacológico , Carcinoma Hepatocelular/genética , Antígeno CD47/metabolismo , Linfocitos T CD8-positivos , Inmunoterapia , Alcaloides Indólicos/metabolismo , Interferón gamma/metabolismo , Neoplasias Hepáticas/tratamiento farmacológico , Neoplasias Hepáticas/genética , Simulación del Acoplamiento Molecular , Triptófano/metabolismoRESUMEN
BACKGROUND: Lung cancer is the primary cause of cancer-related mortality worldwide owing to its strong metastatic ability. EGFR-TKI (Gefitinib) has demonstrated efficacy in metastatic lung cancer therapy, but most patients ultimately develop resistance to Gefitinib, leading to a poor prognosis. Pedunculoside (PE), a triterpene saponin extracted from Ilex rotunda Thunb., has shown anti-inflammatory, lipid-lowering and anti-tumor effects. Nevertheless, the therapeutic effect and potential mechanisms of PE on NSCLC treatment are unclear. PURPOSE: To investigate the inhibitory effect and prospective mechanisms of PE on NSCLC metastases and Gefitinib-resistant NSCLC. METHODS: In vitro, A549/GR cells were established by Gefitinib persistent induction of A549 cells with a low dose and shock with a high dose. The cell migratory ability was measured using wound healing and Transwell assays. Additionally, EMT-related Markers or ROS production were assessed by RT-qPCR, immunofluorescence, Western blotting, and flow cytometry assays in A549/GR and TGF-ß1-induced A549 cells. In vivo, B16-F10 cells were intravenously injected into mice, and the effect of PE on tumor metastases were determined using hematoxylin-eosin staining, Caliper IVIS Lumina, DCFH2-DA staining, and western blotting assays. RESULTS: PE reversed TGF-ß1-induced EMT by downregulating EMT-related protein expression through MAPK and Nrf2 pathways, decreasing ROS production, and inhibiting cell migration and invasion ability. Moreover, PE treatment enabled A549/GR cells to retrieve the sensitivity to Gefitinib and mitigate the biological characteristics of EMT. PE also significantly inhibited lung metastasis in mice by reversing EMT proteins expression, decreasing ROS production, and inhibiting MAPK and Nrf2 pathways. CONCLUSIONS: Collectively, this research presents a novel finding that PE can reverse NSCLC metastasis and improve Gefitinib sensitivity in Gefitinib-resistant NSCLC through the MAPK and Nrf2 pathways, subsequently suppressing lung metastasis in B16-F10 lung metastatic mice model. Our findings indicate that PE is a potential agent for inhibiting metastasis and improving Gefitinib resistance in NSCLC.
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Carcinoma de Pulmón de Células no Pequeñas , Neoplasias Pulmonares , Triterpenos , Animales , Ratones , Carcinoma de Pulmón de Células no Pequeñas/patología , Gefitinib/farmacología , Neoplasias Pulmonares/patología , Factor de Crecimiento Transformador beta1/farmacología , Factor 2 Relacionado con NF-E2 , Transición Epitelial-Mesenquimal , Especies Reactivas de Oxígeno , Línea Celular Tumoral , Triterpenos/farmacología , Resistencia a AntineoplásicosRESUMEN
Heat stress (HS) is a major abiotic factor influencing fungal growth and metabolism. However, the genetic basis of thermotolerance in Ganoderma lingzhi (G. lingzhi) remains largely unknown. In this study, we investigated the thermotolerance capacities of 21 G. lingzhi strains and screened the thermo-tolerant (S566) and heat-sensitive (Z381) strains. The mycelia of S566 and Z381 were collected and subjected to a tandem mass tag (TMT)-based proteome assay. We identified 1493 differentially expressed proteins (DEPs), with 376 and 395 DEPs specific to the heat-tolerant and heat-susceptible genotypes, respectively. In the heat-tolerant genotype, upregulated proteins were linked to stimulus regulation and response. Proteins related to oxidative phosphorylation, glycosylphosphatidylinositol-anchor biosynthesis, and cell wall macromolecule metabolism were downregulated in susceptible genotypes. After HS, the mycelial growth of the heat-sensitive Z381 strain was inhibited, and mitochondrial cristae and cell wall integrity of this strain were severely impaired, suggesting that HS may inhibit mycelial growth of Z381 by damaging the cell wall and mitochondrial structure. Furthermore, thermotolerance-related regulatory pathways were explored by analyzing the protein-protein interaction network of DEPs considered to participate in the controlling the thermotolerance capacity. This study provides insights into G. lingzhi thermotolerance mechanisms and a basis for breeding a thermotolerant germplasm bank for G. lingzhi and other fungi.
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Ganoderma , Termotolerancia , Termotolerancia/genética , Proteómica , Respuesta al Choque Térmico/genética , Ganoderma/genéticaRESUMEN
RAS, the most frequently mutated oncogene that drives tumorigenesis by promoting cell proliferation, survival, and motility, has been perceived as undruggable for the past three decades. However, intense research in the past has mainly focused on KRAS mutations, and targeted therapy for NRAS mutations remains an unmet medical need. NRAS mutation is frequently observed in several cancer types, including melanoma (15-20%), leukemia (10%), and occasionally other cancer types. Here, we report using miRNA-708, which targets the distinct 3' untranslated region (3'UTR) of NRAS, to develop miRNA-based precision medicine to treat NRAS mutation-driven cancers. We first confirmed that NRAS is a direct target of miRNA-708. Overexpression of miRNA-708 successfully reduced NRAS protein levels in melanoma, leukemia, and lung cancer cell lines with NRAS mutations, resulting in suppressed cell proliferation, anchorage-independent growth, and promotion of reactive oxygen species-induced apoptosis. Consistent with the functional data, the activities of NRAS-downstream effectors, the PI3K-AKT-mTOR or RAF-MEK-ERK signaling pathway, were impaired in miR-708 overexpressing cells. On the other hand, cell proliferation was not disturbed by miRNA-708 in cell lines carrying wild-type NRAS. Collectively, our data unveil the therapeutic potential of using miRNA-708 in NRAS mutation-driven cancers through direct depletion of constitutively active NRAS and thus inhibition of its downstream effectors to decelerate cancer progression. Harnessing the beneficial effects of miR-708 may therefore offer a potential avenue for small RNA-mediated precision medicine in cancer treatment.
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Leucemia , Melanoma , MicroARNs , Humanos , Fosfatidilinositol 3-Quinasas/metabolismo , Transducción de Señal/genética , Melanoma/metabolismo , MicroARNs/genética , Mutación , Línea Celular Tumoral , Proteínas Proto-Oncogénicas B-raf/genética , Proteínas de la Membrana/genética , GTP Fosfohidrolasas/genética , GTP Fosfohidrolasas/metabolismoAsunto(s)
Neoplasias , Bancos de Esperma , Humanos , Masculino , Criopreservación , Pueblos del Este de Asia , Semen , Espermatozoides , ChinaRESUMEN
In order to realize accurate marketing by analyzing customer individual demand, a new quantitative Kano model method is put forward, and it is helpful to provide customized products for heterogeneous customer classification groups. By improving the traditional Kano model, the customer satisfaction and the importance degree of products are defined, and the quantitative Kano demand model is established. Customers are classified as the price preference group, the brand preference group, and the service priority group, and decision-making of product attribute quality improvement for customer classification is realized. Lastly, electric vehicles (EVs) are selected as a study case, and their various demands for different classifications of customers are discussed by questionnaire survey and calculation of satisfaction and the importance degree. Furthermore, different customer group demands are classified as attractive demands, expected demands, nondifferential demands, or essential demands, and the important product attribute acquisition process for various customers is discussed to improve enterprise market competitiveness.
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Comportamiento del Consumidor , Mercadotecnía , Nigeria , Proyectos de Investigación , Encuestas y CuestionariosRESUMEN
Whether and how innate antiviral response is regulated by humoral metabolism remains enigmatic. We show that viral infection induces progesterone via the hypothalamic-pituitary-adrenal axis in mice. Progesterone induces downstream antiviral genes and promotes innate antiviral response in cells and mice, whereas knockout of the progesterone receptor PGR has opposite effects. Mechanistically, stimulation of PGR by progesterone activates the tyrosine kinase SRC, which phosphorylates the transcriptional factor IRF3 at Y107, leading to its activation and induction of antiviral genes. SARS-CoV-2-infected patients have increased progesterone levels, and which are co-related with decreased severity of COVID-19. Our findings reveal how progesterone modulates host innate antiviral response, and point to progesterone as a potential immunomodulatory reagent for infectious and inflammatory diseases.
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COVID-19 , SARS-CoV-2 , Animales , Antivirales , COVID-19/genética , Humanos , Sistema Hipotálamo-Hipofisario , Inmunidad Innata/genética , Ratones , Sistema Hipófiso-Suprarrenal , Progesterona/farmacologíaRESUMEN
BACKGROUND: Lung cancer is the leading cause of cancer mortality worldwide, and most of the patients after treatment with EGF-TKIs develop drug resistance, which is closely correlated with EMT. Cucurbitacin B (CuB) is a natural product of the Chinese herb Cucurbitaceae plant, which has a favorable role in anti-inflammation and anti-cancer activities. However, the effect of CuB on EMT is still far from fully explored. In this study, the inhibition effect of CuB on EMT was investigated. METHODS: In this study, TGF-ß1 was used to induce EMT in A549 cells. MTS assay was used to detect the cell viability of CuB co-treated with TGF-ß1. Wound healing assay and transwell assay were used to determine the migration and invasion capacity of cells. Flow cytometry and fluorescence microscope were used to detect the ROS level in cells. Western blotting assay and immunofluorescence assay were used to detect the proteins expression. Gefitinib was used to establish EGF-TKI resistant NSCLC cells. B16-F10 intravenous injection mice model was used to evaluate the effect of CuB on lung cancer metastasis in vivo. Caliper IVIS Lumina and HE staining were used to detect the lung cancer metastasis of mice. RESULTS: In this study, the results indicated that CuB inhibited TGF-ß1-induced EMT in A549 cells through reversing the cell morphology changes of EMT, increasing the protein expression of E-cadherin, decreasing the proteins expression of N-cadherin and Vimentin, suppressing the migration and invasion ability. CuB also decreased the ROS production and p-PI3K, p-Akt and p-mTOR expression in TGF-ß1-induced EMT in A549 cells. Furthermore, Gefitinib resistant A549 cells (A549-GR) were well established, which has the EMT characteristics, and CuB could inhibit the EMT in A549-GR cells through ROS and PI3K/Akt/mTOR pathways. In vivo study showed that CuB inhibited the lung cancer metastasis effectively through intratracheal administration. CONCLUSION: CuB inhibits EMT in TGF-ß1-induced A549 cells and Gefitinib resistant A549 cells through decreasing ROS production and PI3K/Akt/mTOR signaling pathway. In vivo study validated that CuB inhibits lung cancer metastasis in mice. The study may be supporting CuB as a promising therapeutic agent for NSCLC and Gefitinib resistant NSCLC.
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Over the past decades, Ganoderma lingzhi spores have received considerable attention as a great potential pharmaceutical resource. However, the genetic regulation of sporulation is not well understood. In this study, a comparative transcriptome analysis of the low-sporing HZ203 and high-sporing YW-1 was performed to characterize the mechanism underlying sporulation. A total of 917 differentially expressed genes were identified in HZ203 and 1,450 differentially expressed genes in YW-1. Differentially expressed genes involved in sporulation were identified, which included HOP1, Mek1, MSH4, MSH5, and Spo5 in meiosis. Positive regulatory pathways of sporulation were proposed as 2 transcriptional factors had high connectivity with MSH4 and Spo5. Furthermore, we found that the pathways associated with energy production were enriched in the high-sporing genotype, such as the glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism. Finally, we performed a weighted gene coexpression network analysis and found that the hub genes of the module which exhibit strong positive relationship with the high-sporing phase purportedly participate in signal transduction, carbohydrate transport and metabolism. The dissection of differentially expressed genes during sporulation extends our knowledge about the genetic and molecular networks mediating spore morphogenesis and sheds light on the importance of energy source during sporulation.
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Perfilación de la Expresión Génica , Transcriptoma , Ganoderma , Redes y Vías Metabólicas/genética , Esporas Fúngicas/genéticaRESUMEN
Russula griseocarnosa is a well-known ectomycorrhizal mushroom, which is mainly distributed in the Southern China. Although several scholars have attempted to isolate and cultivate fungal strains, no accurate method for culture of artificial fruiting bodies has been presented owing to difficulties associated with mycelium growth on artificial media. Herein, we sequenced R. griseocarnosa genome using the second- and third-generation sequencing technologies, followed by de novo assembly of high-throughput sequencing reads, and GeneMark-ES, BLAST, CAZy, and other databases were utilized for functional gene annotation. We also constructed a phylogenetic tree using different species of fungi, and also conducted comparative genomics analysis of R. griseocarnosa against its four representative species. In addition, we evaluated the accuracy of one already sequenced genome of R. griseocarnosa based on the internal transcribed spacer (ITS) sequencing of that type of species. The assembly process resulted in identification of 230 scaffolds with a total genome size of 50.67 Mbp. The gene prediction showed that R. griseocarnosa genome included 14,229 coding sequences (CDs). In addition, 470 RNAs were predicted with 155 transfer RNAs (tRNAs), 49 ribosomal RNAs (rRNAs), 41 small noncoding RNAs (sRNAs), 42 small nuclear RNAs (snRNAs), and 183 microRNAs (miRNAs). The predicted protein sequences of R. griseocarnosa were analyzed to indicate the existence of carbohydrate-active enzymes (CAZymes), and the results revealed that 153 genes encoded CAZymes, which were distributed in 58 CAZyme families. These enzymes included 78 glycoside hydrolases (GHs), 34 glycosyl transferases (GTs), 30 auxiliary activities (AAs), 2 carbohydrate esterases (CEs), 8 carbohydrate-binding modules (CBMs), and only one polysaccharide lyase (PL). Compared with other fungi, R. griseocarnosa had fewer CAZymes, and the number and distribution of CAZymes were similar to other mycorrhizal fungi, such as Tricholoma matsutake and Suillus luteus. Well-defined effector proteins that were associated with mycorrhiza-induced small-secreted proteins (MiSSPs) were not found in R. griseocarnosa, which indicated that there may be some special effector proteins to interact with host plants in R. griseocarnosa. The genome of R. griseocarnosa may provide new insights into the energy metabolism of ectomycorrhizal (ECM) fungi, a reference to study ecosystem and evolutionary diversification of R. griseocarnosa, as well as promoting the study of artificial domestication.
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Basidiomycota/genética , Basidiomycota/metabolismo , Agaricales/genética , China , Genoma Fúngico/genética , Genómica/métodos , Anotación de Secuencia Molecular/métodos , Micorrizas/genética , Micorrizas/metabolismo , Filogenia , Secuenciación Completa del Genoma/métodosRESUMEN
Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. Ganoderma leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with an N50 scaffold size of 3.06 Mb, 78,206 coding sequences, and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and Ganoderma lucidum. Ganoderma leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.
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Ganoderma , China , Ganoderma/genética , Terpenos , TibetRESUMEN
In this study, we used genotyping by sequencing (GBS) to examine the genetic diversity of 22 strains of Lingzhi and the quality differences in 15 fruit bodies of Lingzhi from different Chinese regions. The phylogenetic trees of 22 strains were constructed based on ITS (Internal transcribed spacer) and SNP (single nucleotide polymorphism). Moisture, ash, water-soluble extracts, alcohol-soluble extracts, polysaccharides, and triterpenoids from 15 fruit bodies of Lingzhi were detected and analyzed based on Chinese Pharmacopoeia and the US Pharmacopoeia references. Moreover, the monosaccharide composition of polysaccharides was studied using PMP-HPLC, and the effect of polysaccharides on the proliferation rate of splenocytes was investigated in vitro. The identification results of these strains by the phylogenetic trees which were constructed based on ITS sequences and SNPs showed that most of the strains applied in the main producing areas of Lingzhi in China were accurate except for a few inaccurate strains. The moisture, ash, water and alcohol soluble extractive, polysaccharide and triterpenoid content of all samples were meet the requirements of the Chinese Pharmacopoeia, while the polysaccharide and triterpenoid content of less than half of the samples meet the requirements of the U.S. Pharmacopoeia. The polysaccharide extracted from these samples have different effects on the proliferation rate of spleen cells. To sum up, this is the first study that reported on the differences in Lingzhi strains from the main producing areas in China. The quality of some fruit bodies did not meet the pharmacopeia requirements, and wrong strains were used in some production areas; thus, strains should be given special attention before legal processing.