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BACKGROUND: Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identified by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq. RESULTS: We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. CONCLUSION: Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.
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Processamento Alternativo , Poliadenilação , Isoformas de Proteínas/genética , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
BACKGROUND: Numerous studies have highlighted the crucial value of the heavy chain of ferritin (FTH1) as a key regulator of iron metabolism and a suppressor of ferroptosis, intimately tied to the tumor immune microenvironment (TIME). Nevertheless, the precise impact of FTH1 on cancer immunotherapy remains vague. Our study aims to systematically explore the prognostic significance and immune role of FTH1 in pan-cancers immunotherapy. METHODS: Our study delves into the potential of FTH1 as an immunotherapeutic target within the TIME of various solid cancers. The immune landscape and underlying mechanisms of FTH1 in the TIME were investigated by multiple algorithms and bioinformatics methods. Single-cell sequencing analysis and multiplex immunofluorescence staining techniques are applied to observe FTH1 co-expression on both tumor and immune cells. RESULTS: FTH1 exhibited aberrant expression patterns across multiple cancers, which is strongly correlated with immunotherapy resistance. Patients with high FTH1 expression levels tended to derive less benefit from immunotherapies. Moreover, FTH1 demonstrated a significant correlation with TIME infiltration, immune checkpoint molecules, and immune-related pathways. Notably, FTH1 showed a positive association with macrophage infiltrations, its expression was particularly noteworthy in malignant cells and macrophages. Inhibiting FTH1-related signaling pathways appeared to be a potential strategy to counteract tumor immunotherapy resistance. CONCLUSION: Our comprehensive analyses may offer valuable insights into the role of FTH1 in tumor immunotherapy. The observed correlations pave the way for further functional experiments, fostering an enhanced understanding that could shape future research endeavors.
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Neoplasias , Humanos , Prognóstico , Neoplasias/terapia , Algoritmos , Biologia Computacional , Imunoterapia , Microambiente Tumoral , Ferritinas , OxirredutasesRESUMO
BACKGROUND: Little is known about the effects of night shifts and their interactions with genetic factors on chronic obstructive pulmonary disease (COPD). In this study, we aim to investigate relationships between long-term night shift work exposure and COPD risk, and assess modification effects of genetic predisposition. METHODS: A total of 277,059 subjects who were in paid employment or self-employed were included in the UK Biobank. Information on current and lifetime employment was obtained, and a weighted COPD-specific genetic risk score (GRS) was constructed. We used Cox proportional hazard models to investigate associations between night shift work and COPD risk, and their interaction with COPD-specific GRS. RESULTS: The cohort study included 277,059 participants (133,063 men [48.03%]; mean [SD] age, 52.71 [7.08] years). During a median follow-up of 12.87 years, we documented 6558 incidents of COPD. From day work, irregular night shifts to regular night shifts, there was an increased trend in COPD incidence (P for trend < 0.001). Compared with day workers, the hazard ratio (HR) and 95% confidence interval (CI) of COPD was 1.28 (1.20, 1.37) for subjects with rarely/sometimes night shifts and 1.49 (1.35, 1.66) for those with permanent night shifts. Besides, the longer durations (especially in subjects with night shifts ≥ 10 years) and increasing monthly frequency of night shifts (in workers with > 8 nights/month) were associated with a higher COPD risk. Additionally, there was an additive interaction between night shifts and genetic susceptibility on the COPD risk. Subjects with permanent night shifts and high genetic risk had the highest risk of COPD (HR: 1.90 [95% CI: 1.63, 2.22]), with day workers with low genetic risk as a reference. CONCLUSIONS: Long-term night shift exposure is associated with a higher risk of COPD. Our findings suggest that decreasing the frequency and duration of night shifts may offer a promising approach to mitigating respiratory disease incidence in night shift workers, particularly in light of individual susceptibility.
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Doença Pulmonar Obstrutiva Crônica , Jornada de Trabalho em Turnos , Masculino , Humanos , Pessoa de Meia-Idade , Jornada de Trabalho em Turnos/efeitos adversos , Tolerância ao Trabalho Programado , Estudos de Coortes , Incidência , Estudos Prospectivos , Bancos de Espécimes Biológicos , Biobanco do Reino Unido , Fatores de Risco , Doença Pulmonar Obstrutiva Crônica/epidemiologiaRESUMO
Organic cathode materials show excellent prospects for sodium-ion batteries (SIBs) owing to their high theoretical capacity. However, the high solubility and low electrical conductivity of organic compounds result in inferior cycle stability and rate performance. Herein, an extended conjugated organic small molecule is reported that combines electroactive quinone with piperazine by the structural designability of organic materials, 2,3,7,8-tetraamino-5,10-dihydrophenazine-1,4,6,9-tetraone (TDT). Through intermolecular condensation reaction, many redox-active groups CâO and extended conjugated structures are introduced without sacrificing the specific capacity, which ensures the high capacity of the electrode and enhances rate performance. The abundant NH2 groups can form intermolecular hydrogen bonds with the CâO groups to enhance the intermolecular interactions, resulting in lower solubility and higher stability. The TDT cathode delivers a high initial capacity of 293 mAh g-1 at 500 mA g-1 and maintains 90 mAh g-1 at an extremely high current density of 70 A g-1. The TDT || Na-intercalated hard carbon (Na-HC) full cells provide an average capacity of 210 mAh g-1 during 100 cycles at 500 mA g-1 and deliver a capacity of 120 mAh g-1 at 8 A g-1.
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LAIR1, a receptor found on immune cells, is capable of binding to collagen and is involved in immune-related diseases. However, the precise contribution of LAIR1 expressed on hepatocellular carcinoma (HCC) cells to tumor microenvironment is still unclear. In our study, bioinformatics analysis and immunofluorescence were employed to study the correlation between LAIR1 levels and clinical indicators. Transwell and scratch tests were used to evaluate how LAIR1 affected the migration and invasion of HCC cells. The chemotactic capacity and alternative activation of macrophages were investigated using RT-qPCR, transwell, and immunofluorescence. To investigate the molecular mechanisms, transcriptome sequencing analysis, Western blot, nucleus/cytoplasm fractionation, ELISA, and cytokine microarray were employed. We revealed a significant correlation between the presence of LAIR1 and an unfavorable outcome in HCC. We indicated that LAIR1 promoted migration and invasion of HCC cells through the AKT-IKKß-p65 axis. Additionally, the alternative activation and infiltration of tumor-associated macrophages induced by LAIR1 were reliant on the upregulation of IL6 and CCL5 within this axis, respectively. In conclusion, blocking LAIR1 was found to be an effective approach in combating the cancerous advancement of HCC.
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Carcinoma Hepatocelular , Movimento Celular , Neoplasias Hepáticas , Proteínas Proto-Oncogênicas c-akt , Receptores Imunológicos , Carcinoma Hepatocelular/patologia , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/genética , Humanos , Neoplasias Hepáticas/patologia , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/genética , Proteínas Proto-Oncogênicas c-akt/metabolismo , Receptores Imunológicos/metabolismo , Receptores Imunológicos/genética , Quinase I-kappa B/metabolismo , Quinase I-kappa B/genética , Fator de Transcrição RelA/metabolismo , Fator de Transcrição RelA/genética , Linhagem Celular Tumoral , Microambiente Tumoral , Regulação Neoplásica da Expressão Gênica , Transdução de Sinais , Macrófagos/metabolismo , Macrófagos/patologia , Proliferação de Células , Macrófagos Associados a Tumor/metabolismo , Macrófagos Associados a Tumor/patologia , Macrófagos Associados a Tumor/imunologia , Invasividade NeoplásicaRESUMO
The non-specific cytotoxic cell receptor protein 1 (NCCRP1) is considered the universal marker for teleost non-specific cytotoxic cells (NCCs). However, the specific distribution characteristics and response patterns of NCCRP1, and the confirmed existence of NCCs in fish species remain debatable. In this study, we investigated the distribution of NCCRP1 in the croaker and observed the most dominant abundance in the head kidney. While most common markers of cytotoxicity were localized in the trunk kidney lymphocytes (TKLs) and spleen lymphocytes (SPLs), NCCRP1-positive cells were predominantly detected in head kidney lymphocytes (HKLs) with a positive rate of approximately 10 %, where present a huge amount of macrophages (MÏ) as well. Furthermore, the remarkable induction evidence of NCCRP1 in HKLs was determined. Collectively, these findings contribute significantly to comprehending the immunological function of NCCRP1 in fish species and enhancing our understanding of its evolutionary development.
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Proteínas de Peixes , Perciformes , Animais , Perciformes/imunologia , Proteínas de Peixes/imunologia , Proteínas de Peixes/genética , Rim Cefálico/imunologia , Imunidade Inata , Linfócitos/imunologiaRESUMO
BACKGROUND: Impact of outdoor and household air pollution on physical function remains unelucidated. This study examined the influence of various ambient particulate sizes (PM1, PM2.5, and PM10) and household fuel usage on physical function. METHODS: Data from the China Health and Retirement Longitudinal Study (CHARLS) spanning 2011 and 2015 were utilized. The physical functional score was computed by summing scores from four tests: grip strength, gait speed, chair stand test, and balance. Multivariate linear and linear mixed-effects models were used to explore the separate and combined effects of PM1, PM2.5, PM10 and household fuel use on physical function in the cross-sectional and longitudinal analyses, respectively, and to further observe the effects of fuel cleanup on physical function in the context of air pollution exposure. RESULTS: Both cross-sectional and longitudinal analyses revealed negative correlations between PM1 (ß = -0.044; 95% CI: -0.084, -0.004), PM2.5 (ß = -0.024; 95% CI: -0.046, -0.001), PM10 (ß = -0.041; 95% CI: -0.054, -0.029), and physical function, with a more pronounced impact observed for fine particulate matter (PM1). Cleaner fuel use was associated with enhanced physical function compared to solid fuels (ß = 0.143; 95% CI: 0.070, 0.216). The presence of air pollutants and use of solid fuels had a negative impact on physical function, while cleaner fuel usage mitigated the adverse effects of air pollutants, particularly in areas with high exposure. CONCLUSION: This study underscores the singular and combined detrimental effects of air pollutants and solid fuel usage on physical function. Addressing fine particulate matter, specifically PM1, and prioritizing efforts to improve household fuel cleanliness in regions with elevated air pollution levels are crucial for preventing physical disability.
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Poluentes Atmosféricos , Poluição do Ar em Ambientes Fechados , Material Particulado , Material Particulado/análise , China , Humanos , Estudos Transversais , Estudos Longitudinais , Pessoa de Meia-Idade , Masculino , Poluentes Atmosféricos/análise , Poluição do Ar em Ambientes Fechados/análise , Poluição do Ar em Ambientes Fechados/efeitos adversos , Feminino , Idoso , Estudos de Coortes , Tamanho da Partícula , Exposição Ambiental , Culinária , Poluição do Ar/estatística & dados numéricos , Poluição do Ar/efeitos adversosRESUMO
BACKGROUND: Non-optimum temperatures are associated with increased risk of respiratory diseases, but the effects of apparent temperature (AT) on respiratory diseases remain to be investigated. METHODS: Using daily data from 2016 to 2020 in Ganzhou, a large city in southern China, we analyzed the impact of AT on outpatient and inpatient visits for respiratory diseases. We considered total respiratory diseases and five subtypes (influenza and pneumonia, upper respiratory tract infection (URTI), lower respiratory tract infection (LRTI), asthma and chronic obstructive pulmonary disease [COPD]). Our analysis employed a distributed lag nonlinear model (DLNM) combined with a generalized additive model (GAM). RESULTS: We recorded 94,952 outpatients and 72,410 inpatients for respiratory diseases. We found AT significantly non-linearly associated with daily outpatient and inpatient visits for total respiratory diseases, influenza and pneumonia, and URTI, primarily during comfortable AT levels, while it was exclusively related with daily inpatient visits for LRTI and COPD. Moderate heat (32.1 °C, the 75.0th centile) was observed with a significant effect on both daily outpatient and inpatient visits for total respiratory diseases at a relative risk of 1.561 (1.161, 2.098) and 1.276 (1.027, 1.585), respectively (both P < 0.05), while the results of inpatients became insignificant with the adjustment for CO and O3. The attributable fractions in outpatients and inpatients were as follows: total respiratory diseases (24.43% and 18.69%), influenza and pneumonia (31.54% and 17.33%), URTI (23.03% and 32.91%), LRTI (37.49% and 30.00%), asthma (9.83% and 3.39%), and COPD (30.67% and 10.65%). Stratified analyses showed that children ≤5 years old were more susceptible to moderate heat than older participants. CONCLUSIONS: In conclusion, our results indicated moderate heat increase the risk of daily outpatient and inpatient visits for respiratory diseases, especially among children under the age of 5.
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Poluentes Atmosféricos , Poluição do Ar , Asma , Influenza Humana , Pneumonia , Doença Pulmonar Obstrutiva Crônica , Transtornos Respiratórios , Infecções Respiratórias , Criança , Humanos , Pré-Escolar , Pacientes Ambulatoriais , Temperatura , Pacientes Internados , Poluição do Ar/efeitos adversos , Influenza Humana/epidemiologia , Fatores de Tempo , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/etiologia , Asma/epidemiologia , Asma/etiologia , Pneumonia/epidemiologia , Pneumonia/etiologia , Doença Pulmonar Obstrutiva Crônica/epidemiologia , Doença Pulmonar Obstrutiva Crônica/etiologia , China/epidemiologia , Poluentes Atmosféricos/análise , Material Particulado/análiseRESUMO
Immunotherapy, which aims to enhance the function of T cells, has emerged as a novel therapeutic approach for hepatocellular carcinoma (HCC). Nevertheless, the clinical utility of using flow cytometry to assess immune cell infiltration (ICI) is hindered by its cumbersome procedures, prompting the need for more accessible methods. Here, we acquired gene expression profiles and survival data of HCC from TCGA and GSE10186 datasets. The patients were categorized into two clusters of ICI, and a set of 11 characteristic genes responsible for the differentiation performance of these ICI clusters were identified. Subsequently, we successfully developed a modified ICI score (mICIS) by utilizing the expression levels of these genes. The efficacy of our mICIS was confirmed via mass cytometry, flow cytometry, and immunohistochemistry. Our research indicated that the favorable overall survival (OS) rate could be attributed to the improved function of anti-tumor leukocytes rather than their infiltration. Furthermore, we observed that the low score group exhibited lower expression levels of T-cell exhaustion-associated genes, which was confirmed in both HCC tissues from patients and mice, which demonstrated that the benefits of the low scores were due to enhanced active/cytotoxic CD8+ T cells and reduced exhausted CD8+ T cells. Additionally, our mICIS stratified the benefits derived from immunotherapies. Lastly, we observed a misalignment between CD8+ T-cell infiltration and function in HCC. In summary, our mICIS demonstrated proficiency in assessing the OS rate of HCC and offering significant stratified data pertaining to distinct responses to immunotherapy.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Animais , Camundongos , Carcinoma Hepatocelular/metabolismo , Neoplasias Hepáticas/metabolismo , Linfócitos T CD8-Positivos , Imuno-Histoquímica , Imunoterapia , Microambiente TumoralRESUMO
CircRNAs exist widely in plants, but the regulatory mechanisms for the biogenesis and function of plant circRNAs remain largely unknown. Using extensive mutagenesis of expression plasmids and genetic transformation methods, we analyzed the biogenesis and anti-salt functions of a new grape circRNA Vv-circSIZ1. We identified Vv-circSIZ1 that is mainly expressed in the cytoplasm of xylem. CircSIZ1 is species-specific, and genomic circSIZ1-forming region of seven tested species could be backspliced in Nicotiana benthamiana, but not in Arabidopsis. The retention length of Vv-circSIZ1 flanking introns was significantly positively correlated with its generation efficiency. The precise splicing of Vv-circSIZ1 does not depend on its mature exon sequence or internal intron sequences, but on the AG/GT splicing signal sites and branch site of the flanking introns. The spliceosome activity was inversely proportional to the expression level of Vv-circSIZ1. Furthermore, RNA-binding proteins can regulate the expression of Vv-circSIZ1. The overexpression of Vv-circSIZ1 improved salt tolerance of grape and N. benthamiana. Additionally, Vv-circSIZ1 could relieve the repressive effect of VvmiR3631 on its target VvVHAc1. Vv-circSIZ1 also promoted transcription of its parental gene. Overall, these results broaden our understanding of circRNAs in plants.
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Arabidopsis , Precursores de RNA , Precursores de RNA/metabolismo , RNA Circular/genética , RNA Circular/metabolismo , Tolerância ao Sal/genética , Splicing de RNA/genética , Processamento Pós-Transcricional do RNA , Íntrons/genética , Plantas/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismoRESUMO
The process of ripening and softening in grape begins at veraison and is closely related to the depolymerization of pectin components. A variety of enzymes are involved in pectin metabolism and one class of enzyme, pectin lyases (PLs), have been reported to play an important role in softening in many fruits; however, little information is available on the VvPL gene family in grape. In this study, 16 VvPL genes were identified in the grape genome using bioinformatics methods. Among them, VvPL5, VvPL9, and VvPL15 had the highest expression levels during grape ripening, which suggests that these genes are involved in grape ripening and softening. Furthermore, overexpression of VvPL15 affects the contents of water-soluble pectin (WSP) and acid-soluble pectin (ASP) in the leaves of Arabidopsis and significantly changes the growth of Arabidopsis plants. The relationship between VvPL15 and pectin content was further determined by antisense expression of VvPL15. In addition, we also studied the effect of VvPL15 on fruit in transgenic tomato plants, which showed that VvPL15 accelerated fruit ripening and softening. Our results indicate that VvPL15 plays an important role in grape berry softening during ripening by depolymerizing pectin.
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Arabidopsis , Vitis , Vitis/metabolismo , Frutas/metabolismo , Arabidopsis/genética , Pectinas/metabolismo , Plantas Geneticamente Modificadas/metabolismo , Regulação da Expressão Gênica de PlantasRESUMO
Ferroptosis is a new type of programmed cell death different from other cell death pathways such as apoptosis,autophagy,necrosis,and pyroptosis in terms of initiation,mechanisms,and molecular characteristics.As the accumulation of phospholipid hydroperoxides is the hallmark of ferroptosis,the balance between oxidative damage and antioxidant defense is critical to the regulatory mechanism of ferroptosis.In cancer,the upregulation of antioxidant defense pathways can inhibit ferroptosis,thereby promoting cancer cells to survive the oxidative stress and develop drug resistance.This review systematically introduces the main features and regulatory mechanisms of ferroptosis.In addition,we summarize the role of ferroptosis in the progression and drug resistance of malignant tumors,providing novel implications for further research on the pathogenesis of malignant tumors and discovery of new targets for anti-cancer therapy.
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Ferroptose , Neoplasias , Humanos , Antioxidantes , Apoptose , AutofagiaRESUMO
Wide-bandgap perovskite solar cells (PSCs) with an optimal bandgap between 1.7 and 1.8 eV are critical to realize highly efficient and cost-competitive silicon tandem solar cells (TSCs). However, such wide-bandgap PSCs easily suffer from phase segregation, leading to performance degradation under operation. Here, it is evident that ammonium diethyldithiocarbamate (ADDC) can reduce the detrimental I2 back to I- in precursor solution, thereby reducing the density of deep level traps in perovskite films. The resultant perovskite film exhibits great phase stability under continuous illumination and 30-60% relative humidity conditions. Due to the suppression of defect proliferation and ion migration, the PSCs deliver great operation stability which retain over 90% of the initial power conversion efficiency (PCE) after 500 h maximum power point tracking. Finally, a highly efficient semitransparent PSC with a tailored bandgap of 1.77 eV, achieving a PCE approaching 18.6% with a groundbreaking open-circuit voltage (VOC ) of 1.24 V enabled by ADDC additive in perovskite films is demonstrated. Integrated with a bottom silicon solar cell, a four-terminal (4T) TSC with a PCE of 30.24% is achieved, which is one of the highest efficiencies in 4T perovskite/silicon TSCs.
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Salt stress significantly affects the growth, development, yield, and quality of plants. MicroRNAs (miRNAs) are involved in various stress responses via target gene regulation. Their role in regulating salt stress has also received significant attention from researchers. Various transcription factor families are the common target genes of plant miRNAs. Thus, regulating the expression of miRNAs is a novel method for developing salt-tolerant crops. This review summarizes plant miRNAs that mediate salt tolerance, specifically miRNAs that have been utilized in genetic engineering to modify plant salinity tolerance. The molecular mechanism by which miRNAs mediate salt stress tolerance merits elucidation, and this knowledge will promote the development of miRNA-mediated salt-tolerant crops and provide new strategies against increasingly severe soil salinization.
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MicroRNAs , Tolerância ao Sal , Regulação da Expressão Gênica de Plantas/genética , MicroRNAs/genética , MicroRNAs/metabolismo , Tolerância ao Sal/genética , Plantas Tolerantes a Sal/genética , Estresse Fisiológico/genéticaRESUMO
Silicosis is one of the most severe interstitial lung fibrosis diseases worldwide, caused by crystalline silica exposure. While the mechanisms and pathogenesis underlying silicosis remained unknown. N6-methyladenosine (m6A) methylation has received significant attention in a variety of human diseases. However, whether m6A methylation is involved in silicosis has not been clarified. In this study, we conducted methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and transcriptome sequencing (RNA-Seq) to profile the m6A modification in normal and silicosis mouse models (n = 3 pairs). The global levels of m6A methylation were further assessed by m6A RNA methylation quantification kits, and the major regulators of m6A RNA methylation were verified by qRT-PCR. Our results showed that long-term exposure to crystalline silica led to silicosis, accompanied by increasing levels of m6A methylation. Upregulation of METTL3 and downregulation of ALKBH5, FTO, YTHDF1, and YTHDF3 might contribute to aberrant m6A modification. Compared with controls, 359 genes showed differential m6A methylation peaks in silicosis (P < 0.05 and FC ≥ 2). Among them, 307 genes were hypermethylated, and 52 genes were hypomethylated. RNA-Seq analysis revealed 1091 differentially expressed genes between the two groups, 789 genes were upregulated and 302 genes were downregulated in the lungs of silicosis mice (P < 0.05 and FC ≥ 2). In the conjoint analysis of MeRIP-Seq and RNA-Seq, we identified that 18 genes showed significant changes in both m6A modification and mRNA expression. The functional analysis further noted that these 18 m6A-mediated mRNAs regulated pathways that were closely related to "phagosome", "antigen processing and presentation", and "apoptosis". All findings suggested that m6A methylation played an essential role in the formation of silicosis. Our discovery with multi-omics approaches not only gives clues for the epigenetic mechanisms underlying the pathogenesis of silicosis but also provides novel and viable strategies for the prevention and treatment of silicosis.
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Fibrose Pulmonar , Silicose , Humanos , Camundongos , Animais , Fibrose Pulmonar/induzido quimicamente , Fibrose Pulmonar/genética , Fibrose Pulmonar/metabolismo , Transcriptoma , Dióxido de Silício/toxicidade , Metilação , Silicose/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Metiltransferases/genética , Metiltransferases/metabolismo , Dioxigenase FTO Dependente de alfa-Cetoglutarato/genética , Dioxigenase FTO Dependente de alfa-Cetoglutarato/metabolismoRESUMO
BACKGROUND: In plants, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is a key negative regulator in photoperiod response. However, the biological function of COP1-interacting protein 1 (CIP1) and the regulatory mechanism of the CIP1-COP1 interaction are not fully understood. RESULTS: Here, we identified the apple MdCIP1 gene based on the Arabidopsis AtCIP1 gene. Expression pattern analysis showed that MdCIP1 was constitutively expressed in various tissues of apple, and responded to stress and hormone signals at the transcriptional level. Ectopic expression of MdCIP1 complemented the phenotypes of the Arabidopsis cip1 mutant, and MdCIP1 inhibited anthocyanin biosynthesis in apple calli. In addition, the biochemical assay demonstrated that MdCIP1 could interact with MdCOP1 protein by their coiled-coil domain, and MdCIP1-OX/cop1-4 had a similar phenotype in photomorphogenesis with the cop1-4 mutant, suggesting that COP1 is epistatic to CIP1. Furthermore, the transient transformation assay indicated that MdCIP1 repressed anthocyanin biosynthesis in an MdCOP1-mediated pathway. CONCLUSION: Take together, this study finds that MdCIP1 acts as a repressor in regulating hypocotyl elongation and anthocyanin biosynthesis through MdCOP1 in apple.
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Antocianinas/biossíntese , Antocianinas/genética , Arabidopsis/genética , Hipocótilo/crescimento & desenvolvimento , Hipocótilo/genética , Malus/crescimento & desenvolvimento , Malus/genética , Reguladores de Crescimento de Plantas/genética , Produtos Agrícolas/genética , Produtos Agrícolas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Reguladores de Crescimento de Plantas/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente ModificadasRESUMO
MAIN CONCLUSION: This study identified a new bHLHm1 transcription factor MdSAT1 which functioned in mediating tolerance to salt and drought resistance. Changes in the expression of stress-related genes play crucial roles in response to environmental stress. Basic helix-loop-helix (bHLH) proteins are the largest superfamily of transcription factors and a large number of bHLH proteins function in plant responses to abiotic stresses. We identified a new bHLHm1 transcription factor from apple and named it MdSAT1. ß-Glucuronidase (GUS) staining showed that MdSAT1 expressed in various tissues with highly expressed in leaves. Promoter analysis revealed that MdSAT1 contained multiple response elements and its transcription was induced by several environmental cues, particularly salt and drought stresses. Overexpression of MdSAT1 in apple calli and Arabidopsis resulted in a phenotype of increased tolerance to salt and drought. Altering abscisic acid (ABA) treatment increased the sensitivity of MdSAT1-OE Arabidopsis to ABA, and heavy metal stress, osmotic stress, and ethylene did not participate in MdSAT1 mediated plant development. These findings reveal the abiotic stress functions of MdSAT1 and pave the way for further functional investigation.
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Secas , Malus , Proteínas de Plantas , Estresse Fisiológico , Ácido Abscísico , Regulação da Expressão Gênica de Plantas , Malus/genética , Malus/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/metabolismo , Salinidade , Estresse Fisiológico/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismoRESUMO
Pangolin metagenomic data obtained from public databases were used to assemble partial or complete viral genomes showing genetic relationship to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sendai virus, flavivirus, picornavirus, parvovirus, and genomovirus, respectively. Most of these virus genomes showed genomic recombination signals. Phylogeny based on the SARS-CoV-2-related virus sequences assembled in this study and those recently published indicated that pangolin SARS-CoV-2-related viruses were clustered into two sub-lineages according to geographic sampling sites. These findings suggest the need for further pangolin samples, from different countries, to be collected and analyzed for coronavirus to elucidate whether pangolins are intermittent hosts for SARS-CoV-2.
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COVID-19/virologia , Genoma Viral/genética , Metagenoma/genética , Pangolins/virologia , SARS-CoV-2/genética , Animais , Especificidade de Hospedeiro/genética , Metagenômica/métodos , Filogenia , Recombinação Genética/genéticaRESUMO
A novel bacterial strain, designated K2CV101002-2T, was isolated from forest soil collected at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that it belonged to the genus Chitinophaga and was most closely related to Chitinophaga terrae KP01T (99.0â%), followed by Chitinophaga extrema Mgbs1T (98.3â%) and Chitinophaga solisilvae O9T (98.1â%). The draft genome sequence was 6.8 Mb long with a relative low G+C content of 39.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the novel strain and closely related type strains were 71.4â76.2â% and 18.4â19.6â%, respectively. Meanwhile the corresponding values between C. extrema Mgbs1T and C. solisilvae O9T were 98.6 and 88.1â%, respectively. The novel strain contained iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH as the major fatty acids and MK-7 as the predominant respiratory quinone. The polyphasic study clearly supported that strain K2CV101002-2T represents a new species of the genus Chitinophaga, for which the name Chtinophaga silvatica sp. nov. (type strain K2CV101002-2T=GDMCC 1.1288T=JCM 32696T) is proposed. In addition, Chitinophaga extrema Goh et al. 2020 should be taken as a later heterotypic synonym of Chitinophaga solisilvae Ping et al. 2020.
Assuntos
Bacteroidetes/classificação , Florestas , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
BACKGROUND: Melatonin can regulate plant growth, development and biotic responses by causing global changes in gene expression; however, the melatonin-induced changes in gene expression via the modification of DNA methylation remain unclear in plants. RESULTS: A total of 1,169,852 and 1,008,894 methylated cytosines (mCs) were identified in the control and melatonin-treated grape berries, respectively, and mCs occurred primarily at CG sites, followed by CHG sites and CHH sites. Compared to the control, melatonin treatment broadly decreased methylation levels at CHG and particularly CHH sites in various gene regions. Melatonin treatment generated a total of 25,125 differentially methylated regions (DMRs), which included 6517 DMR-associated genes. RNA-Seq demonstrated that 2479 genes were upregulated, and 1072 genes were repressed by melatonin treatment. The evaluation of the interconnection of the DNA methylome and transcriptome identified 144 genes showing a negative correlation between promoter methylation and gene expression, which were primarily related to biotic stress responses and flavonoid biosynthesis. Additionally, the application of 5Ì-azacytidine and melatonin led to similar effects on mycelial growth of B. cinerea, berry decay rate and flavonoid biosynthesis. Moreover, EDS1 was used to show that melatonin increased gene expression by decreasing promoter methylation levels. CONCLUSION: Our results demonstrated that melatonin broadly decreased DNA methylation and altered gene expression in grape berries. We propose that melatonin increases disease resistance and flavonoid biosynthesis by decreasing the methylation levels of the promoters of the genes involved.