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Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.

Stropharia rugosoannulata is not only a popular edible mushroom, but also has excellent potential in bioremediation. In this study, we present a high-quality genome of a monokaryotic strain of the S. rugosoannulata commercial cultivar in China. The assembly yielded an N50 length of 2.96 Mb and a total size of approximately 48.33 Mb, encoding 11,750 proteins. The number of heme peroxidase-encoding genes in the genome of S. rugosoannulata was twice the average of all of the tested Agaricales. The genes encoding lignin and xenobiotic degradation enzymes accounted for more than half of the genes encoding plant cell wall degradation enzymes. The expansion of genes encoding lignin and xenobiotic degradation enzymes, and cytochrome P450 involved in the xenobiotic metabolism, were responsible for its strong bioremediation and lignin degradation abilities. S. rugosoannulata was classified as a litter-decomposing (LD) fungus, based on the analysis of the cell wall degrading enzymes. Substrate selection for fruiting body cultivation should consider both the nutritional strategy of LD and a strong lignin degradation ability. Consistent with safe usage as an edible mushroom, the S. rugosoannulata genome does not contain genes for known psilocybin biosynthesis. Genome analysis will be helpful for understanding its nutritional strategy to guide fruiting body cultivation and for providing insight into its application in bioremediation.

Purpose This study was designed to analyze the liver tissue changes among the CHB patients who received treatment for at least 6 months and follow-up for at least 1 year, together with the correlation between the different disease condition and serum markers. Methods One-hundred and eighty-five CHB patients underwent antiviral therapy for at least 6 months were enrolled. In the 12-month follow-up, ultrasonography-guided biopsy was performed. The patients were grouped based on the serum markers and pathological changes in liver tissues. Then we determined the serum markers, virological tests and Tim-3 expression among these groups. Results Antiviral therapy significantly reduced liver inflammation indicators and serum Tim-3 level. However, the fibrosis process of liver tissue was not changed, and there are still disputes on the serum marker and hepatic lesion outcomes. Under normal liver function or negative hepatitis B e antigen (HBeAg) of CHB patients, there might be consensus between Tim-3 change and liver pathological outcome. According to the liver tissue inflammation and fibrosis conditions, Tim-3 was positively correlated with liver function indices. Besides, it was also related to fibrosis stage and inflammation grade. Conclusion There were inconsistent changes between serum markers and liver tissue conditions after anti-viral therapy. Tim-3 expression was more suitable to indicate the changes of liver inflammatory and fibrosis response to some extent than ALT and AST. It may serve as a certain indicator to predict the CHB prognosis, which could be used as one of the monitoring indicators in liver pathological changes of chronic HBV infection, especially in monitoring liver tissue inflammation.

Background Hepatocellular carcinoma (HCC) is one of the most prevalent and aggressive malignancies worldwide. Studies seeking to advance the overall understanding of lncRNA profiling in HCC remain rare. Methods The transcriptomic profiling of 12 HCC tissues and paired adjacent normal tissues was determined using high-throughput RNA sequencing. Fifty differentially expressed mRNAs (DEGs) and lncRNAs (DELs) were validated in 21 paired HCC tissues via quantitative real-time PCR. The correlation between the expression of DELs and various clinicopathological characteristics was analyzed using Student’s t -test or linear regression. Co-expression networks between DEGs and DELs were constructed through Pearson correlation co-efficient and enrichment analysis. Validation of DELs’ functions including proliferation and migration was performed via loss-of-function RNAi assays. Results In this study, we identified 439 DEGs and 214 DELs, respectively, in HCC. Furthermore, we revealed that multiple DELs, including NONHSAT003823, NONHSAT056213, NONHSAT015386 and especially NONHSAT122051, were remarkably correlated with tumor cell differentiation, portal vein tumor thrombosis, and serum or tissue alpha fetoprotein levels. In addition, the co-expression network analysis between DEGs and DELs showed that DELs were involved with metabolic, cell cycle, chemical carcinogenesis, and complement and coagulation cascade-related pathways. The silencing of the endogenous level of NONHSAT122051 or NONHSAT003826 could significantly attenuate the mobility of both SK-HEP-1 and SMMC-7721 HCC cells. Conclusion These findings not only add knowledge to the understanding of genome-wide transcriptional evaluation of HCC but also provide promising targets for the future diagnosis and treatment of HCC.

Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Nextgeneration sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.

Sweet cherry ( Prunus avium L.), one of the most appreciated and most important commercial temperate fruits, has high sensory quality and nutritional value. Investigating its metabolic variations provides valuable information on the formation of fruit quality. In this study, widely targeted LC-MS/MS based metabolomics was used to identify and quantify metabolic changes during ‘Black Pearl’ sweet cherry development and ripening. A total of 263 significant differentially expressed metabolites (DEMs) were detected during the four fruit-development stages. Significant differences were observed in the composition and content of compounds in the four stages of cherry development, especially sugars, organic acids, and flavonoids. Moreover, transcriptome analysis provided a molecular basis for metabolic variations during fruit development. A total of 6724 significant differentially expressed genes (DEGs) were identified. Further correlation analysis of major DEMs and DEGs showed that 19 key DEGs were involved in sugar metabolism, 23 key DEGs in organic acid metabolism, and 13 key DEGs in flavonoid metabolism. The upregulated genes involved in the flavonoid pathway probably play an important role in regulating the rapid increase of anthocyanin content during fruit development. These comprehensive analysis data provide a better understanding to improve fruit quality traits based on molecular and metabolic levels.

Prunus tomentosa Thunb. has excellent nutritional, economic, and ornamental values with different fruit color. The red coloration of fruit is determined by anthocyanin pigmentation, which is an attractive trait for consumers. However, the mechanisms underlying fruit color formation in the P. tomentosa cherry are not well understood. In this research, the pigmentation patterns in red-color P. tomentosa (RP) fruit and white-color P. tomentosa (WP) were evaluated. Anthocyanin content in matured RP fruit was significantly abundant compared with WP fruit. Metabolomic profiling revealed that pelargonidin 3- O -glucoside, cyanidin 3- O -rutinoside, and pelargonidin 3- O -rutinoside were the predominant anthocyanin compounds in the RP fruit, while, WP fruit had less anthocyanin compositions and lower level. Then, integrative analyses of transcriptome and metabolome identified 285 significant differentially expressed genes (DEGs) closely related to anthocyanin differentially expressed metabolites (DEMs). Among them, nine genes were involved in anthocyanin biosynthesis, transport and degradation pathway, including four biosynthesis genes ( PtPAL1 , PtDFR , PtANS, and PtUFGT ), two transport genes ( PtGST11 , PtABC10 ), and three degradation genes ( PtPOD1 , PtPOD16, PtPOD73 ). Transcriptome data and real-time PCR showed that the transcript levels of biosynthesis and transport genes were significantly higher in RP than in WP, especially PtANS, PtUFGT, and PtGST11 , suggesting they may play key roles in red-colored fruit formation. Meanwhile, the degradation-related genes PtPOD1/16/73 took on exactly opposite trend, suggesting their potential effects on anthocyanin degradation. These results provide novel insights into color patterns formation mechanisms of cherries fruit, and the candidate key genes identified in anthocyanin biosynthesis, transport and degradation may provide a valuable resource for cherry breeding research in future.

Anions are always considered to explain most of the cellulose dissolution in the ionic liquid; where electron donor theory is always used to elaborate cellulose dissolution in the ionic liquids with different anions. However, the theory does not apply to ionic liquids with different alkyl chain anions. Herein, the hydrogen bond theory was proposed to further explain cellulose dissolution by density functional theory (DFT) calculations. 1-allyl-3-methylimidazole carboxylate ionic liquids with different alkyl chains including ([Amim][HCOO], [Amim][CH3COO], [Amim][CH3CH2COO], [Amim][CH3CH2CH2COO]) were investigated. The DFT results indicated that the alkyl chains of the anions directly affect the hydrogen bond and the interaction energy between the cations and anions; where the length of the hydrogen bonds between cation and anion is the most predominant factor for determining the polarity parameter β value of the ionic liquid itself and therefore governing cellulose dissolution. Moreover, a shorter length of hydrogen bonds between the anions of ionic liquid and cellobiose referred to a better solubility of cellulose in the ionic liquids.

Efficient photocatalytic performance plays a pivotal role in tackling our present energy challenges. A well-designed arrangement of nanoscale semiconductors and metallic components within multi-heterojunction photocatalysts can establish rapid transport pathways, enhancing the separation and migration of charge carriers. This approach offers a viable strategy towards achieving optimal photocatalytic efficiency. Herein, the glancing angle deposition technique (GLAD) technology of electron beam evaporation and spin-coating method were used to construct Fe 2 O 3 /TiO 2 /WO 3 /Ti 3 C 2 T x quaternary composite materials with serial heterojunctions. Photocatalytic activity was assessed through photoelectrochemical tests, revealing that the Fe 2 O 3 /TiO 2 /WO 3 /Ti 3 C 2 T x composite material outperformed its counterparts under visible-light irradiation. Notably, it achieved the highest photocurrent response, with a maximum photocurrent density of 1.09 mA/cm 2 . This represented a substantial improvement, surpassing Fe 2 O 3 , Fe 2 O 3 /TiO 2 , and Fe 2 O 3 /TiO 2 /WO 3 photocatalysts by factors of 36, 2.8 and 1.25, respectively. This remarkable enhancement can be attributed to the formation of three heterojunctions in series, creating multiple pathways for efficient charge transfer and separation during the photocatalytic process. Furthermore, we proposed a photocatalytic mechanism for quaternary heterojunctions based on band structure analysis.

Cold atmospheric plasma has been widely applied in medical treatment clinically, especially skin diseases. However, the mechanism of cold atmospheric plasma on the treatment of skin diseases is still undefined. In this study, dinitrofluorobenzene-induced atopic dermatitis mice model was constructed. Cold atmospheric plasma was able to decrease skin cells apoptosis, relieve skin inflammation, ER stress and oxidative stress caused by dinitrofluorobenzene stimulation, which was mediated by cold atmospheric plasma-induced MANF expression. In terms of mechanism, hypoxia-inducible factor-1α expression was increased intracellularly after cold atmospheric plasma treatment, which further bound to the promoter region of manf gene and enhanced MANF transcriptional expression. This study reveals that cold atmospheric plasma has a positive effect on atopic dermatitis treatment, also demonstrates the regulatory mechanism of cold atmospheric plasma on MANF expression via HIF-1α, which indicates the potential medical application of cold atmospheric plasma for atopic dermatitis treatment.