Integrating single-cell and bulk RNA sequencing to predict prognosis and immunotherapy response in prostate cancer.

Prostate cancer (PCa) stands as a prominent contributor to morbidity and mortality among males on a global scale. Cancer-associated fibroblasts (CAFs) are considered to be closely connected to tumour growth, invasion, and metastasis. We explored the role and characteristics of CAFs in PCa through bioinformatics analysis and built a CAFs-based risk model to predict prognostic treatment and treatment response in PCa patients. First, we downloaded the scRNA-seq data for PCa from the GEO. We extracted bulk RNA-seq data for PCa from the TCGA and GEO and adopted "ComBat" to remove batch effects. Then, we created a Seurat object for the scRNA-seq data using the package "Seurat" in R and identified CAF clusters based on the CAF-related genes (CAFRGs). Based on CAFRGs, a prognostic model was constructed by univariate Cox, LASSO, and multivariate Cox analyses. And the model was validated internally and externally by Kaplan-Meier analysis, respectively. We further performed GO and KEGG analyses of DEGs between risk groups. Besides, we investigated differences in somatic mutations between different risk groups. We explored differences in the immune microenvironment landscape and ICG expression levels in the different groups. Finally, we predicted the response to immunotherapy and the sensitivity of antitumour drugs between the different groups. We screened 4 CAF clusters and identified 463 CAFRGs in PCa scRNA-seq. We constructed a model containing 10 prognostic CAFRGs by univariate Cox, LASSO, and multivariate Cox analysis. Somatic mutation analysis revealed that TTN and TP53 were significantly more mutated in the high-risk group. Finally, we screened 31 chemotherapeutic drugs and targeted therapeutic drugs for PCa. In conclusion, we identified four clusters based on CAFs and constructed a new CAFs-based prognostic signature that could predict PCa patient prognosis and response to immunotherapy and might suggest meaningful clinical options for the treatment of PCa.

Identification of atherosclerosis-related prioritizing metabolites based on a multi-omics composite network.

Metabolites are the final products of cellular regulation processes, their level is the ultimate response of biological systems to environmental and genetic changes. Therefore, the identification of key metabolites is required for the diagnosis and therapy of diseases. In this study, atherosclerosis-related gene expression profile information was extracted from ArrayExpress database (GEOD-57691), and analyzed with limma package. Furthermore, we constructed an intricate multi-omics network involved in genes, phenotypes, metabolites and their associations. To identify the prioritization of atherosclerosis-related metabolites, the relation score of each metabolite in the composite network was computed with the random walk with restart (RWR) method. The top 50 metabolites and top 100 genes were chosen based on the score in the weighted composite network. Consequently, several key metabolites that were ranked in the top 5 of relation score or degree greater than 70 were confirmed. Particularly, metabolites Tretinoin and Estraderm not only have high relation scores, but also contain more degrees. Moreover, we obtained 24 co-expression genes that may be regarded as the targets of atherosclerosis therapy. Therefore, identification of metabolite prioritizations by the composite network integrated the information of genes, phenotypes and metabolites may be available to diagnose atherosclerosis, and can provide the potential therapeutic strategies for atherosclerosis.

Enhanced Production of 6-(N-Hydroxyethyl)-Amino-6-Deoxy-α-L-Sorbofuranose by Immobilized Gluconobacter oxydanson Corn Stover with a pH Control Strategy in a Bubble Column Bioreactor.

6-(N-Hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose (6NSL) is a key intermediate in the synthesis of miglitol. Biotransformation of N-2-hydroxyethyl glucamine (NHEG) to 6NSL was performed by immobilized Gluconobacter oxydans, which was prepared by cultivating the cells in a home-made bubble column bioreactor where corn stover particles were loaded. The optimal carrier addition and aeration rate for 6NSL production by immobilized cells in the bioreactor were determined to be 25 g/L and 2.5 vvm respectively. The supplementation of NH4Cl was conducive to the biotransformation of NHEG and was performed by adding aqueous ammonia and HCl, which was taken as the pH controlling agents as well. An optimal pH control strategy using the mixture of aqueous ammonia and NaOH was applied, resulting in a 9.9% increased production of 6NSL, while repeated batches of biotransformation increased from three times to four times. Finally, the 6NSL concentration and the conversion rate of NHEG to 6NSLreached 44.2 ± 1.5 g/L and 88.4 ± 2.0%, respectively, in average after four cycles of biotransformation under the optimized condition.

[Determination of 22 inorganic elements in different parts of Lantana camara by ICP-OES].

OBJECTIVE: To determine the contents of 22 inorganic elements in different parts of Lantana camara by inductively coupled plasma optical emission spectroscopy (ICP-OES). METHODS: HNO3-H2O2 digested system was used to completely decompose the organic compounds effectually by microwave digestion. The 22 inorganic elements such as K, Ca, Mg, Fe, Al, Na, Zn, Mn and Cr were determined by ICP-OES under set up working conditions. RESULTS: The contents of K, Ca and Mg were the most in different parts of Lantana camara; The contents of K, Ca, Mg, Mn, Sr and Cu in the leaf were more those that in the root and branch; The contents of Fe, Na, Cr and Ni in the root were more than those in the leaf and branch; The contents of Mn, Zn, Sr and Cu in the branch were more than those in the root and the leaf; The contents of Pb and Cd were higher than the national standard and Cr had high content in different parts of Lantana camara. CONCLUSION: The determination method is quick, easy and accurate with high sensitivity, which can determine the contents of 22 inorganic elements accurately in different parts of Lantana camara.

[Determination of 22 inorganic elements in different parts of Lantana camara by ICP-OES].

OBJECTIVE: To determine the contents of 22 inorganic elements in different parts of Lantana camara by inductively coupled plasma optical emission spectroscopy (ICP-OES). METHODS: HNO3-H2 02 digested system was used to completely decomposed the organic compounds effectually by microwave digestion. 22 inorganic elements such as K, Ca, Mg, Fe, Al, Na, Zn, Mn and Cr were determined by ICP-OES under set up working conditions. RESULTS: The contents of K, Ca and Mg were the most in different parts of Lantana camrnara; The contents of K, Ca, Mg, Mn, Sr and Cu in the leaves of Lantana camara were more than that in the root and the branch. The contents of Fe and Na in the root of Lantana camara were more than that in the leaves and the branch. The contents of Pb and Cd were higher than the national standard and Cr had high content in different parts of Lantana camara. CONCLUSION: The determination method is quick, easy and accurate with high sensitivity,which can determine the contents of 22 inorganic elements accurately in different parts of Lantana camara.

[Ecological effect of recirculated landfill leachate with different hydraulic loading on plant-soil system].

The ecological effect of irrigating recirculated leachate with different hydraulic loading on bermudagrass (Cynodon dactylon) and soil system was evaluated. The results show that leachate irrigation with hydraulic loading of 2.77-12.00 mm d(-1) leads to high chlorophyll content, low proline (Pro) content, as well as low malondialdehyde (MDA) and H2O2 content. Soil enzyme activities, respirations, microbial biomass and ratio of biomass carbon to organic carbon (Cmic/Corg) are rather higher. Among leachte irrigation group, leachate irrigation with hydraulic loading of 6.46-10.15 mm x d(-1) leads to declined proline, increased chlorophyll content, low POD activity and low content of MDA and H2O2. Soil bio-activity related parameters, such as soil enzyme activities, respirations, microbial biomass and Cmic/Corg are all enhanced at 6.46-10.15 mm x d(-1) of hydraulic loading. However, when hydraulic loading increases to 12.00 mm x d(-1) or declines to 2.77-4.16 mm x d(-1), the stress of irrigation on bermudagrass is aggravated, and soil bioactivity declines. The results reveal that leachate irrigation could alleviate the stress of environment on bermudagrass and improve the bio-activity of soil. The positive effect of leachate irrigation on the plant-soil system might be contributed to changes of soil water and physico-chemical property after leachate irrigated to the soil. The experimental results suggest that leachate irrigation could benefit plant-soil system, especially when controlled at suitable hydraulic loading.

[Studies on organ phytomorphology of leaves from Rehmannia glutinosa].

OBJECTIVE: To set up the fittest medium and optimum condition for leaves from Rehmannia glutinosa to form regenerated plantlets directly and to induce microtubers. METHOD: Leaves of different phases obtained from the virus-free plantlets were incubated in some kinds of media on the back side. RESULT AND CONCLUSION: The fittest medium for the formation of regenerated plantlet was MS + 6-BA 2.0 mg.L-1 and the fittest medium for the induction of microtuber was MS + 6-BA 1.0 mg.L-1 + NAA 0.5 mg.L-1. The optimum incubation temperaue was 25 degrees C and the light length was (2,000-3,000 lx) 12 h.d-1.