Whole-transcriptome sequencing with ceRNA regulation network construction and verification in glioblastoma.

OBJECTIVES: To explore the key genes involved in the occurrence and development of glioblastoma (GBM) by analyzing whole-transcriptome sequencing and biologic data from GBM and normal cerebral cortex tissues and to search for important noncoding RNA (ncRNA) molecular markers based on the competitive endogenous RNA (ceRNA) network. METHODS: Ten GBM and normal cerebral cortex tissues were collected for full transcriptome sequencing, screened for differentially expressed (DE) mRNAs, miRNAs, lncRNAs, and circRNAs, and subjected to bioinformatic analysis. We constructed a Protein-Protein Interaction (PPI) network and a circRNA/lncRNA-miRNA-mRNA regulatory network and identified them using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Finally, The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were used to validate and conduct a survival analysis of the target genes. RESULTS: A total of 5341 DEmRNAs, 259 DEmiRNAs, 3122 DElncRNAs, and 2135 DEcircRNAs were identified. Enrichment analysis showed that target genes regulated by DEmiRNA, DElncRNA, and DEcircRNA were closely related to chemical synaptic transmission and ion transmembrane transport. A PPI network analysis screened 10 hub genes that directly participate in tumor cell mitosis regulation. In addition, the ceRNA composite network showed that hsa-miR-296-5p and hsa-miR-874-5p were the central nodes of the network, and the reliability of relevant key molecules was successfully verified through RT-qPCR identification and the TCGA database. The CGGA database survival analysis produced 8 DEmRNAs closely related to GBM patient survival prognosis. CONCLUSIONS: This study revealed the important regulatory functions and molecular mechanisms of ncRNA molecules and identified hsa-miR-296-5p and hsa-miR-874-5p as key molecules in the ceRNA network. They may play an important role in GBM pathogenesis, treatment, and prognosis.

Phthalates in plastic bottled non-alcoholic beverages from China and estimated dietary exposure in adults.

Concentrations of six phthalates were determined in 69 plastic bottled non-alcoholic beverages collected from marketplaces in China. Di-n-butyl phthalate (DBP) and di-(2-ethylhexyl)-phthalate (DEHP) were the most detected compounds with frequencies of 100%. Dimethyl phthalate was found less, with a mean frequency of almost 34%. The samples were divided into seven groups. The frequencies of phthalates in these groups ranged from 6.67% to 100%, which indicated that different types of beverages were differently contaminated by phthalates. DEHP contained the highest mean and median concentrations (1.60 ng g-1 and 0.62 ng g-1), followed by DBP (1.34 ng g-1 and 0.27 ng g-1). For DBP, the highest phthalate concentration of 14.3 ng g-1 was measured. The results of estimated daily intake (EDI) showed that the risk of Chinese adults exposed to these 6 phthalates in beverages examined was lower than the reference doses as suggested by the United States Environmental Protection Agency. The range of EDI values was between 1.77 × 10-4 µg kg-bw-1 day-1 and 0.478 µg kg-bw-1 day-1.

Reaction of antibiotic sulfadiazine with manganese dioxide in aqueous phase: Kinetics, pathways and toxicity assessment.

Sulfonamide antibiotics are often detected in terrestrial and aquatic environment, but little is known about abiotic degradation of these antibiotics. In the present study, the degradation of the sulfonamide antibiotic sulfadiazine by a synthesized δ-MnO2 was investigated. The initial reaction rate of sulfadiazine oxidized by manganese dioxide increased as the solution pH decreased by weakening electrostatic attraction between sulfadiazine and MnO2 and enhancing the reduction potential of MnO2. The presence of metal ions (Mn2+, Na+ and Ca2+), especially Mn2+, decreased the initial reaction rate by competitively adsorbing and reacting with MnO2. Two different products were identified during the reaction of sulfadiazine with MnO2 and the transformation of parent compound started with the formation of sulfadiazine radicals. Furthermore, toxicity assay results showed that the toxicity of products produced by bacteria decreased with elapse of reaction time. Results from the present study indicate that manganese dioxides in environmental matrix could be helpful in dissipation of sulfadiazine released into the environment.

Chemical oxidation of sulfadiazine by the Fenton process: kinetics, pathways, toxicity evaluation.

This paper investigated sulfadiazine oxidation by the Fenton process under various reaction conditions. The reaction conditions tested in the experiments included the initial pH value of reaction solutions, and the dosages of ferrous ions and hydrogen peroxide. Under the reaction conditions with pH 3, 0.25 mM of ferrous ion and 2 mM of hydrogen peroxide, a removal efficiency of nearly 100% was achieved for sulfadiazine. A series of intermediate products including 4-OH-sulfadiazine/or 5-OH-sulfadiazine, 2-aminopyrimidine, sulfanilamide, formic acid, and oxalic acid were identified. Based on these products, the possible oxidation pathway of sulfadiazine by Fenton's reagent was proposed. The toxicity evaluation of reaction solutions showed increased antimicrobial effects following the Fenton oxidation process. The results from this study suggest that the Fenton oxidation process could remove sulfadiazine, but also increase solution toxicity due to the presence of more toxic products.

[Study on the chemical components of volatile oil from Euphorbia pekinensis radix].

OBJECTIVE: To analyze the volatile oil from Radix Euphorbia Pekinensis. METHODS: Volatile oil was extracted from Radix Euphorbia Pekinensis by steam distillation and GC-MS was employed for detecting the content of the constituents. The relative content of the chemical constituents were calculated using area normalization method. RESULTS: 35 peaks were separated and 29 constituents were identified. The yield rate of volatile oil extracted from the dried radix of Euphorbia Pekinensis was 0.3%. CONCLUSION: The main components of volatile oil were agarospirol and hedycargol and their contents were 49.23% and 20.66% respectively. This paper provides valuable experimental data for further research of Radix Euphorbia Pekinensis.

Biological degradation and microbial function effect of norfloxacin in a soil under different conditions.

This paper investigated the degradation kinetics of norfloxacin in a soil, and its effects on soil respiration and nitrogen transformation under different conditions. Compared to the sterile control, the degradation rates of norfloxacin in the non-sterile soil were greatly enhanced, suggesting that microorganisms played a major role in the degradation. Accelerated degradation for norfloxacin in the soil was observed with decreasing concentrations (30 mg/kg to 5 mg/kg) with its half-life decreasing from 62 days to 31 days. Amending swine manure into the soil and increasing the soil moisture level enhanced the biological degradation of norfloxacin. No obvious inhibition of norfloxacin on soil respiration was observed in the soil, while only slight effect on nitrogen transformation was found. The results suggested that norfloxacin at the reported environmental concentrations (<100 mg/kg) would have little effect on microbial activity and functions in the soils.

[Association of IL-8 gene polymorphisms with inflammatory bowel disease in Chinese patients].

OBJECTIVE: To investigate the association of interleukin 8 (IL-8) gene polymorphisms with the risks of inflammatory bowel disease (IBD). METHODS: Single nucleotide polymorphisms (SNPs) of IL-8 gene at -845 T/C, -738 T/A, -353 A/T, -251 T/A and +678 T/C were analyzed in 183 IBD patients. They included Crohn's disease (CD, n = 41), ulcerative colitis (UC, n = 142) and healthy controls (n = 160). The methods of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and polymerase chain reaction-sequence specific primers (PCR-SSP) were employed. RESULTS: No association was observed between any of these five SNPs in IL-8 gene with the occurrence of IBD. A specific haplotype AAT (-353 A/T, -251 T/A & +678 T/C) was over-represented in UC cases when compared with controls (31.0% vs 23.7%, P = 0.046). But the distributions of this haplotype did not show significant difference between CD cases and controls. CONCLUSION: Our data support a significant but modest association between the AAT haplotype of IL-8 gene and UC (OR = 1.441, 95%CI 1.007 - 2.063).

Transcriptome analysis of adaptive heat shock response of Streptococcus thermophilus.

Streptococcus thermophilus, a gram-positive facultative anaerobe, is one of the most important lactic acid bacteria widely used in the dairy fermentation industry. In this study, we have analyzed the global transcriptional profiling of S. thermophilus upon temperature change. During a temperature shift from 42°C to 50°C, it is found that 196 (10.4%) genes show differential expression with 102 up-regulated and 94 down-regulated at 50°C. In particular, 1) Heat shock genes, such as DnaK, GroESL and clpL, are identified to be elevated at 50°C; 2) Transcriptional regulators, such as HrcA, CtsR, Fur, MarR and MerR family, are differentially expressed, indicating the complex molecular mechanisms of S. thermophilus adapting to heat shock; 3) Genes associated with signal transduction, cell wall genes, iron homeostasis, ABC transporters and restriction-modification system were induced; 4) A large number of the differentially expressed genes are hypothetical genes of unknown function, indicating that much remains to be investigated about the heat shock response of S. thermophilus. Experimental investigation of selected heat shock gene ClpL shows that it plays an important role in the physiology of S. thermophilus at high temperature and meanwhile we confirmed ClpL as a member of the CtsR regulon. Overall, this study has contributed to the underlying adaptive molecular mechanisms of S. thermophilus upon temperature change and provides a basis for future in-depth functional studies.

Notch signaling dependent differentiation of cholangiocyte-like cells from rhesus monkey embryonic stem cells.

Rhesus monkey embryonic stem (rES) cells have similar characteristics to human ES cells, and might be useful as a substitute model for preclinical research. Notch signaling is involved in the formation of bile ducts, which are composed of cholangiocytes. However, little is known about the role of Notch signaling in cholangiocytic commitment of ES cells. We analyzed the effect of Notch signaling on the induction of cholangiocyte-like cells from rES cells. About 80% of definitive endoderm (DE) cells were generated from rES cells after treatment with activin A. After treatment with BMP4 and FGF1 on matrigel coated wells in serum-free medium, rES-derived DE gave rise to cholangiocyte-like cells by expression of cholangiocytic specific proteins (CK7, CK18, CK19, CK20, and OV-6) and genes (GSTPi, IB4, and HNF1ß). At the same time, expression of Notch 1 and Notch 2 mRNA were detected during cell differentiation, as well as their downstream target genes such as Hes 1 and Hes 5. Inhibition of the Notch signal pathway by L-685458 resulted in decreased expression of Notch and their downstream genes. In addition, the proportion of cholangiocyte-like cells declined from approximately 90% to approximately 20%. These results suggest that Notch signaling may play a critical role in cholangiocytic development from ES cells.

[Association of combined polymorphisms in MIP-1α and ApoE genes with the susceptibility of inflammatory bowel disease].

OBJECTIVE: To investigate whether the macrophage inflammatory protein 1 alpha (MIP-1α) and apolipoprotein E (ApoE) gene polymorphisms, either alone or in combination, affect the susceptibility to inflammatory bowel disease (IBD). METHODS: Genomic DNA of IBD patients with Crohn's disease (CD, n = 41) and with ulcerative colitis (UC, n = 142) and healthy controls (n = 160) was extracted and genotyped for the MIP-1α and ApoE gene polymorphisms by restriction fragment length polymorphism assay. RESULTS: MIP-1α -906(TA)(6)/(TA)(6) homozygotes had a significantly elevated risk of UC (OR = 1.909, 95%CI = 1.204 - 3.028). The carriers of APOE4ε4 were at a significantly higher risk for UC with OR of 2.379 (95% CI = 1.451 - 3.896). And a combination of these two loci, MIP-1α -906(TA)(6)/(TA)(6)/APOE4ε4 were strongly associated with a higher risk of UC (OR = 3.288; 95%CI = 1.777 - 6.084). CONCLUSION: The polymorphisms of MIP-1α -906 (TA)(6)/(TA)(6) and ApoE are probably independent genetic risk factors for UC. And the coexistence of both may exert an additive effect on the UC risks.

Trends in the occurrence of human and veterinary antibiotics in the sediments of the Yellow River, Hai River and Liao River in northern China.

The occurrence of four classes of 17 commonly used antibiotics (including fluoroquinolones, tetracycline, sulfonamides, and macrolides) was investigated in the sediments of the Yellow River, Hai River and Liao River in northern China by using rapid resolution liquid chromatography-tandem mass spectrometry. Higher concentrations were detected for most antibiotics in the sediments of the Hai River than in the sediments of the other rivers. Norfloxacin, ofloxacin, ciprofloxacin and oxytetracycline in the three rivers were most frequently detected with concentrations up to 5770, 1290, 653 and 652 ng/g, respectively. High frequencies and concentrations of the detected antibiotics were often found in the downstream of large cities and areas influenced by feedlot and fish ponds. Good fitted linear regression equations between antibiotic concentration and sediment physicochemical properties (TOC, texture and pH) were also found, indicating that sediment properties are important factors influencing the distribution of antibiotics in the sediment of rivers.

Spatial and seasonal distribution of selected antibiotics in surface waters of the Pearl Rivers, China.

The distribution and occurrence of 15 antibiotics in surface water of the Pearl River System (Liuxi River, Shijing River and Zhujiang River) and effluents of four wastewater treatment plants (WWTPs) were investigated in two sampling events representing wet season and dry season by using rapid resolution liquid chromatography-electrospray tandem mass spectrometry (RRLC-MS/MS) in positive ionization mode. Only eight antibiotics (sulfadiazine, sulfapyridine, sulfamethazine, sulfamethoxazole, trimethoprim, roxithromycin, erythromycin-H2O and norfloxacin) were detected in the water samples of the three rivers and the effluents. The detection frequencies and levels of antibiotics in the dry season were higher than those in the wet season. This could be attributed to the dilution effects in the wet season and relatively lower temperature in the dry season under which antibiotics could persist for a longer period. The levels of the detected antibiotics in different sites are generally in a decreasing order as follows: Shijing River ≥WWTP effluent ≥Zhujiang River ≥ Liuxi River. Risk assessment based on the calculated risk quotients showed that only erythromycin-H2O and roxithromycin detected in the Pearl Rivers might have adverse effects on aquatic organisms.

Rapid resolution liquid chromatography-tandem mass spectrometry method for the determination of endocrine disrupting chemicals (EDCs), pharmaceuticals and personal care products (PPCPs) in wastewater irrigated soils.

A multiresidue analytical method was developed for the determination of 9 endocrine disrupting chemicals (EDCs) and 19 pharmaceuticals and personal care products (PPCPs) including acidic and neutral pharmaceuticals in water and soil samples using rapid resolution liquid chromatography-tandem mass spectrometry (RRLC-MS/MS). Solid phase extraction (SPE), and ultrasonic extraction combined with silica gel purification were applied as pretreatment methods for water and soil samples, respectively. The extracts of the EDCs and PPCPs in water and soil samples were then analyzed by RRLC-MS/MS in electrospray ionization (ESI) mode in three independent runs. The chromatographic mobile phases consisted of Milli-Q water and acetonitrile for EDCs and neutral pharmaceuticals, and Milli-Q water containing 0.01 % acetic acid (v/v) and acetonitrile: methanol (1:1, v/v) for acidic pharmaceuticals at a flow rate of 0.3 mL/min. Most of the target compounds exhibited signal suppression due to matrix effects. Measures taken to reduce matrix effects included use of isotope-labeled internal standards, and application of matrix-match calibration curves in the RRLC-MS/MS analyses. The limits of quantitation ranged between 0.15 and 14.08 ng/L for water samples and between 0.06 and 10.64 ng/g for solid samples. The recoveries for the target analytes ranged from 62 to 208 % in water samples and 43 to 177 % in solid samples, with majority of the target compounds having recoveries ranging between 70­120 %. Precision, expressed as the relative standard deviation (RSD), was obtained less than 7.6 and 20.5 % for repeatability and reproducibility, respectively. The established method was successfully applied to the water and soil samples from four irrigated plots in Guangzhou. Six compounds namely bisphenol-A, 4-nonylphenol, triclosan, triclocarban, salicylic acid and clofibric acid were detected in the soils.

Occurrence and a screening-level risk assessment of human pharmaceuticals in the Pearl River system, South China.

Ten nonsteroidal antiinflammatory drugs (NSAIDs), two blood lipid regulators (BLRs), and two antiepileptic drugs (AEDs) were analyzed in the Pearl River system in China (i.e., Liuxi, Zhujiang, and Shijing Rivers) and four sewage effluents during the dry and wet seasons, and the environmental risks they posed were assessed. Eight pharmaceuticals were detected in the rivers and effluents, including five NSAIDs (salicylic acid, ibuprofen, diclofenac, mefenamic acid, and naproxen), two BLRs (clofibric acid and gemfibrozil), and one AED (carbamazepine). The median concentrations for the eight pharmaceuticals ranged from 11.2 to 102 ng/L. Seasonal variations were not obvious for most pharmaceuticals in the three rivers, except for salicylic acid and clofibric acid in the Zhujiang River, and diclofenac in the Zhujiang and Shijing Rivers. However, spatially considerable variations in the concentrations were observed for the eight pharmaceuticals in all three rivers. For most of the pharmaceuticals, the effluents from the four wastewater treatment plants and Shijing River water were found to be the major discharge sources for the Zhujiang River, but with additional discharge sources from some small urban streams in the wet season. Diclofenac in the Shijing River was the only pharmaceutical that had a risk quotient (RQ) >1, indicating a high risk to aquatic organisms in the river. Although higher RQs were calculated for the mixture of the pharmaceuticals in each river, the risk rating remained the same for the three rivers with the RQ being >1 only in Shijing River.

Simultaneous determination of four classes of antibiotics in sediments of the Pearl Rivers using RRLC-MS/MS.

A simultaneous extraction and analysis method was developed for four classes of antibiotics: sulfonamides (SAs), macrolides (MLs), fluoroquinolones (FQs) and tetracyclines (TCs) in sediment. The antibiotics in the sediment were extracted by using an optimized mixed solution (citric buffer: acetonitrile, 50:50 v/v), and analyzed by rapid resolution liquid chromatography-tandem mass spectrometry (RRLC-MS/MS) equipped with electrospray ionization source in the positive mode. The recoveries for the antibiotics in the spiked sediment were: 66.3-123.5%, 48.2-72.0%, 61.8-160.4% and 60.6-151.9% for the SAs, TCs, FQs and MLs, respectively. The LOD ranged from 0.08 microg/kg to 4.2 microg/kg and LOQ from 0.26 microg/kg (erythromycin-H(2)O) to 14.01 microg/kg (norfloxacin). The developed analytical method was applied in the determination of the antibiotics in sediment samples collected from the Pearl Rivers, China. The antibiotics were found at the levels of microg/kg in the sediments of the three rivers. Ofloxacin was found to have the highest concentration of 1560 microg/kg in sediment. However, no significant seasonal variation could be found for the antibiotics in the sediments between wet season and dry season.

Occurrence and risks of triclosan and triclocarban in the Pearl River system, South China: from source to the receiving environment.

We investigated two commonly used antimicrobial agents triclosan (TCS) and triclocarban (TCC) in the Pearl River system in China (i.e., Liuxi, Zhujiang and Shijing Rivers) and four sewage effluents during dry and wet seasons. The median values for TCS and TCC were the highest in the surface water and sediments of the Shijing River, followed by the Zhujiang River and Liuxi River. Screening level risk assessment using the risk quotient (RQ) method showed that TCS and TCC in surface water posed median risks in the Zhujiang and Liuxi Rivers (RQs: 0.28-0.62 for TCS, and 0.15-0.80 for TCC) and high risks in the Shijing River (RQs: 5.15-9.55 for TCS, and 3.32-5.83 for TCC). Higher risks (RQs: 3.63-28.47 for TCS, and 3.13-24.54 for TCC) were found in the sediments than in surface water of the Pearl River system. The four sewage effluents and Shijing River as well as other urban streams in Guangzhou metropolitan area were identified as the sources of the two compounds in the main river Zhujiang River. The mass inventories of TCS and TCC in the Pearl River system indicate that the sediments are not only an important sink but also a potential source for the two compounds in surface water.

Dissipation of oxytetracycline in soils under different redox conditions.

This study investigated the dissipation kinetics of oxytetracycline in soils under aerobic and anoxic conditions. Laboratory experiments showed that the dissipation of oxytetracycline in soil followed first-order reaction kinetics and its dissipation rates decreased with increasing concentration. Oxytetracycline dissipated faster in soil under aerobic conditions than under anoxic conditions. The half-lives for oxytetracycline in soil under aerobic conditions ranged between 29 and 56 days for non-sterile treatments and 99-120 days for sterile treatments, while under anoxic conditions the half-lives of oxytetracycline ranged between 43 and 62 days in the non-sterile soil and between 69 and 104 days in the sterile soil. This suggests microbes can degrade oxytetracycline in agricultural soil. Abiotic factors such as strong sorption onto soil components also played a role in the dissipation of oxytetracycline in soil.

Degradation behavior of sulfadiazine in soils under different conditions.

This study investigated the degradation of sulfadiazine in three soils and also determined its sorption and hydrolysis behaviors as well. At the spike concentration of 10 mg/kg, the half-lives for sulfadiazine in the aerobic nonsterile soils ranged from 12 days to 18 days. Sulfadiazine was more persistent in the anoxic soils with the half-lives ranging between 57 days and 237 days and soil microorganisms played little role in the dissipation process under anoxic conditions. The decline in sulfadiazine concentrations was also observed in the sterile soils under aerobic conditions. Hydrolysis could not explain this phenomena as hydrolysis of sulfadiazine was pH dependent. Sulfadiazine only hydrolyzed to a very limited degree at acidic pH. Increased sorption was observed for sulfadiazine in soil 1 (pH 4.3) when the contact time increased to 14 days, but no significant increase in sorption was found for soil 2 (pH 7.2) and soil 3 (pH 8.5).

Effects of six selected antibiotics on plant growth and soil microbial and enzymatic activities.

The potential impact of six antibiotics (chlortetracycline, tetracycline and tylosin; sulfamethoxazole, sulfamethazine and trimethoprim) on plant growth and soil quality was studied by using seed germination test on filter paper and plant growth test in soil, soil respiration and phosphatase activity tests. The phytotoxic effects varied between the antibiotics and between plant species (sweet oat, rice and cucumber). Rice was most sensitive to sulfamethoxazole with the EC10 value of 0.1 mg/L. The antibiotics tested inhibited soil phosphatase activity during the 22 days' incubation. Significant effects on soil respiration were found for the two sulfonamides (sulfamethoxazole and sulfamethazine) and trimethoprim, whereas little effects were observed for the two tetracyclines and tylosin. The effective concentrations (EC10 values) for soil respiration in the first 2 days were 7 mg/kg for sulfamethoxazole, 13 mg/kg for sulfamethazine and 20 mg/kg for trimethoprim. Antibiotic residues in manure and soils may affect soil microbial and enzyme activities.

Determination of phenolic endocrine disrupting chemicals and acidic pharmaceuticals in surface water of the Pearl Rivers in South China by gas chromatography-negative chemical ionization-mass spectrometry.

An analytical method for phenolic endocrine disrupting chemicals and acidic pharmaceuticals in river water was developed using gas chromatography mass spectrometry (GC-MS) coupled with negative chemical ionization (NCI) technique, and used for the determination of these compounds in the Pearl Rivers (Liuxi, Zhujiang and Shijing Rivers). Derivatization using pentafluorobenzoyl chloride (PFBOCl) and pentafluorobenzyl bromide (PFBBr) before GC-MS analysis were applied and optimized for phenolic compounds and acidic compounds, respectively. The target compounds were analyzed for river waters from the upstream to downstream of the Pearl Rivers. Phenolic compounds 4-tert-octylphenol (4-t-OP), 4-nonylphenol (4-NP), bisphenol-A (BPA), estrone (E1), estradiol (E2) and triclosan (TCS) were detected at trace or low levels in the water samples from Liuxi River and Zhujiang River. Diethylstilbestrol (DES) was not detected in the Pearl Rivers. The highest concentrations of the phenolic compounds were found in Shijing River, and they were 3150 ng/L for 4-t-OP, 11,300 ng/L for 4-NP, 1040 ng/L for BPA, 79 ng/L for E1, 7.7 ng/L for E2 and 355 ng/L for TCS, respectively. Only a few acidic pharmaceuticals were detected at low concentrations in water from Liuxi River and Zhujiang River, but the highest concentrations for the acidic pharmaceuticals were also found in Shijing River. The highest concentrations detected for clofibric acid, ibuprofen, gemfibrozil, naproxen, mefenamic acid and diclofenac were 17 ng/L, 685 ng/L, 19.8 ng/L, 125 ng/L, 24.6 ng/l and 150 ng/L, respectively. The results suggest Liuxi and Zhujiang Rivers are only slightly contaminated and can be used as drinking water sources, but Shijing River is heavily polluted by the wastewater from nearby towns.