Identification and Validation of Inflammatory Response-Related Gene Signatures to Predict the Prognosis of Neuroblastoma.

Background: Neuroblastoma (NB) is the third most common malignant tumor in children. The inflammation is believed to be closely related to NB patients' prognosis. However, there is no comprehensive research to study the role of inflammatory response-related gene (IRRG) in NB patients. Methods: We downloaded the gene expression profiles of NB patients from GEO and TARGET database, and the expression of 200 IRRGs was extracted. Then, we performed differentially analysis between INSS stage 4 and INSS stage 4S NB patients. The univariate and multivariate Cox regression analyses were performed to screen out the overall survival- (OS-) and event-free survival- (EFS-) related IRRGs in GSE49710, and two signatures were constructed; both signatures were evaluated by Kaplan-Meier (K-M) survival curve and receiver operating characteristic (ROC) curve. Finally, the TARGET cohort was used to validate IRRG signatures, and the independence of the prognostic IRRG signatures was evaluated by integrating clinical information. Results: We screened out 10 OS-related IRRGs and 11 EFS-related IRRGs. Then, we identified that OS- and EFS-related IRRG signatures and found that the OS and EFS of NB patients in the low-risk group were significantly superior than those in the high-risk group (both P value < 0.0001). The AUC values of 3-, 5-, and 7-year OS are 0.910, 0.933, and 0.921, respectively, and 3-, 5-, and 7-year EFS are 0.840, 0.835, and 0.837, respectively. In addition, we found that both IRRG signatures can be used as independent prognostic indicators for patients with NB. Both IRRG signatures still have good predictive ability in validation cohort. Conclusions: We constructed and validated two prognostic gene signatures based on IRRGs. Our study helped us to better understand the role of inflammation in NB and provided new insights for the prognosis assessment and treatment strategy for NB patients.

Novel pathway and acetate-facilitated complete atenolol degradation by Hydrogenophaga sp. YM1 isolated from activated sludge.

Atenolol is a widely prescribed beta-blocker that has been detected in wastewater at concentrations up to 300 µg/L. The parent compound and its transformation products pose risks to aquatic organisms. Efficient atenolol degrading microorganism has yet to be identified, and its biodegradation pathway is unknown. In this study, Hydrogenophaga sp. YM1 isolated from activated sludge can degrade atenolol efficiently (286.1 ± 4.0 µg/g dry wt/h in actual wastewater), where atenolol acid, and four newly detected products (4-hydroxyphenylacetic acid, 3-(isopropylamino)-1,2-propanediol, 3-amino-1,2-propanediol and 4-(1-amino-2-hydroxy-3-propoxy) benzeneacetic acid) were the main intermediates. Key genes involved in atenolol degradation were proposed based on RNA-seq and validated by RT-qPCR. The ether bond cleavage of atenolol acid was the rate-limiting step likely catalyzed by the α-ketoglutarate dependent 2,4-dichlorophenoxyacetate dioxygenase. The further degradation of 4-hydroxyphenylacetic acid followed the homoprotocatechuate degradation pathway, enabling complete conversion to CO2. Acetate addition (39-156 mg COD/L) under aerobic condition enhanced atenolol degradation by 29-37% and decreased the accumulation of atenolol acid, likely because acetate oxidation provided α-ketoglutarate and additional reducing power. Activated sludge core microorganisms have limited atenolol mineralization potentials. Enriching Hydrogenophaga-like populations and/or providing such as acetate can drive more complete conversion of atenolol in natural and engineered biosystems.

Genetic characterization and modification of a bioethanol-producing yeast strain.

Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem.

In this study, time-series samples were taken from a gravel beach to ascertain whether a periodic oil input induced by tidal action at the early stage of an oil spill can be a trigger to stimulate the development of hydrocarbon-degrading bacteria under natural in situ attenuation. High-throughput sequencing shows that the microbial community in beach sediments is characterized by the enrichment of hydrocarbon-degrading bacteria, including Alcanivorax, Dietzia, and Marinobacter. Accompanying the periodic floating-oil input, dynamic successions of microbial communities and corresponding fluctuations in functional genes (alkB and RDH) are clearly indicated in a time sequence, which keeps pace with the ongoing biodegradation of the spilled oil. The microbial succession that accompanies tidal action could benefit from the enhanced exchange of oxygen and nutrients; however, regular inputs of floating oil can be a trigger to stimulate an in situ "seed bank" of hydrocarbon-degrading bacteria. This leads to the continued blooming of hydrocarbon-degrading consortia in beach ecosystems. The results provide new insights into the beach microbial community structure and function in response to oil spills.

Trehalose promotes Rhodococcus sp. strain YYL colonization in activated sludge under tetrahydrofuran (THF) stress.

Few studies have focused on the role of compatible solutes in changing the microbial community structure in bioaugmentation systems. In this study, we investigated the influence of trehalose as a biostimulant on the microbial community in tetrahydrofuran (THF)-treated wastewater bioaugmentation systems with Rhodococcus sp. YYL. Functional gene profile changes were used to study the variation in the microbial community. Soluble di-iron monooxygenases (SDIMO), particularly group-5 SDIMOs (i.e., tetrahydrofuran and propane monooxygenases), play a significant role in the initiation of the ring cleavage of tetrahydrofuran. Group-5 SDIMOs genes are enriched upon trehalose addition, and exogenous tetrahydrofuran monooxygenase (thmA) genes can successfully colonize bioaugmentation systems. Cytochrome P450 monooxygenases (P450s) have a significant role in catalyzing the region- and stereospecific oxidation of non-activated hydrocarbons, and THF was reported to inhibit P450s in the environment. The CYP153 family was chosen as a representative P450 to study the inhibitory effects of THF. The results demonstrated that CYP153 family genes exhibited significant changes upon THF treatment and that trehalose helped maintain a rich diversity and high abundance of CYP153 family genes. Biostimulation with trehalose could alleviate the negative effects of THF stress on microbial diversity in bioaugmentation systems. Our results indicated that trehalose as a compatible solute plays a significant role for environmental strains under extreme conditions.

Effect of Pseudomonas sp. HF-1 inoculum on construction of a bioaugmented system for tobacco wastewater treatment: analysis from quorum sensing.

To better construct a bioaugmented system for tobacco wastewater treatment, activated sludge was inoculated with different concentrations of the nicotine-degrading bacterium Pseudomonas sp. HF-1. The results showed that inoculum concentrations of 0.55 ± 0.01 and 1.10 ± 0.03 mg/g (dry weight of strain HF-1/dry weight of activated sludge) were best to ensure strain HF-1 survival and successful bioaugmentation. The release pattern of autoinducer (AI) for quorum sensing in the bioaugmented system was also investigated. During the period of HF-1 inoculation, compared with failed bioaugmented systems, AI-2 was significantly increased in the successful systems, suggesting that AI-2-mediated bacterial communication played an important role in the colonization of HF-1. When inoculation of strain HF-1 was stopped, the amount of AI-2 decreased and leveled out in all systems. Notably, there was a greater than threefold increase of short-chain AHLs in failed bioaugmented systems, but no increase in successful ones, implying that the fluctuation of short-chain AHLs could be an indicator of the failure of bioaugmentation. Thus, AI-2-mediated quorum sensing could be implemented to facilitate HF-1 colonization.

Bioaugmentation of activated sludge with Acinetobacter sp. TW enhances nicotine degradation in a synthetic tobacco wastewater treatment system.

Bioaugmentation (BA) using Acinetobacter sp. TW with high nicotine-degrading efficiency was applied in a bioreactor receiving a load of COD (3,200 ± 50 mg/L) and nicotine (1.0 ± 0.1g/L). The results showed that because of the colonization of strain TW, the COD removal was stable at 80-90%, while nicotine removal reached 98% in the BA system. Furthermore, according to PCR-DGGE fingerprinting, compared with the originally activated sludge, more bacteria existed in the BA systems while some bacteria disappeared from the non-BA system. In terms of the quorum sensing, short chain AHLs increased to assist colonization of strain TW, and long chain AHLs were secreted and helped to resist the nicotine toxicity. Compared with the non-BA system, the amounts of ROS, protein carbonyls and 8-OHdG were significant lower in the BA systems, which suggested that strain TW played an important role in eliminating the nicotine toxicity from the bioreactors.

Optimization of Fenton process for decoloration and COD removal in tobacco wastewater and toxicological evaluation of the effluent.

Decoloration and chemical oxygen demand (COD) removal in tobacco wastewater by Fenton process has been optimized under 25 +/- 2 degrees C. The results showed that the optimal range of conditions were pH 4.13-4.66, Fe(2+) 0.29-0.34 g/L and H2O2 > or = 2.73 g/L. Within this range, up to 95% of colour and 90% of COD was removed. In an enlarged system, setting the optimal conditions as pH 4.50, Fe(2+) 0.34 g/L and H2O2 4.00 g/L, the colour removal rate was 96.03 +/- 2.57%, with COD removal rate of 93.30 +/- 2.92%. The residual COD of 73.67 +/- 19.70 mg/L in effluent had hit the State's first-class standard for the industrial discharge in China (< 100 mg/L COD, GB8978-1996). The ecological safety of Fenton process has also been evaluated. When reaction completed, the content of hydroxyl free radical (OH) was 3.26 +/- 0.44 mg/L. There was no inhibition of Fenton effluent in growth of Escherichia coli, Pseudomonas putida, Pseudomonas sp. HF-1, Acinetobacter sp. TW and Sphingomonas sp. TY. No oxidative stress was induced on strain HF-1 by Fenton effluent. Thus, Fenton process was one of high-efficiency and ecologically safe strategy for tobacco wastewater advanced treatment.

Bioaugmentation with the nicotine-degrading bacterium Pseudomonas sp. HF-1 in a sequencing batch reactor treating tobacco wastewater: degradation study and analysis of its mechanisms.

The highly effective nicotine-degrading bacterium Pseudomonas sp. HF-1 was augmented in an SBR system that is used to treat tobacco wastewater. Compared to the non-bioaugmented (non-BA) system, the bioaugmented (BA) system exhibited considerably stronger pollution disposal abilities, with 100% nicotine degradation and more than 84% chemical oxygen demand (COD) removal within 12h. Nicotine degradation had a significant effect on COD removal in SBRs (r=0.928, p<0.01). The mechanisms of bioaugmentation were systematically investigated using a combination of polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and a toxicity assay (protein carbonyl (PC) and DNA-protein crosslinking (DPC)). DGGE fingerprint profiles showed that the number of bands and the Shannon-Wiener index decreased at a nicotine load of 250mg/L compared to a 40-130mg/L nicotine load in the non-BA system. However, a stepwise increase in the Shannon-Wiener index was found during all periods in the BA system. A comparison of sequences excised from DGGE gels demonstrated significant differences in the dominant microbial species between the two SBRs. This result suggested that bioaugmentation of strain HF-1 could select cooperators for treating complicated tobacco wastewater. The PC content and the DPC coefficient increased significantly at levels higher than 80mg/L in the non-BA system; nevertheless, no increase was observed in the BA system during the stepwise nicotine load. This indicated that bioaugmentation of strain HF-1 resulted in the maintenance of high treatment activity by minimizing the nicotine toxicity for other microbes in the BA system. In conclusion, the rapid nicotine degradation of strain HF-1 performed a vital function in SBR by influencing the microbial community structure, dynamics and activity of the activated sludge system.

A novel nicotine catabolic plasmid pMH1 in Pseudomonas sp. strain HF-1.

Attempts were made to acquire a plasmid-loss mutant via various methods (spontaneous mutation, SDS, and mitomycin C), among which the method involving mitomycin C (10 microg/mL) has been proven successful. Concomitant with the loss of the plasmid in Pseudomonas sp. strain HF-1, the cured derivative was identified as having a nicotine-negative (Nic-) phenotype, named mutant strain 6-13 (Nic-). After plasmids were transferred from strain HF-1 (named plasmid pMH1) to the mutant strain 6-13, the mutant strain acquired nicotine-degrading ability, called 6-13 transformant (Nic+). There were no differences in growth or nicotine-degrading efficiency between strain HF-1 (wild-type strain) and strain 6-13 transformant. After pMH1 was transferred to Escherichia coli strain Top10 (Nic-), a distant relative of Pseudomonas, it also gained nicotine-degrading ability, showing the highest nicotine degradation efficiency at pH 7.0, the optimal pH for growth of E. coli. The hsp gene, which encodes 6-hydroxy-3-succinoylpyridine hydroxylase, is involved in nicotine degradation in Pseudomonas putida strain S16 and was present in pMH1 but not in pAO1, the well-known nicotine degradation plasmid in Arthrobacter nicotinovorans. It was demonstrated that plasmid pMH1 is a novel nicotine-degrading plasmid.

Antimicrobial activity of isolate HL-12 against Clavibacter michiganensis subsp. michiganensis in the presence of cadmium.

An actinomycete, strain HL-12, that was isolated from a farmland on the Huajiachi campus of Zhejiang University was capable of inhibiting the growth of Clavibacter michiganensis subsp. michiganensis (Cmm) and was identified as a member of Streptomyces. Its antimicrobial activity against Cmm was measured using the agar plate sensitivity method in pure culture and evaluated by the inhibition ratio of Cmm in soil. The inhibitory activity of strain HL-12 against Cmm following exposure to low concentrations of Cd was greater than the inhibitory activity following exposure to high concentrations of Cd both in liquid culture and in soil. A stronger inhibition was also seen following a 24 h preculture in the presence of Cd in liquid culture. The growth of Cmm in soil was stimulated at low concentrations of Cd (<5.0 mg Cd kg(-1) dry soil) but inhibited when cultured in high concentrations of Cd (5.0 and 10.0 mg Cd kg(-1) dry soil). A higher inhibition ratio of strain HL-12 against Cmm, which was over 40% after soil incubation for 2 weeks, was observed following exposure to low concentrations of Cd (<5.0 mg Cd kg(-1) dry soil).

Isolation, identification and characterization of a novel Rhodococcus sp. strain in biodegradation of tetrahydrofuran and its medium optimization using sequential statistics-based experimental designs.

Statistics-based experimental designs were applied to optimize the culture conditions for tetrahydrofuran (THF) degradation by a newly isolated Rhodococcus sp. YYL that tolerates high THF concentrations. Single factor experiments were undertaken for determining the optimum range of each of four factors (initial pH and concentrations of K(2)HPO(4).3H(2)O, NH(4)Cl and yeast extract) and these factors were subsequently optimized using the response surface methodology. The Plackett-Burman design was used to identify three trace elements (Mg(2+), Zn(2+)and Fe(2+)) that significantly increased the THF degradation rate. The optimum conditions were found to be: 1.80 g/L NH(4)Cl, 0.81 g/L K(2)HPO(4).3H(2)O, 0.06 g/L yeast extract, 0.40 g/L MgSO(4).7H(2)O, 0.006 g/L ZnSO(4).7H(2)O, 0.024 g/L FeSO(4).7H(2)O, and an initial pH of 8.26. Under these optimized conditions, the maximum THF degradation rate increased to 137.60 mg THF h(-1) g dry weight in Rhodococcus sp. YYL, which was nearly five times of that by the previously described THF degrading Rhodococcus strain.

MTH1745, a protein disulfide isomerase-like protein from thermophilic archaea, Methanothermobacter thermoautotrophicum involving in stress response.

MTH1745 is a putative protein disulfide isomerase characterized with 151 amino acid residues and a CPAC active-site from the anaerobic archaea Methanothermobacter thermoautotrophicum. The potential functions of MTH1745 are not clear. In the present study, we show a crucial role of MTH1745 in protecting cells against stress which may be related to its functions as a disulfide isomerase and its chaperone properties. Using real-time polymerase chain reaction analyses, the level of MTH1745 messenger RNA (mRNA) in the thermophilic archaea M. thermoautotrophicum was found to be stress-induced in that it was significantly higher under low (50 degrees C) and high (70 degrees C) growth temperatures than under the optimal growth temperature for the organism (65 degrees C). Additionally, the expression of MTH1745 mRNA was up-regulated by cold shock (4 degrees C). Furthermore, the survival of MTH1745 expressing Escherichia coli cells was markedly higher than that of control cells in response to heat shock (51.0 degrees C). These results indicated that MTH1745 plays an important role in the resistance of stress. By assay of enzyme activities in vitro, MTH1745 also exhibited a chaperone function by promoting the functional folding of citrate synthase after thermodenaturation. On the other hand, MTH1745 was also shown to function as a disulfide isomerase on the refolding of denatured and reduced ribonuclease A. On the basis of its single thioredoxin domain, function as a disulfide isomerase, and its chaperone activity, we suggest that MTH1745 may be an ancient protein disulfide isomerase. These studies may provide clues to the understanding of the function of protein disulfide isomerase in archaea.

Dynamic changes of microbial community diversity in a photohydrogen producing reactor monitored by PCR-DGGE.

A PCR-DGGE (denaturing gradient gel electrophoresis of polymerase chain reaction) protocol was used for monitoring the dynamic changes in the microbial population during photohydrogen production. Total DNA was extracted directly from the mixed bacterial community in the reactor and subjected to PCR with V3-16S rDNA and pufM gene primers, and the amplifications were then analyzed by DGGE. The DGGE patterns demonstrated the dynamics of community structure and the shift of microbial diversity, which corresponded to different running periods of the reactor. The optimal hydrogen producing community formed on day 10. Using DGGE analysis with the pufM gene fragments was superior to V3-16S rDNA region genes for detecting the dynamic variations of the photosynthetic bacteria population during hydrogen production. The comparative sequence analysis of excised DGGE bands showed the relationship between specific population structures and system performance. Rhodopseudomonas palustris was presumed as one of the dominant community members for hydrogen production in the reactor. The PCR-DGGE protocol was proven to be a good tool for monitoring the photohydrogen production in real time and offered the available information to improve the photohydrogen producing system.

Effect of tetrahydrofuran on enzyme activities in activated sludge.

Tetrahydrofuran is an important solvent with wide usage in industry and laboratory research work. However, little information was known about the influence and fate of tetrahydrofuran (THF) in the environments. Several attempts have failed to enrich microorganisms in activated sludge to degrade THF. Effects of THF on the activities of dehydrogenase, protease, phosphatase, urease and catalase in activated sludge were investigated in this paper. The activated sludge was taken from the secondary sedimentation pool in the Sibao sewage treatment plant in Hangzhou China for observation of enzyme activities variation at the existence of tetrahydrofuran. The results obtained showed that tetrahydrofuran at over the range of selected concentrations could completely inhibit dehydrogenase activity during period of incubation, in the contrary, not to the protease activity, and strongly affected the phosphatase, urease and catalase activities which declined with increasing of tetrahydrofuran concentration. EC(10), EC(50), and EC(90) of tetrahydrofuran on phosphatase, urease and catalase activities was calculated according to the equation obtained from regression model of dose-effect curve. Realizing the effect of THF on the enzymatic diversity in activated sludge can help us to understand the influence and fate of tetrahydrofuran in the environments, and help us to enrich THF-degrading pure isolates or activated sludge.

Response of superoxide dismutase, catalase, and ATPase activity in bacteria exposed to acetamiprid.

OBJECTIVE: To investigate how acetamiprid, a new insecticide, affects the activity of superoxide dismutase (SOD), catalase (CAT), and ATPase and the SOD isozyme patterns in two G bacteria, E. coli K12 and Pse.FH2, and one G+ bacterum, B. subtilis. METHODS: The SOD, CAT, and ATPase specific activities of cell lysates were determined spectrophotometrically at 550 nm, 240 nm, and 660 nm, respectively, with kits A001, A016, and A007. SOD isozyme patterns were detected by native PAGE analysis. RESULTS: SOD and CAT activities in the tested bacteria increased significantly in a concentration-dependent manner after different concentrations of acetamiprid were applied. The activity of SOD in B. subtilis and Pse.FH2 was stimulated and reached the highest level after treatment with 100 mg/L acetamiprid for 0.5 h. For Pse.FH2, there was another stimulation of SOD activity after acetamiprid application for about 8.0 h and the second stimulation was stronger than the first. The stimulation by acetamiprid showed a relative lag for E. coli K12. Acetamiprid seemed to exhibit a similar effect on CAT activity of the two G bacteria and had an evident influence on ATPase activity in the three bacteria within a relatively short period. Only one SOD isozyme was detectable in Pse.FH2 and B. subtilis, while different isozyme compositions in E. coli could be detected by native PAGE analysis. CONCLUSION: Acetamiprid causes a certain oxidative stress on the three bacteria which may not only elevate SOD and CAT activities but also generate new SOD isozymes to antagonize oxidative stress. However, this oxidative stress lasts for a relatively short time and does not cause a long-term damage.

Isolation and characterization of phenanthrene-degrading Sphingomonas paucimobilis strain ZX4.

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2,3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type metapathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.