Global gene expression profiling of blast lung injury of goats exposed to shock wave.

PURPOSE: Blast lung injury (BLI) is the most common damage resulted from explosion-derived shock wave in military, terrorism and industrial accidents. However, the molecular mechanisms underlying BLI induced by shock wave are still unclear. METHODS: In this study, a goat BLI model was established by a fuel air explosive power. The key genes involved in were identified. The goats of the experimental group were fixed on the edge of the explosion cloud, while the goats of the control group were 3 km far away from the explosive environment. After successful modeling for 24 h, all the goats were sacrificed and the lung tissue was harvested for histopathological observation and RNA sequencing. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis were performed to identify the main enriched biological functions of differentially expressed genes (DEGs). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the consistency of gene expression. RESULTS: Of the sampled goat lungs, 895 genes were identified to be significantly differentially expressed, and they were involved in 52 significantly enriched GO categories. KEGG analysis revealed that DEGs were highly enriched in 26 pathways, such as cytokine-cytokine receptor interaction, antifolate resistance, arachidonic acid metabolism, amoebiasis and bile secretion, JAK-STAT, and IL-17 signaling pathway. Furthermore, 15 key DEGs involved in the biological processes of BLI were confirmed by qRT-PCR, and the results were consistent with RNA sequencing. CONCLUSION: Gene expression profiling provide a better understanding of the molecular mechanisms of BLI, which will help to set strategy for treating lung injury and preventing secondary lung injury induced by shock wave.

Genome-wide identification and characterization of genes encoding cyclohexylamine degradation in a novel cyclohexylamine-degrading bacterial strain of Pseudomonas plecoglossicida NyZ12.

The Gram-negative strain of Pseudomonas plecoglossicida NyZ12 isolated from soil has the ability to degrade cyclohexylamine (CHAM). The genes encoding CHAM degradation by gram-negative bacteria, however, have not been reported previously. In this study, ORFs predicted to encode CHAM degradation by NyZ12 were identified by bioinformatics analysis. Differential expression of the proposed ORFs was analyzed via RNA-seq and quantitative reverse transcription-PCR (qRT-PCR), using RNA extracted from NyZ12 cultured with or without CHAM addition. One CHAM-inducible ORF, RK21_02867 predicted to encode a cyclohexanone monooxygenase (ChnB) was disrupted, as were five ORFs, RK21_00425, RK21_02631, RK21_04207, RK21_04637 and RK21_05539, that had weak homology to the only known cyclohexylamine oxidase (CHAO encoded by chaA) found in Brevibacterium oxydans IH-35A. We also found that a tandem array of five ORFs (RK21_02866-02870) shared homology with those in an operon responsible for oxidation of cyclohexanone to adipic acid, although the ORFs in strain NyZ12 were arranged in a different order with previously found in cyclohexane, cyclohexanol or cyclohexanone degradation strains. The ORFs in this cluster were all up-regulated when CHAM was supplied as the sole carbon source. When one of these five genes, RK21_02867 encoding cyclohexanone (CHnone) monooxygenase, was knocked out, NyZ12 could not grow on CHAM, but it accumulated equimolar amounts of CHnone. Our results show that strain NyZ12 metabolized CHAM directly to CHnone which was then further metabolized to adipate. Despite clearly identifying genes encoding the steps for metabolism of CHAM metabolites, not every one of the putative chaAs was differentially expressed in the presence of CHAM and deletion of each one individually did not completely eliminate the capacity of NyZ12 to degrade CHAM, though it did reduce its growth in several instances. Our results suggest that there is genetic redundancy encoding the initial step in the oxidation of CHAM to CHnone in NyZ12 and that its CHAOs differ considerably from the ChaA, originally described in Brevibacterium oxydans IH-35A.

Complete genome sequence of the cyclohexylamine-degrading Pseudomonas plecoglossicida NyZ12.

Pseudomonas plecoglossicida NyZ12 (CCTCC AB 2015057), a Gram-negative bacterium isolated from soil, has the ability to degrade cyclohexylamine. The complete genome sequence of this strain (6,233,254bp of chromosome length) is presented, with information about the genes of characteristic enzymes responsible for cyclohexylamine oxidation to cyclohexanone and the integrated gene cluster for the metabolic pathway of cyclohexanone oxidation to adipate.

Biodegradation of hexachlorobenzene by a constructed microbial consortium.

A consortium comprised of an engineered Escherichia coli DH5α and a natural pentachlorophenol (PCP) degrader, Sphingobium chlorophenolicum ATCC 39723, was assembled for degradation of hexachlorobenzene (HCB), a persistent organic pollutant. The engineered E. coli strain, harbouring a gene cassette (camA (+) camB (+) camC) that encodes the F87W/Y96F/L244A/V247L mutant of cytochrome P-450cam (CYP101), oxidised HCB to PCP. The resulting PCP was then further completely degraded by ATCC 39723. The results showed that almost 40 % of 4 µM HCB was degraded by the consortium at a rate of 0.033 nmol/mg (dry weight)/h over 24 h, accompanied by transient accumulation and immediate consumption of the intermediate PCP, detected by gas chromatography. In contrast, in the consortium comprised of Pseudomonas putida PaW340 harbouring camA (+) camB (+) camC and ATCC 39723, PCP accumulated in PaW340 cells but could not be further degraded, which may be due to a permeability barrier of Pseudomonas PaW340 for PCP transportation. The strategy of bacterial co-culture may provide an alternative approach for the bioremediation of HCB contamination.