The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficient nutrient uptake and detoxification, and genes for a flexible respiration system including an aerobic branch comprising five terminal oxidases and an anaerobic branch comprising a complete denitrification pathway for quick response to dissolved oxygen fluctuation. The identification of a nitrous oxide reductase gene has not been previously described in Gram-positive bacteria. The proteome further reveals the presence of a long-chain alkane degradation pathway; and the function of the key enzyme in the pathway, the long-chain alkane monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oil pollutions and biosynthesis of complex molecules.adaptation ͉ degradation ͉ monooxygenase

Recent reports highlight the impact of copper on lactate metabolism: CHO cell cultures with higher initial copper levels shift to net lactate consumption and yield lower final lactate and higher titers. These studies investigated the effects of copper on metabolite and transcript profiles, but did not measure in detail the dependences of cell culture performance and product quality on copper concentrations. To more thoroughly map these dependences, we explored the effects of various copper treatments on four recombinant CHO cell lines. In the first cell line, when extracellular copper remained above the limit of detection (LOD), cultures shifted to net lactate consumption and yielded comparable performances irrespective of the differences in copper levels; when extracellular copper dropped below LOD (∼13 nM), cultures failed to shift to net lactate consumption, and yielded significantly lower product titers. Across the four cell lines, the ability to grow and consume lactate seemed to depend on the presence of a minimum level of copper, beyond which there were no further gains in culture performance. Although this minimum cellular copper requirement could not be directly quantified, we estimated its probable range for the first cell line by applying several assumptions. Even when different copper concentrations did not affect cell culture performance, they affected product quality profiles: higher initial copper concentrations increased the basic variants in the recombinant IgG1 products. Therefore, in optimizing chemically defined media, it is important to select a copper concentration that is adequate and achieves desired product quality attributes.

A thermophilic Bacillus strain NG80-2 growing within the temperature range of 45-73 degrees C (optimum at 65 degrees C) was isolated from a deep subterranean oil-reservoir in northern China. The strain was able to utilize crude oil and liquid paraffin as the sole carbon sources for growth, and the growth with crude oil was accompanied by the production of an unknown emulsifying agent. Further examination showed that NG80-2 degraded and utilized only long-chain (C15-C36) n-alkanes, but not short-chain (C8-C14) n-alkanes and those longer than C40. Based on phenotypic and phylogenic analyses, NG80-2 was identified as Geobacillus thermodenitrificans. The strain NG80-2 may be potentially used for oily-waste treatment at elevated temperature, a condition which greatly accelerates the biodegradation rate, and for microbial enhancing oil recovery process.

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Banana is a key staple food and fruit in countries all over the world. However, the development of the global banana industry is seriously threatened by Fusarium wilt disease, which is caused by Fusarium oxysporum f. sp. cubense (Foc). In particular, Foc tropical race 4 (Foc TR4) could infect more than 80% of global banana and plantain crops. Until now, there were no commercial chemicals or resistant cultivars available to control the disease. Biological control using actinomycetes is considered a promising strategy. In this study, 88 actinomycetes were isolated from a banana orchard without symptoms of Fusarium wilt disease for more than 10 years. An actinobacterial strain labeled as JBS5-6 has exhibited strong antifungal activities against Foc TR4 and other selected 10 phytopathogenic fungi. Based on phenotypic and biochemical traits as well as complete genome analysis, strain JBS5-6 was assigned to Streptomyces violaceusniger. Extracts of the strain inhibited the mycelial growth and spore germination of Foc TR4 by destroying membrane integrity and the ultrastructure of cells. The complete genome of strain JBS5-6 was sequenced and revealed a number of key function gene clusters that contribute to the biosynthesis of active secondary metabolites. Sixteen chemical compounds were further identified by gas chromatography-mass spectrometry (GC-MS). 5-hydroxymethyl-2-furancarboxaldehyde was one of the dominant components in strain JBS5-6 extracts. Moreover, fermentation broth of strain JBS5-6 significantly reduced the disease index of banana seedlings by inhibiting the infection of Foc TR4 in a pot experiment. Hence, strain JBS5-6 is a potential biocontrol agent for the management of disease and the exploitation of biofertilizer.

cDuck tembusu virus (DTMUV) is an emerging agent that causes a severe disease in ducks. We report herein the first complete genome sequences of duck tembusu virus strains YY5, ZJ-407, and GH-2, isolated from Shaoxing ducks, breeder ducks, and geese, respectively, in China. The genomes of YY5, ZJ-407, and GH-2 are all 10,990 nucleotides (nt) in length and encode a putative polyprotein of 3,426 amino acids. It is flanked by a 5= and a 3= noncoding region (NCR) of 94 and 618 nt, respectively. Knowledge of the whole sequence of DTMUV will be useful for further studies of the mechanisms of virus replication and pathogenesis. In 2010, a novel infectious agent emerged in China and caused extensive epidemics in egg-laying and breeder ducks. The affected ducks showed a severe drop in egg production and paralysis. We isolated the causative agent, a virus, from affected ducks and determined the partial genome sequence. All of Koch's postulates were fulfilled, including duck trials. The isolated virus is considered to belong to a new genotype of tembusu virus (TMUV) and was designated duck TMUV (DTMUV) (1).To date, the complete genome sequence of DTMUV has not been reported. To provide more information about DTMUV, we determined the entire genome sequences of two duck-origin isolates (YY5 and ZJ-407) and a goose-origin isolate (GH-2).The 5= and 3= ends of the genomes were amplified using 5= and 3= rapid amplification of cDNA ends (RACE) strategies (5). Based on partial genomic sequences obtained (1), the remainder of the sequences were generated by five overlapping cDNA fragments covering each of the entire genomes and were sequenced using an Applied Biosystems (ABI) 3730xl DNA analyzer. Overlapping consensus sequences were assembled using the SeqMan II programs to generate contiguous full-genome sequences.The complete genomes of the three DTMUV strains are 10,990 nucleotides (nt) in length, with an open reading frame (ORF) extending from nt 95 to 10,278 that encodes a putative polyprotein of 3,426 amino acids (aa). Aligning the sequence of the polyprotein with those of other mosquito-borne flaviviruses, we observed the highest aa similarity with those of Bagaza virus (BAGV; 82%), St. Louis encephalitis virus (SLEV; 66%), Ilheus virus (ILHV; 63.7%), West Nile virus (WNV; 63.4%), and Japanese encephalitis virus (JEV; 63.3%). Like that of other mosquitoborne flaviviruses, the polyprotein of DTMUV is processed into three structural proteins and seven nonstructural proteins by the viral or host cell proteases.We analyzed the secondary structures and cyclization between the 5= and 3= noncoding regions (NCRs) of DTMUV the mfold program of Zuker et al. (6). The predicted results showed that the folding pattern of the three DTMUVs was similar to those of other mosquito-borne flaviviruses (2, 3, 4). The organization of conserved sequences (CS) of 3= NCRs is RCS3-CS3-RCS2-CS2-CS1 for DTMUV, which is the same as that of the JEV subgroup but different from that of Ntaya subgroup members BAGV and ILHV, in which there is no RCS2 or RCS3,...

Duck reovirus (DRV) is an typical aquatic bird pathogen belonging to the Orthoreovirus genus of the Reoviridae family. Reovirus causes huge economic losses to the duck industry. Although DRV has been identified and isolated long ago, the responses of Cairna moschata to classical/novel duck reovirus (CDRV/NDRV) infections are largely unknown. To investigate the relationship of pathogenesis and immune response, proteomes of C. moschata liver cells under the C/NDRV infections were analyzed, respectively. In total, 5571 proteins were identified, among which 5015 proteins were quantified. The differential expressed proteins (DEPs) between the control and infected liver cells displayed diverse biological functions and subcellular localizations. Among the DEPs, most of the metabolism-related proteins were down-regulated, suggesting a decrease in the basal metabolisms under C/NDRV infections. Several important factors in the complement, coagulation and fibrinolytic systems were significantly up-regulated by the C/NDRV infections, indicating that the serine protease-mediated innate immune system might play roles in the responses to the C/NDRV infections. Moreover, a number of molecular chaperones were identified, and no significantly changes in their abundances were observed in the liver cells. Our data may give a comprehensive resource for investigating the regulation mechanism involved in the responses of C. moschata to the C/NDRV infections.