Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.     

Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges

The biosynthesis of non-ribosomal peptide and polyketide natural products is facilitated by multimodular enzymes that contain domains responsible for the sequential condensation of amino and carboxylic subunits. These conserved domains provide molecular targets for the discovery of natural products from microbial metagenomes. This study demonstrates the application of tag-encoded FLX amplicon pyrosequencing (TEFAP) targeting non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes as a method for determining the identity and diversity of natural product biosynthesis genes. To validate this approach, we assessed the diversity of NRPS and PKS genes within the microbiomes of six Australian marine sponge species using both TEFAP and metagenomic whole-genome shotgun sequencing approaches. The TEFAP approach identified 100 novel ketosynthase (KS) domain sequences and 400 novel condensation domain sequences within the microbiomes of the six sponges. The diversity of KS domains within the microbiome of a single sponge species Scopalina sp. exceeded that of any previously surveyed marine sponge. Furthermore, this study represented the first to target the condensation domain from NRPS biosynthesis and resulted in the identification of a novel condensation domain lineage. This study highlights the untapped potential of Australian marine sponges for the isolation of novel bioactive natural products. Furthermore, this study demonstrates that TEFAP approaches can be applied to functional genes, involved in natural product biosynthesis, as a tool to aid natural product discovery. It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites.     

The PathoChip,a functional gene array for assessing pathogenic properties of diverse microbial communities

Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.     

Jagged-1/Notch3 signaling transduction pathway is involved in apelin-13-induced vascular smooth muscle cells proliferation

The apelin/apelin receptor （APJ, apelin-angiotensin receptor-like 1） system is a newly deorphanized G protein- coupled receptor system. Both apelin and APJ that are important regulatory factors are expressed in the cardio- vascular system. Our previous studies demonstrated that apelin-13 significantly stimulated vascular smooth muscle cell （VSMC） proliferation. In this paper, our data sug- gested that the Jagged-l/Notch3 signaling transduction pathway is involved in apelin-13-induced VSMC prolifer- ation by promoting the expression of Cyclin D1. Results indicated that apelin-13 stimulates the proliferation of VSMC and the expression of Jagged-1 and Notch3 in con- centration- and time-dependent manners. The increased expression of Jagged-1 and Notch3 induced by apelin-13 could be abolished by extracellular signal-regulated protein kinase （ERK） blockade. PD98059 （ERK inhibitor） can inhibit the activation of Jagged-I/Notch3 induced by apelin- 13. Down-regulation of Notch3 using small interfering RNA inhibits the expression of Cyclin DI and prevents apelin- 13-induced VSMC proliferation. In conclusion, Jagged-I/ Notch3 signaling transduction pathway is involved in VSMC proliferation induced by apelin-13.     

Quantitative analysis of site-specific N-glycans on sera haptoglobin βchain in liver diseases

The site-specific characterization of N-glycans in glycopro- teins with the potential of clinical application is important. In our previous report, the overall N-glycans of sera haptoglobin （Hp） β chain were found to be different in liver diseases. Hp β chain contains four potential sites of N-glycosylation. In this study, we investigated the potential change of N-glycans on Hp β chain in a site-specific fashion. Sera Hp β chain in healthy individuals as well as patients with hepatitis B virus （HBV）, liver cirrhosis （LC） and hepatocellular carcinoma （HCC） were purified, digested and subjected to liquid chromatography-electro- spray ionization-higher energy collision dissociation mass spectrometry, which allowed identification and structure determination of the glycopeptide, as well as the relative quantification of glycans present on each glycopeptide. The quantitative results revealed that the sialylation of NLFLN207HSEN211 ATAK and the fucosylated structure at all glycopeptides increased significantly in LC and HCC patients compared with those in HBV patients and healthy individuals. A set of different N-glycan patterns of Hp β chain in various liver diseases has been determined. Thus, the sialylated and fucosylated glycoforms of Hp β chain might be related to early hepatocarcinogenesis and also might be useful as novel differential markers for LC and HCC patients.     

Potential antitumor mechanisms of phenothiazine drugs

In this study, three kinds of phenothiazine drugs were analyzed to explore their potential antitumor mechanisms. First, target proteins that could interact with chlorpromazine, fluphenazine and trifluoperazine were predicted. Then, the target proteins of the three drugs were intersected. Cell signaling pathway enrichment and related disease enrichment were conducted for the intersected proteins to extract the enrichment categories associated with tumors. By regulation network analysis of the protein interactions, the mechanisms of action of these target proteins in tumor tissue were clarified, thus confirming the potential antitumor mechanisms of the phenothiazine drugs. The final results of cell signaling pathway enrichment and related disease enrichment showed that the categories with the highest score were all found in tumors. Target proteins belonging to the tumor category included signaling pathway members such as Wnt, MAPK and retinoic acid receptor. Moreover, another target protein, MAPK8, could indirectly act on target proteins CDK2, IGF1R, GSK3B, RARA, FGFR2 and MAPK10, thereby affecting tumor cell division and proliferation. Therefore, phenothiazine drugs may have potential antitumor effects, and tumor-associated target proteins play important roles in the process of cell signaling transduction cascades.     

Duck egg drop syndrome virus: an emerging Tembusu-related flavivirus in China

Duck egg drop syndrome virus(DEDSV) is a newly emerging pathogenic flavivirus isolated from ducks in China.DEDSV infection mainly results in severe egg drop syndrome in domestic poultry,which leads to huge economic losses.Thus,the discovery of ways and means to combat DEDSV is urgent.Since 2010,a remarkable amount of progress concerning DEDSV research has been achieved.Here,we review current knowledge on the epidemiology,symptomatology,and pathology of DEDSV.A detailed dissection of the viral genome and polyprotein sequences,comparative analysis of viral antigenicity and the corresponding potential immunity against the virus are also summarized.Current findings indicate that DEDSV should be a distinct species from Tembusu virus.Moreover,the adaption of DEDSV in wildlife and its high homology to pathogenic flaviviruses(e.g.,West Nile virus,Japanese encephalitis virus,and dengue virus),illustrate its reemergence and potential to become a zoonotic pathogen that should not be overlooked.Detailed insight into the antigenicity and corresponding immunity against the virus is of clear significance for the development of vaccines and antiviral drugs specific for DEDSV.     

Spatio-temporal changes in biomass carbon sinks in China’s forests from 1977 to 2008

Forests play a leading role in regional and global carbon (C) cycles. Detailed assessment of the temporal and spatial changes in C sinks/sources of China’s forests is critical to the estimation of the national C budget and can help to constitute sustainable forest management policies for climate change. In this study, we explored the spatio-temporal changes in forest biomass C stocks in China between 1977 and 2008, using six periods of the national forest inventory data. According to the definition of the forest inventory, China’s forest was categorized into three groups: forest stand, economic forest, and bamboo forest. We estimated forest biomass C stocks for each inventory period by using continuous biomass expansion factor (BEF) method for forest stands, and the mean biomass density method for economic and bamboo forests. As a result, China’s forests have accumulated biomass C (i.e., biomass C sink) of 1896 Tg (1 Tg=10¹² g) during the study period, with 1710, 108 and 78 Tg C in forest stands, and economic and bamboo forests, respectively. Annual forest biomass C sink was 70.2 Tg C a^?1, offsetting 7.8% of the contemporary fossil CO₂ emissions in the country. The results also showed that planted forests have functioned as a persistent C sink, sequestrating 818 Tg C and accounting for 47.8% of total C sink in forest stands, and that the old-, mid- and young-aged forests have sequestrated 930, 391 and 388 Tg C from 1977 to 2008. Our results suggest that China’s forests have a big potential as biomass C sink in the future because of its large area of planted forests with young-aged growth and low C density.     

Optimization of fermentation medium for xylanase-producing strain Xw2

To improve the fermentation yield of xylanase by optimizing the fermentation conditions for strain Xw2, a Plackett-Burman design was used to evaluate the effects of eight variables on xylanase production by strain Xw2. The steepest ascent （descent） method was used to approach the optimal response surface experimental area. The optimal fermentation conditions were obtained by central composite design and response surface analysis. The results showed that the composition of the optimal fermentation medium was corn cob ＋ 1.5% wheat bran （1：1）, 0.04% MnSO4, 0.04% K2HPO4. 3H2O, and an inoculum size of 6% in 50 mL liquid volume （pH = 6.0）. The optimal culture conditions were 28oc at 150 r/min for 54.23 h. The results of this study can serve as the basis for the industrial production and application of xylanase.