Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms

Genomic Characterization Provides New Insights Into the Biosynthesis of the Secondary Metabolite Huperzine a in the Endophyte Colletotrichum gloeosporioides Cg01

A reliable source of Huperzine A (HupA) meets an urgent need due to its wide use in Alzheimer's disease treatment. In this study, we sequenced and characterized the whole genomes of two HupA-producing endophytes, Penicillium polonicum hy4 and Colletotrichum gloeosporioides Cg01, to clarify the mechanism of HupA biosynthesis. The whole genomes of hy4 and Cg01 were 33.92 and 55.77 Mb, respectively. We compared the differentially expressed genes (DEGs) between the induced group (with added extracts of Huperzia serrata) and a control group. We focused on DEGs with similar expression patterns in hy4 and Cg01. The DEGs identified in GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were primarily located in carbon and nitrogen metabolism and nucleolus, ribosome, and rRNA processing. Furthermore, we analyzed the gene expression for HupA biosynthesis genes proposed in plants, which include lysine decarboxylase (LDC), copper amine oxidase (CAO), polyketides synthases (PKS), etc. Two LDCs, one CAO, and three PKSs in Cg01 were selected as prime candidates for further validation. We found that single candidate biosynthesis-gene knock-out did not influence the HupA production, while both LDC gene knock-out led to increased HupA production. These results reveal that HupA biosynthesis in endophytes might differ from that proposed in plants, and imply that the HupA-biosynthesis genes in endophytic fungi might co-evolve with the plant machinery rather than being acquired through horizontal gene transfer (HGT). Moreover, we analyzed the function of the differentially expressed epigenetic modification genes. HupA production of the histone acetyltransferase (HAT) deletion mutant ΔCgSAS-2 was not changed, while that of the histone methyltransferase (HMT) and histone deacetylase (HDAC) deletion mutants ΔCgClr4, ΔCgClr3, and ΔCgSir2-6 was reduced. Recovery of HupA-biosynthetic ability can be achieved by retro-complementation, demonstrating that HMT and HDACs associated with histone modification are involved in the regulation of HupA biosynthesis in endophytic fungi. This is the first report on epigenetic modification in high value secondary metabolite- producing endophytes. These findings shed new light on HupA biosynthesis and regulation in HupA-producing endophytes and are crucial for industrial production of HupA from fungi

Full-length single-cell RNA-seq applied to a viral human cancer:applications to HPV expression and splicing analysis in HeLa S3 cells

Background: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied HeLa is a well characterized HPV+ cervical cancer cell line Result: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins Conclusion: Our results reveal the heterogeneity of a virus-infected cell line It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers

Biosynthesis of Gold Nanoparticles by Foliar Broths: Roles of Biocompounds and Other Attributes of the Extracts

Biosynthesis of nanoparticles has arisen as a promising alternative to conventional synthetic methodologies owing to its eco-friendly advantages, and the involved bioprotocol still needs further clarification. This research, for the first time from the standpoint of statistics, confirmed an electrostatic force or ionic bond-based interaction between the chloroauric ions and the involved bioconstituents and manifested that reducing sugars and flavonoids were both important reductants responsible for conversion of Au(III) to Au(0). The result also demonstrated that the proteins were not the reducing agents, yet they might be protection agents in biosynthesis of gold nanoparticles (GNPs). Besides, a significant linear relationship was found between the anti-oxidant ability of the foliar broths and their capability to reduce Au(III) into Au(0). Furthermore, the preliminary investigation based on the boxplot on the size/shape distribution of the biosynthesized GNPs revealed that gold nanospheres with higher degree of homogeneity in size tended to be promoted by foliar broths containing higher content of reducing sugars/flavonoids and proteins. Otherwise, i.e., for those broths with lower content of the above biocompounds, sphere GNPs of wider size distribution or even gold nanotriangles tended to be fabricated

DV-Hop Node Location Algorithm Based on GSO in Wireless Sensor Networks

Node location is one of the most important problems to be solved in practical application of WSN. As a typical location algorithm without ranging, DV-Hop is widely used in node localization of wireless sensor networks. However, in the third phase of DV-Hop, a least square method is used to solve the nonlinear equations. Using this method to locate the unknown nodes will produce large coordinate errors, poor stability of positioning accuracy, low location coverage, and high energy consumption. An improved localization algorithm based on hybrid chaotic strategy (MGDV-Hop) is proposed in this paper. Firstly, a glowworm swarm optimization of hybrid chaotic strategy based on chaotic mutation and chaotic inertial weight updating (MC-GSO) is proposed. The MC-GSO algorithm is used to control the moving distance of each firefly by chaos mutation and chaotic inertial weight when the firefly falls into a local optimum. The experimental results show that MC-GSO has better convergence and higher accuracy and avoids the premature convergence. Then, MC-GSO is used to replace the least square method in estimating node coordinates to solve the problem that the localization accuracy of the DV-Hop algorithm is not high. By establishing the error fitness function, the linear solution of coordinates is transformed into a two-dimensional combinatorial optimization problem. The simulation results and analysis confirm that the improved algorithm (MGDV-Hop) reduces the average location error, increases the location coverage, and decreases and balances the energy consumption as compared to DV-Hop and the location algorithm based on classical GSO (GSDV-Hop)

Experimental Investigation of Relationship between Infiltration Rate and Soil Moisture under Rainfall Conditions

In this study, a mathematical expression describing the relationship between infiltration rate and soil moisture content was deduced based on the Horton equation in order to study the relationship between infiltration rate and soil moisture content during the rainfall infiltration process. Specific experimental data on infiltration processes were used to verify the validity of the equations and to analyze the main factors affecting the infiltration rate. The results indicate the following: (1) The experimental data demonstrated a high degree of accuracy. The volumetric error of soil moisture increase and cumulative infiltration was 3.5% and the coefficient of determination (R2) was 0.87 in the 42 tests. (2) The equation obtained in this paper can well describe the relationship between infiltration rate and soil moisture content; the R2 of the fitted results was greater than 0.80 in more than 80% of the experiments. (3) The relationship between infiltration rate and soil moisture content is mainly influenced by initial soil moisture content; the higher the initial soil moisture content, the lower the initial infiltration rate, the faster the infiltration rate decreases with soil moisture content, and the lower the “relative stable infiltration rate” in the process of infiltration