基于ceRNA网络识别登革热诊断标志物

通过比较登革热患者和健康人群转录组数据,识别差异基因,构建失调ceRNA网络,筛选关键基因富集分析,解析潜在生物学功能,助力登革热诊断标志物的研究。从GEO数据库下载登革热外周血芯片数据,识别差异基因并进行富集分析。结合miRNA-mRNA互作数据,利用超几何算法和皮尔森相关性计算方法识别登革热失调ceRNA互作对,使用Cytoscape软件可视化ceRNA网络与模块挖掘,对网络模块进行功能富集及外部数据验证表达模式。筛选出251个差异基因,发现其富集在细胞周期等生物学通路中。经外部数据验证,网络模块基因的表达趋势与训练集数据大致相同,表明模块基因在登革热疾病中的潜在诊断效能。本研究可为确定有效的疾病诊断分子标志物提供思路。     

THE EFFECTS OF SOME ECOLOGICAL FACTORS ON CELL SIZE OF THE HOT SPRING ALGA SYNECHOCOCCUS LIVIDUS (CYANOPHYTA)1

Algae were sampled along temperature gradients of 30 thermal springs in Colorado, Idaho, Montana and Wyoming. From a maximum temperature of 74.5 C downstream, to ca. 62 C, the diversity of the algae was limited to the various forms of Synechococcus lividus Copeland; from ca. 62 to 40–45 C it coexisted with other algae. When S. lividus was in direct sunlight the mean length was greatest at the highest temperatures of its existence, becoming shorter as the water cooled; the mean reduction in length was 0.132 μm for each 1 C reduction in temperature. The cells in a shaded stream did not exhibit the reduction in size with reduced temperature, but remained about the same length from 73 C downstream to 45 C. The longer cells from the highest temperatures of their existence in any stream could not become established in the cooler water downstream, so the range of cell lengths (diversity) became less as the water cooled. Unknown dissolved substance(s) depressed the upper temperature limit in two streams and had a reverse effect on the expected length–temperature relationship; the shortest cells were at the higher temperatures. Generally, total dissolved substances had a positive effect on the length; the longest cells were in the water with the highest total dissolved solids (TDS) at the upper temperature limits of 70–74.5 C. In the temperature range of 55–60 C the higher TDS were not as effective in developing longer cells.     

Review of the Potential Environmental and Human Health–Related Hazards and Risks from Long-Term Exposure to p-tert-Octylphenol

Para-tert-octylphenol (OP) is an important chemical intermediate mainly used for production of phenolic resins and lacquers. OP has weak estrogen-like activity in vitro, with induction of vitellogenin in fish hepatocytes and competitive estrogen receptor binding and estrogen-responsive gene expression in mammalian systems. Induction of vitellogenin in fish plasma and liver, in vivo, has also been measured and weak estrogen-like activity in rodent screening assays occurs but at much lower potency than predicted by the in vitro activity. Conventional aquatic wildlife toxicity testing shows effects on survival, growth and development, and reproduction occurring at concentrations lower than the estrogen-like responses predicted from screening assays. Studies in rodents have provided evidence of metabolic saturation at high doses of OP, and a multigeneration reproductive study confirms the lack of estrogen-like activity below this metabolic saturation as well as the lack of reproductive toxicity. This article reviews the weight of evidence for the aquatic and mammalian data and compares the results of the definitive assays to those of the screening tests. The results show that the estrogen-like activity in screening tests is not predictive of results from definitive testing, and that risk assessment decisions should be made using conventional toxicity endpoints.     

The Structure of a New Piperidine Derivative from Buckwheat Seeds (Fagopyrum esculentum Moench)

Streptomyces hygroscopicus No. B–5050-HA, which produces a mixture of six maridomycins, yielded a mutant which produced 75% of the mixture as maridomycin III (MDM III).

Growth of S. hygroscopicus No. B–5050-HA, an improved MDM producer, was almost completely inhibited by 20 µg/ml of valine. This inhibition was counteracted by the addition of isoleucine, threonine, homoserine, methionine, α-amino-n-butyrate and α-ketobutyrate.

A valine resistant mutant, strain AV was isolated and found to produce increased level of MDM III at the expense of other maridomycins. Production of MDM III by the parent strain depended on the addition of isoleucine to the medium, but that by this mutant did not.

The properties of strain AV were discussed.     

Characterisation of a Tunisian coastal lagoon through hyperspectral underwater irradiance

North African coastal lagoons are unique ecosystems that often suffer degradation due to human activities. Therefore, monitoring methods are required to identify stressors and assist with the management of these valuable and often understudied ecosystems. A synthetic indicator of water ecological quality would be desirable for regular monitoring of these ecosystems under pressure. In 2008 an optical procedure was developed and applied in Ghar El Melh, a Tunisian lagoon which has been increasingly impacted by pollutant loading, especially from agriculture. In situ hyperspectral irradiance was measured at several stations, from which the apparent optical properties (AOPs), namely the irradiance attenuation coefficient K(λ) and the reflectance ratio R(λ), were obtained in order to relate them to water composition, in terms of light-attenuating substances (LASs). The significant relationships observed between R and LAS values enabled the application of a hyperspectral optical classification, which effectively highlighted threatened sectors of the lagoon. The pattern of differing water quality across the lagoon system that was derived from the hyperspectral classification agreed well with that obtained from a conventional optical classification that included AOPs and LASs. We suggest that hyperspectral analysis and classification is a useful monitoring tool for the assessment of change in coastal lagoons, and perhaps also in other shallow-water ecosystems.     

Transformation of humic acids by two-domain laccase from Streptomyces anulatus

The properties of two-domain laccase of Streptomyces anulatus (SaSL) and its role in transformation of humic acids (HA) from chernozem, sod-podzolic soil and peat at alkaline pH values were studied. The SaSL was cloned, expressed in E. coli and obtained in an electrophoretically homogeneous state. SaSL is an oligomeric protein with a molecular weight of 235-300 kDa and six or eight subunits in the molecule. The molecular weight of the subunit is 37.7 kDa. Its catalytic properties are similar to those of the previously described two-domain laccase. The enzyme catalyzed oxidation of electron donors (K₄[Fe(CN)₆], ABTS) at acidic pH and phenolic substrates (2-methoxyphenol, 2,6-dimethixyphenol) at alkaline pH values. The efficiency of catalysis was higher in the case of electron donors than phenolic substrates. The enzyme showed a high thermal stability and was more stable at neutral and alkaline pH values. The enzyme effectively transformed humic acids at alkaline pH values. It was found that polymerization reactions took place during interaction of SaSL with HA, as well as with their high-molecular weight (>80 kDa) and low-molecular weight (<5 kDa) fractions. Our results suggest a possible involvement of the two-domaim laccases in humification processes in alkaline soils.     

Bioflocculation in natural and engineered systems: current perspectives

Microorganisms have the tendency to accumulate at interfaces through the release of extracellular polymeric substances to form aggregates such as films or flocs. This physical association leads to different modes of interactions among cells and the subsequent development of functionally and metabolically diverse consortia. Aggregation of cells in aqueous suspensions often results in the formation of flocs, which are hotspots of enhanced microbial processes. This has important implications for the dynamics of organic and inorganic matter in varied ecosystems. These microbial flocs are not only important components in nutrient turnover, decomposition, and sinking flux but also facilitate contaminant removal and treatment of wastewater and biomass harvesting. Greater insight into the multitude of interactions between microorganisms in flocs would be useful to enhance the efficiency of bioflocculation processes. This review covers the fundamental aspects and outlines the role of bioflocculation in controlled industrial processes and in nature.     

Long noncoding RNA HOXA-AS2 regulates the expression of SCN3A by sponging miR-106a in breast cancer

Breast cancer is the most commonly diagnosed cancer that affects women worldwide. This study aimed to investigate the competing endogenous RNAs (ceRNAs) mechanism in breast cancer. Microarray data were downloaded from the University of California Santa Cruz (UCSC) Xena database. The limma package was used to screen the differentially expressed messenger RNAs (DEMs) and differentially expressed long noncoding RNAs (DELs). Subsequently, functional analysis was performed using DAVID tool. After constructing the protein-protein interaction (PPI) network, we identified the major gene modules using the Cytoscape software. Univariate survival analysis in the survival package was performed. Finally, the ceRNA regulatory network was constructed to identify the critical genes. A total of 1380 DEMs and 345 DELs were identified in breast cancer samples compared with normal samples. Functional enrichment analysis showed that DEMs were mainly involved in cell division, and cell cycle. We screened four major gene modules and identified the hub nodes in these functional modules. Several DEMs (including FABP7, C4BPA, and LAMB3) and three long noncoding RNAs (lncRNAs) (LINC00092, SLC26A4.AS1, and COLCA1) exhibited significant correlation with patients' survival outcomes. In the ceRNA network, the lncRNA HOXA-AS2 regulated the expression level of SCN3A by interacting with hsa-miR-106a-5p. Thus, our study investigated the ceRNA mechanism in breast cancer. The results showed that lncRNA HOXA-AS2 might modulate the expression of SCN3A by sponging miR-106a in breast cancer.