Systematic identification and characterization of miRNAs and piRNAs from porcine testes

microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) execute important regulatory roles in testis development and spermatogenesis, while previous studies mainly focus on the expression profiles in immature and mature porcine testes, which may cause a bottleneck for further understanding their complex physiological processes in porcine testes development and spermatogenesis. Thus, we presented the expression and characterization of miRNAs and piRNAs in DS (60-day-old), DN (90-day-old), DT (120-day-old) and DF (150-day-old) pig testes. In total, 12,834,628, 13,359,726, 12,851,249 and 12,938,601 clean reads were generated from these libraries, respectively. 293 mature and 36 novel miRNAs as well as 4923 piRNA clusters were identified from pig testes, and they showed an age-dependent manner. GO enrichment analysis of miRNA target genes and piRNA generated genes showed that they participated widely in regulating the pig spermatogenesis process. In addition, 12 differentially expressed miRNAs were randomly selected to validate using qRT-PCR. Our results provided novel comprehensive expression profiles of miRNAs and piRNAs in pig testes at different stages of sexual maturity, which will promote our knowledge of them in regulating the pig testes development and spermatogenesis process.     

Continuous treatment with recombinant Mycobacterium tuberculosis CFP-10-ESAT-6 protein activated human monocyte while deactivated LPS-stimulated macrophage

Influence of the recombinant culture filtered protein 10 (CFP-10) and early-secreted antigenic target 6kDa protein (ESAT-6) (r-CFP-10-ESAT-6, rCE) of Mycobacterium tuberculosis (Mtb) on human monocyte and macrophage activation was investigated using human monocyte, monocyte like THP-1 cell line and monocyte derived macrophage (MDM). rCE solely enhanced TNF-alpha release from human monocytes and THP-1 cells in a dose- and time-dependent manner. rCE enhanced expression of CD80 and CD40, it also synergized with IFN-gamma in induction of TNF-alpha production and HLA-DR expression. Pharmacological agents that selectively inhibit mitogen activated protein kinase activation markedly suppressed rCE-induced TNF- alpha release. However, continuous presence of rCE (>72h) during monocyte to macrophage differentiation inhibited macrophage response to LPS stimulation. Collectively, these data suggest that rCE might have differential influence on monocyte and macrophage activation, which might be correlated with Mtb immune evasion.     

转Bt + CpTI基因棉花对根际土壤细菌及氨氧化细菌数量的影响

摘要:转基因棉花对根际土壤微生物的影响在转基因作物风险评估中具有重要意义。【目的】通过研究转基因棉花根际微生物群落变化来评估转基因棉花的生态风险。【方法】以转Bt + CpTI基因抗虫棉(SGK321)及非转基因亲本棉花石远321(SY321)根际土壤总细菌和氨氧化细菌为研究对象,分别在种植前和棉花的不同生长时期(蕾期、花期、铃期和絮期)取样。采用微滴数码PCR方法对土壤中总细菌16S rRNA和氨氧化细菌的功能基因amoA基因进行定量分析。【结果】结果发现两种棉花根际土壤中的总细菌数量随棉花生长的不同时期没有显著差异。但是对氨氧化细菌的定量结果表明随棉花不同生长时期,两种棉花根际土壤中的氨氧化细菌数量均发生显著变化,但变化趋势不同:在蕾期,SY321和SGK321根际土壤中的氨氧化细菌数量分别增加了4倍和2倍;在花期,SY321根际氨氧化细菌与蕾期相比显著降低至5.96×105 copies/g dry soil,而SGK321根际氨氧化细菌则显著增加至1.25×106 copies/g dry soil;在铃期,SY321根际氨氧化细菌显著增加至1.49×106 copies/g dry soil,而SGK321根际土壤中氨氧化细菌数量没有发生显著变化;絮期两者均表现为降低,但差异显著。与非转基因棉花相比,转基因棉花根际土壤中的氨氧化细菌变化相对较为平缓。【结论】这表明氨氧化细菌数量既受棉花生长时期的影响,同时也受转基因棉花的影响,转基因棉花通过影响氨氧化细菌的数量减缓氨的转化速度,这在一定程度上有利于植物生长。     

SRC-1 and Twist1 Expression Positively Correlates with a Poor Prognosis in Human Breast Cancer

To evaluate the possible prognostic value of Steroid Receptor Coactivator-1 (SRC-1) and Twist1 expression in human breast cancer, we examined SRC-1 and Twist1 expression using immunohistochemistry on tissue microarray sections containing 137 breast cancer specimens. All patients were followed up for a median of 5 years following surgery. Survival curves were generated using the Kaplan-Meier method. Multivariate analysis was performed using the Cox proportional hazard regression model to assess the prognostic values. The results showed a positive correlation between SRC-1 and Twist1 expression at protein levels (P < 0.001). Also, SRC-1 expression positively correlated with HER2 expression (P = 0.024). The protein expression of Twist1 positively associated with lymph node metastasis (P < 0.001), but inversely correlated with PR status (P = 0.041). Patients with SRC-1 or Twist1-positive expression exhibited poorer overall survival (OS) and disease-free survival (DFS) than did those with SRC-1 or Twist1-negative expression (P < 0.05 for all). In addition, SRC-1-negativeive/Twist1-negative patients had the best OS and DFS (P < 0.01 for both). In multivariate survival analysis, SRC-1 expression, tumor stage, and PR were found to be independent prognostic factors related to OS (P = 0.019, < 0.001 and 0.02, respectively) and Twist1 expression, lymph node status and PR were independent predictors of DFS (P = 0.006, 0.001 and 0.029, respectively). These results suggest that a combined SRC-1/Twist1 expression status could improve the prognostic judgment for breast cancer patients.     

Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants,as revealed by analysis of the extensins super-gene family

Background

All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.

Results

The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.

Conclusions

Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-612) contains supplementary material, which is available to authorized users.     

Effect of Brominated Furanones on the Formation of Biofilm by Escherichia coli on Polyvinyl Chloride Materials

To study the influence of brominated furanones on the biofilm (BF) formation by Escherichia coli (E. coli) on polyvinyl chloride (PVC) material, and to provide new ways of surface modification of materials to clinically prevent biomaterial centered infection. Three brominated furanones, dissolved in ethanol, furanone-1(3,4-dibromo-5-hydroxyl-furanone), furanone-2(4-bromo-5-(4-methoxypheny)-3-(methylamino)-furanone), and furanone-3(3,4-dibromo-5,5-dimethoxypheny-2(5H)-furanone) with representative chemical structure, were coated on the surfaces of separate PVC materials (1 × 1 cm), respectively. The surface-modified PVC materials were incubated with E. coli and for controls, 75 % ethanol-treated PVC materials were used. This treatment played as control group. The cultivation incubations were for 6, 12, 18, and 24 h. The thickness of bacterial BF and bacterial community quantity unit area on the PVC materials was determined by confocal laser scanning microscopy (CLSM), and the surface structure of bacterial BF formation was examined by scanning electron microscopy (SEM). The results of CLSM indicated the thickness of bacterial BF and bacterial community quantity unit area on PVC materials treated with furanone-3 were significantly lower than that of control at all time points (P < 0.05), whereas, the differences between furanone-1 and furanone-2 groups and control group were not significantly different (P > 0.05). The results of SEM indicated that after 6 h incubation, the quantity of bacterial attachment to the surface of PVC material treated with furanone-3 was lower than the control group. By 18 h incubation there was completely formed BF structure on the surface of control PVC material. However, there was no significant BF formation on the surface of PVC material treated with furanone-3. The impact of different brominated furanones on SA biofilm formation on the surface of PVC materials are different, furanone-3 can inhibit E. coli biofilm formation on the surface of PVC material.     

Activation of Notch pathway is linked with epithelial-mesenchymal transition in prostate cancer cells

Notch signaling has been reported to play an essential role in tumorigenesis. Several studies have suggested that Notch receptors could be oncoproteins or tumor suppressors in different types of human cancers. Emerging evidence has suggested that Notch pathway regulates cell growth, apoptosis, cell cycle, and metastasis. In the current study, we explore whether Notch-1 could regulate the cell invasion and migration as well as EMT (epithelial-mesenchymal transition) in prostate cancer cells. We found that overexpression of Notch-1 enhanced cell migration and invasion in PC-3 cells. However, downregulation of Notch-1 retarded cell migration and invasion in prostate cancer cells. Importantly, we observed that overexpression of Notch-1 led to EMT in PC-3 cells. Notably, we found that EMT-type cells are associated with EMT markers change and cancer stem cell phenotype. Taken together, we concluded that downregulation of Notch-1 could be a promising approach for inhibition of invasion in prostate cancer cells, which could be useful for the treatment of metastatic prostate cancer.     

Biosynthesis of the regulatory oxysterol, 5-cholesten-3beta,25-diol 3-sulfate, in hepatocytes

Cellular cholesterol homeostasis is maintained through coordinated regulation of cholesterol synthesis, degradation, and secretion. Nuclear receptors for oxygenated cholesterol derivatives (oxysterols) are known to play key roles in the regulation of cholesterol homeostasis. We recently identified a sulfated oxysterol, 5-cholesten-3beta,25-diol 3-sulfate (25HC3S), that is localized to liver nuclei. The present study reports a biosynthetic pathway for 25HC3S in hepatocytes. Assays using mitochondria isolated from rats and sterol 27-hydroxylase (Cyp27A1) gene knockout mice indicated that 25-hydroxycholesterol (25HC) is synthesized by CYP27A1. Incubation of cholesterol or 25HC with mitochondrial and cytosolic fractions in the presence of 3'-phosphoadenosyl 5'-phosphosulfate resulted in the synthesis of 25HC3S. Real-time RT-PCR and Western blot analysis showed the presence of insulin-regulated hydroxycholesterol sulfotransferase 2B1b (SULT2B1b) in hepatocytes. 25HC3S, but not 25HC, decreased SULT2B1b mRNA and protein levels. Specific small interfering RNA decreased SULT2B1b mRNA, protein, and activity levels. These findings demonstrate that mitochondria synthesize 25HC, which is subsequently 3beta-sulfated to form 25HC3S.