Integrating high-throughput microRNA and mRNA expression data to identify risk mRNA signature for pancreatic cancer prognosis

Pancreatic cancer is a malignancy of the digestive system characterized by poor prognosis. A number of prognostic messenger RNA (mRNA) signatures have been identified by using the high-throughput expression profiles. MicroRNAs (miRNA) play a critical role in regulating multiple cellular functions. However, no such integrated analysis of miRNAs and mRNAs for studying the prognostic mechanisms of pancreatic cancer has been reported. In this study, we first identified prognostic mRNAs and miRNAs based on The Cancer Genome Atlas datasets, and then performed an enrichment analysis to explore the underlying biological mechanisms involved in pancreatic cancer prognosis at the mRNA level. Furthermore, we performed an integrated analysis of mRNAs and miRNAs to identify prognostic subpathways, which were closely associated with pancreatic cancer genes and tumor hallmarks and involved in hypoxia, oxidative phosphyorylation and xenobiotic metabolisms. Meanwhile, we performed a random walk algorithm based on global network, prognostic mRNAs and miRNAs, and identified top risk mRNAs as the prognostic signature. Finally, an independent testing set was used to confirm the predictive power of the top mRNA signature, and most of these genes involved were known oncogenes. In conclusion, we performed a series of integrated analyses by comprehensively exploring pancreatic cancer prognosis and systematically optimized the prognostic signature for clinical use.     

Enhanced thermotolerance and ethanol tolerance in Saccharomyces cerevisiae mutated by high-energy pulse electron beam and protoplast fusion

To increase thermotolerance and ethanol tolerance in Saccharomyces cerevisiae strain YZ1, the strategies of high-energy pulse electron beam (HEPE) and three rounds of protoplast fusion were explored. The YF31 strain had the characteristics of resistant to high-temperature, high-ethanol tolerance, rapid growth and high yield. The YF31 could grow on plate cultures up to 47?°C, containing 237.5?g?L^?1 of ethanol. In particular, the mutant strain YF31 generated 94.2?±?4.8?g?L^?1 ethanol from 200?g glucose L^?1 at 42?°C, which was 2.48 times the production of the wild strain YZ1. Results demonstrated that the variant phenotypes from the strains screening by HEPE irradiation could be used as parent stock for yeast regeneration and the protoplast fusion technology is sufficiently powerful in combining suitable characteristics in a single strain for ethanol fermentation.     

Rituximab sensitizes a Burkitt lymphoma cell line to cell killing by X-irradiation

Clinical trials with rituximab in combination with chemotherapeutic regimens have shown promising results. Data on the effects of rituximab treatment in combination with irradiation are, however, limited and inconsistent. This study aims to investigate the effects of rituximab (R) on cell death induced by X-irradiation in Raji lymphoma cells and to evaluate its mechanisms. We found the cell growth inhibition by irradiation was enhanced by additional rituximab exposure both in cells precultured with rituximab followed by irradiation (R + irradiation) or in cells treated in the reverse sequence (irradiation + R). R + irradiation combination treatment induced more apoptotic cells than irradiation and irradiation + R treatment as early as 12 h after treatment. At 24 h, both combination treatments, R + irradiation and irradiation + R, showed apoptotic cells, which were significantly different from irradiation alone. G2/M cell cycle arrest was observed after irradiation alone and the combination treatment. The combination treatment revealed an elevation in reactive oxygen species (ROS) generation in a radiation dose-dependent manner. In addition, rituximab enhanced the cell growth inhibition and apoptotic cell death induced by the oxidative agent, H₂O₂. We propose that rituximab mediates a significant in vitro radiosensitizing effect and induces cell cycle changes and apoptosis in Raji cells. ROS probably play an important role in these events.     

Simultaneous Removal of Lindane,Lead and Cadmium from Soils by Rhamnolipids Combined with Citric Acid

This study investigated the performance of rhamnolipids-citric acid mixed agents in simultaneous desorption of lindane and heavy metals from soils. The capacity of the mixed agents to solubilize lindane, lead and cadmium in aqueous solution was also explored. The results showed that the presence of citric acid greatly enhanced the solubilization of lindane and cadmium by rhamnolipids. A combined effect of the mixed agents on lindane and heavy metals removal from soils was observed. The maximum desorption ratios for lindane, cadmium and lead were 85.4%, 76.4% and 28.1%, respectively, for the mixed agents containing 1% rhamnolipidsand 0.1 mol/L citric acid. The results also suggest that the removal efficiencies of lead and cadmium were strongly related to their speciations in soils, and metals in the exchangeable and carbonate forms were easier to be removed. Our study suggests that the combining use of rhamnolipids and citric acid is a promising alternative to simultaneously remove organochlorine pesticides and heavy metals from soils.     

基于改进遥感生态指数的宁夏沿黄平原区生态环境质量评价

区域生态环境质量评价是国民经济建设与可持续性发展规划的基础，是生态学研究的主要方向之一。以土地利用/覆盖数据和Landsat OLI数据为基础，分别在ArcGIS和GEE平台上进行景观多样性指数（Landscape Diversity Index，LDI）与归一化植被指数（Normalized Difference Vegetation Index，NDVI）、湿度（Wet Index，WI）、归一化裸土和建筑指数（Normalized Difference Building-Soil Index，NDBSI）、遥感生态指数（Remote Sensing Based Ecological Index，RSEI）和改进遥感生态指数（Modified Remote Sensing Ecological Index，MRSEI）的计算。在LDI最佳尺度约束下分析表明，宁夏沿黄平原区景观多样性指数具有显著尺度依赖特征（P<0.001），阈值出现在3000 m×3000 m。主成分分析（Principal Component Analysis，PCA）解释了研究区改进遥感生态指数主要受到NDVI和LDI影响，其中NDVI是PC1（特征值贡献率68.98%）的决定因子，特征向量为0.8901；LDI为次要决定因子，特征向量为-0.4146，该分量在MRSEI计算中分值较高。LDI是PC2（特征值贡献率28.76%）的决定因子，特征向量为0.9100；NDVI为次要决定因子，特征向量为0.4056，该分量在MRSEI计算中分值较低。从MRSEI在应用中可信性来看，其在分析中采用LDI替代LST有效地避免了RSEI分析中NDBSI和LST之间存在的生态学意义重复表达和多因子向量投影中的高度聚集。研究区空间异质性主要以"差"和"较差"级别分布在不同土地利用/覆盖类型交错区且以环绕研究区为主要特点。在"差"到"好"梯度上，斑块密度为减少趋势由8.3个/km²减少到5.9个/km²，而平均斑块面积呈增加趋势由0.120 km²增加到0.169 km²。综合来看宁夏沿黄平原区生态环境质量总体MRSEI值为0.0117刚好超过"较好"水平下限。     

Gene Expression Profile Analysis of Type 2 Diabetic Mouse Liver

Liver plays a key role in glucose metabolism and homeostasis, and impaired hepatic glucose metabolism contributes to the development of type 2 diabetes. However, the precise gene expression profile of diabetic liver and its association with diabetes and related diseases are yet to be further elucidated. In this study, we detected the gene expression profile by high-throughput sequencing in 9-week-old normal and type 2 diabetic db/db mouse liver. Totally 12132 genes were detected, and 2627 genes were significantly changed in diabetic mouse liver. Biological process analysis showed that the upregulated genes in diabetic mouse liver were mainly enriched in metabolic processes. Surprisingly, the downregulated genes in diabetic mouse liver were mainly enriched in immune-related processes, although all the altered genes were still mainly enriched in metabolic processes. Similarly, KEGG pathway analysis showed that metabolic pathways were the major pathways altered in diabetic mouse liver, and downregulated genes were enriched in immune and cancer pathways. Analysis of the key enzyme genes in fatty acid and glucose metabolism showed that some key enzyme genes were significantly increased and none of the detected key enzyme genes were decreased. In addition, FunDo analysis showed that liver cancer and hepatitis were most likely to be associated with diabetes. Taken together, this study provides the digital gene expression profile of diabetic mouse liver, and demonstrates the main diabetes-associated hepatic biological processes, pathways, key enzyme genes in fatty acid and glucose metabolism and potential hepatic diseases.     

Determination of Brain-Regional Blood Perfusion and Endogenous cPKCγ Impact on Ischemic Vulnerability of Mice with Global Ischemia

Conventional protein kinase C (cPKC)γ participated in cerebral hypoxic preconditioning-induced neuroprotection and affected the neurological outcome of ischemic stroked mice. As an independent predictor of ischemic stroke, the internal carotid artery occlusion (ICAO)-caused brain-regional ischemic injury may worsen the neurological outcome of patients. However, the brain-regional ischemic vulnerability and its underlying mechanism remain unclear. In this study, the bilateral ICAO (BICAO) model was applied in cPKCγ wild type (WT) and knockout (KO) mice to determine the cPKCγ impact on brain-regional ischemic vulnerability. The arterial spin labeling (ASL) imaging results showed that 7 days BICAO-induced global ischemia could cause significant blood perfusion loss in prefrontal cortex (69.13%), striatum (61.69%), hypothalamus (67.36%), hippocampus (69.82%) and midbrain (40.53%) of WT mice, along with neurological deficits. Nissl staining and Western blot results indicated that hypothalamus and midbrain had more severe neural cell loss than prefrontal cortex, striatum and hippocampus, which negatively coincided with endogenous cPKCγ protein levels but not blood perfusion loss and cPKCγ membrane translocation levels. Furthermore, we found that cPKCγ KO significantly aggravated the neuron loss in prefrontal cortex, striatum and hippocampus and abolish the regional ischemic vulnerability by using immunofluorescent staining with neuron-specific marker NeuN. Similarly, cPKCγ KO also significantly increased Caspase-3, -8 and -9 cleavage levels in prefrontal cortex, striatum, hippocampus, hypothalamus and midbrain of mice with 24 h BICAO. These results suggested that hypothalamus and midbrain are more vulnerable to ischemia, and endogenous cPKCγ affects the regional ischemic vulnerability through modulating Caspase-8 and -9 dependent cell apoptosis.     

Genome‐wide identification and characterization of microRNAs responding to ABA and GA in maize embryos during seed germination

• MicroRNAs (miRNAs) are an important class of non‐coding small RNAs that regulate the expression of target genes through mRNA cleavage or translational inhibition. Previous studies have revealed their roles in regulating seed dormancy and germination in model plants such as Arabidopsis thaliana, rice (Oryza sativa) and maize (Zea mays). However, the miRNA response to exogenous gibberellic acid (GA) and abscisic acid (ABA) during seed germination in maize has yet to be explored.
• In this study, small RNA libraries were generated and sequenced from maize embryos treated with GA, ABA or double‐distilled water as control.
• A total of 247 miRNAs (104 known and 143 novel) were identified, of which 45 known and 53 novel miRNAs were differentially expressed in embryos in the different treatment groups. In total, 74 (37 up‐regulated and 37 down‐regulated) and 55 (23 up‐regulated and 32 down‐regulated) miRNAs were expressed in response to GA and to ABA, respectively, and a total of 18 known and 38 novel miRNAs displayed differential expression between the GA‐ and ABA‐treated groups. Using bioinformatics tools, we predicted the target genes of the differentially expressed miRNAs. Using GO enrichment and KEGG pathway analysis of these targets, we showed that miRNAs differentially expressed in our samples affect genes encoding proteins involved in the peroxisome, ribosome and plant hormonal signalling pathways.
• Our results indicate that miRNA‐mediated gene expression influences the GA and ABA signalling pathways during seed germination.