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PDF file, 125K, Univariate and multivariate analysis of features associated with overall survival.

PDF file, 148K, Univariate and multivariate analysis of features associated with overall survival in the test and independent sets (n = 106).

PDF file, 132K, Differential expression of miRNAs between clinical features.

PDF file, 40K.

PDF file, 148K, Class Prediction with PAM in Test Set and Independent Cohort.

PDF file, 97K, Overall survival (OS) and disease-free survival (DFS) in Training set, Test Set and Independent Cohort.

PDF file, 131K, The relationship between 20-miRNA signature risk score and survival status of HCC patients in combination of training and test sets.

PDF file, 220K, Classification and Prediction of HCC and NC samples by 30-miRNA signature.

PDF file, 118K, The relationship between 20-miRNA signature risk score and survival status of HCC patients.

Purpose: MicroRNAs (miRNAs) play important roles in the development and progression of cancer. The aim of this study is to identify miRNA expression signatures in hepatocellular carcinoma and delineate their clinical significance for hepatocellular carcinoma.Experimental Design: Patients with hepatocellular carcinoma, undergoing hepatectomy were randomly divided into training set (60 patients) and test set (50 patients). Other 56 patients were used as an independent cohort. The miRNA expression levels were detected by microarray and verified by quantitative real-time reverse transcription-PCR (qRT-PCR).Results: A 30-miRNA signature consisting of 10 downregulated and 20 upregulated miRNAs was established for distinguishing hepatocellular carcinoma from noncancerous liver tissues in the training set with 99.2% accuracy. The classification accuracies of this signature were 97% and 90% in the test set and independent cohort, respectively. The expression level of four miRNAs in the 30-miRNA signature was verified by qRT-PCR in the training set. Twenty miRNAs were then selected to construct prognostic signature in the training set. Of the 20 miRNAs, six were risk factors and 14 were protective factors. A formula based on the 20 miRNAs was built to compute prognostic index. Kaplan–Meier analysis showed that patients with a higher prognostic index had a significantly lower survival than those with a low index. This was verified in the test and independent sets. Multivariate analysis indicated that the 20-miRNA signature was an independent prognostic predictor.Conclusions: The 30- and 20-miRNA signatures identified in this study should provide new molecular approaches for diagnosis and prognosis of patients with hepatocellular carcinoma and clues for elucidating molecular mechanism of hepatocarcinogenesis. Clin Cancer Res; 19(17); 4780–91. ©2013 AACR.

In eukaryotes, autophagy maintains cellular homeostasis by recycling cytoplasmic components. The autophagy-related proteins (ATGs) ATG1 and ATG13 form a protein kinase complex that regulates autophagosome formation; however, mechanisms regulating ATG1 and ATG13 remain poorly understood. Here, we show that, under different nutrient conditions, the RING-type E3 ligases SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA1 (SINAT1), SINAT2, and SINAT6 control ATG1 and ATG13 stability and autophagy dynamics by modulating ATG13 ubiquitylation in Arabidopsis (Arabidopsis thaliana). During prolonged starvation and recovery, ATG1 and ATG13 were degraded through the 26S proteasome pathway. TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR1a (TRAF1a) and TRAF1b interacted in planta with ATG13a and ATG13b and required SINAT1 and SINAT2 to ubiquitylate and degrade ATG13s in vivo. Moreover, lysines K607 and K609 of ATG13a protein contributed to K48-linked ubiquitylation and destabilization, and suppression of autophagy. Under starvation conditions, SINAT6 competitively interacted with ATG13 and induced autophagosome biogenesis. Furthermore, under starvation conditions, ATG1 promoted TRAF1a protein stability in vivo, suggesting feedback regulation of autophagy. Consistent with ATGs functioning in autophagy, the atg1a atg1b atg1c triple knockout mutants exhibited premature leaf senescence, hypersensitivity to nutrient starvation, and reduction in TRAF1a stability. Therefore, these findings demonstrate that SINAT family proteins facilitate ATG13 ubiquitylation and stability and thus regulate autophagy.

In order to study the degradation of herbicide----Quinclorac using microorganism, separate and screen the degrading bacteria CSUFTM62 from soil, this paper researched the degradation effect of bacterial strain on the Quinclorac under different situations, including different increments, different temperatures, different concentrations of pesticide, different pH, and different additive amount of nutrients. The results show that the optimal degradation temperature is 30 ° C; the optimum pH is 7; the degradation rate of Quinclorac reaches its maximum when the concentration is 50mg / L. Adding yeast extract could increase the amount of strain growth but never affect its degradation effects on Quinclorac; combined with the morphological characteristics, the strains CSUFTM62 is identified as the Stenotrophomonas maltophilia by measuring the 16S sequence.

In order to explore the relevant molecular genetic mechanisms of photosynthetic rate (PR) and chlorophyll content (CC) in rice (Oryza sativa L.), we conducted a series of related experiments using a population of recombinant inbred lines (Zhenshan97B x IRAT109). We found a significant correlation between CC and PR (R= 0.19**) in well-watered conditions, but no significant correlation during water stress (r= 0.08). We detected 13 main quantitative trait loci (QTLs) located on chromosomes 1, 2, 3, 4, 5, 6, and 10, which were associated with CC, including six QTLs located on chromosomes 1, 2, 3, 4, and 5 during water stress, and seven QTLs located on chromosomes 2, 3, 4, 6, and 10 in well-watered conditions. These QTLs explained 47.39% of phenotypic variation during water stress and 56.19% in well-watered conditions. We detected four main QTLs associated with PR; three of them (qPR2, qPR10, qPR11) were located on chromosomes 2, 10, and 11 during water stress, and one (qPR10) was located on chromosome 10 in well-watered conditions. These QTLs explained 34.37% and 18.41% of the phenotypic variation in water stress and well-watered conditions, respectively. In total, CC was largely controlled by main QTLs, and PR was mainly controlled by epistatic QTL pairs.

Endosymbionts include primary endosymbionts and secondary endosymbionts, accreting with insects. Endosymbionts evolve with insects and benefit from each other. A report was given on the difference of endosymbionts found in Bemisia tabaci (Gennadius 1889) and Trialeurodes vaporariorum (Westwood 1856) before. However, the phylogentic analysis of primary and secondary bacterial symbionts associated with the whitefly B tabaci B biotype are poorly known. Here are presented the results of cloning and sequencing 16S rDNA of primary and secondary endosymbionts in B tabaci living for extended periods on different host plants in Beijing. Molecular phylogenetic trees, including about 1 000bp 16S rDNA of primary endosymbionts, and about 1 250bp 16S rDNA of secondary endosymbionts in B tabaci were constructed. The results indicate that primary endosymbionts in B tabaci were Proteobacteria, Gammaproteobacteria, Oceanospirillales, Halomonadaceae, Zymobacter and Candidatus Portiera aleyrodidarum. Secondary endosymbionts in B tabaci were Proteobacteria, Gammaproteobacteria, Enterobacteriales and Enterobacteriaceae. The primary and secondary endosymbionts in B tabaci from different host plants or other countries might belong to different ecological types from one species specifically. B tabaci independently acquired various endosymbionts when living on different host plants, and these endosymbionts played important roles for B tabaci's accomodation in different environments. The phylogentic trees based on 16S rDNA of primary endosymbionts could be explained by geographical origin more reasonably than those of the secondary endosymbionts, and the phylogentic trees based on 16S rDNA of secondary endosymbionts can be explained by varying host resources more reasonably than those of primary endosymbionts. B tabaci may have been introduced to China via the importation of Poinsettia plants.

Purpose: MicroRNAs (miRNAs) play important roles in the development and progression of cancer. The aim of this study is to identify miRNA expression signatures in hepatocellular carcinoma and delineate their clinical significance for hepatocellular carcinoma. Experimental Design: Patients with hepatocellular carcinoma, undergoing hepatectomy were randomly divided into training set (60 patients) and test set (50 patients). Other 56 patients were used as an independent cohort. The miRNA expression levels were detected by microarray and verified by quantitative real-time reverse transcription-PCR (qRT-PCR). Results: A 30-miRNA signature consisting of 10 downregulated and 20 upregulated miRNAs was established for distinguishing hepatocellular carcinoma from noncancerous liver tissues in the training set with 99.2% accuracy. The classification accuracies of this signature were 97% and 90% in the test set and independent cohort, respectively. The expression level of four miRNAs in the 30-miRNA signature was verified by qRT-PCR in the training set. Twenty miRNAs were then selected to construct prognostic signature in the training set. Of the 20 miRNAs, six were risk factors and 14 were protective factors. A formula based on the 20 miRNAs was built to compute prognostic index. Kaplan–Meier analysis showed that patients with a higher prognostic index had a significantly lower survival than those with a low index. This was verified in the test and independent sets. Multivariate analysis indicated that the 20-miRNA signature was an independent prognostic predictor. Conclusions: The 30- and 20-miRNA signatures identified in this study should provide new molecular approaches for diagnosis and prognosis of patients with hepatocellular carcinoma and clues for elucidating molecular mechanism of hepatocarcinogenesis. Clin Cancer Res; 19(17); 4780–91. ©2013 AACR.

There is no gene signature for predicting relapse and survival of cervical cancer with early stage currently. In this study, we investigate whether gene expression profiling of cervical cancer could be used to predict the prognosis of patient. A series of 100 primary cervical cancer patients who underwent radical hysterectomy between January 2001 and October 2006 were analyzed for gene expression profiles by using a custom oligonucleotide microarray containing probes for 1440 human tumor-related gene transcripts. Supervised analysis of gene expression data identified 19 genes that exhibited differential expression between cervical cancer and normal cervix. Then, all 100 patients were divided into the training (n=50) and testing sets (n=50). Using Cox regression and risk-score analysis, we identified a 7-gene (UBL3, FGF3, BMI1, PDGFRA, PTPRF, RFC4, and NOL7) signature for predicting relapse of patient in the training set. The 7-gene signature was validated by the testing set (sensitivity, 84.6%; specificity, 91.9%; positive predictive value, 78.6%; negative predictive value, 94.4%). Patients with high-risk 7-gene signature had poor relapse-free survivals (RFS) than patients with low-risk 7-gene signature in both training set (P=0.026) and testing set (P=0.042). Multivariate analysis showed that the FIGO stage and 7-gene signature are independent prognostic factors associated with RFS of cervical cancer patients. The 7-gene signature can predict cancer recurrence and survival of cervical cancer patients. This may have prognostic or therapeutic implications for the future management of cervical cancer patients.

A pot experiment with the soils from Yongzhou, Liuyang, and Sangzhi, the high-quality tobacco planting regions of Hunan Province, was conducted to study the effects of climate, soil, and their interaction on some neutral volatile aroma components in flue-cured tobacco leaves. The contents of test neutral volatile aroma components in the flue-cured tobacco leaves were of medium variation, and the variation intensity was decreased in the order of dihydroactinolide, damascenone, furfural, total megastigmatrienone, and beta-ionone. Climate, soil, and their interaction affected the neutral volatile aroma components in different degrees. The furfural content was most affected by climate, the damascenone content was most affected by climate and by soil, the total megastigmatrienone and beta-ionone contents were most affected by the interaction of soil and climate, while the dihydroactinolide content was less affected by soil, climate, and their interaction. The contribution of climate, soil, and their interaction to the contents of the five aroma components was 40.82%, 20.67%, and 38.51%, respectively. During different growth periods of tobacco, different climate factors had different effects on the neutral volatile aroma components. The rainfall, cloudiness, and mean air temperature at rooting stage, the diurnal temperature amplitude, sunshine time, and evaporation at vigorous growth stage, and the rainfall, evaporation, and mean air temperature at maturing stage were the top three climate factors affecting the contents of the neutral volatile aroma components in flue-tobacco leaves. For the soil factors, the available potassium, available phosphorus, and pH were the top three factors affecting the contents of the five components.