Bicluster and Pathway Enrichment Analysis of HCV-induced Cirrhosis and Hepatocellular Carcinoma

Cheng, Peng,Cheng, You,Su, Mei X.,Li, Dong,Zhao, Guo Z.,Gao, Hui,Li, Yan,Zhu, Jie Y.,Li, Hua,Zhang, Tao Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.8

Background: Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the most common form of liver cancer. However, while it is associated frequently with hepatitis C virus (HCV) there is only an elementary understanding of its molecular pathogenesis. Methods: To gain insight into the molecular mechanisms of HCV-induced hepatocarcinogenesis, we performed microarray analysis on 75 surgical liver samples from 48 HCV-infected patients. Results: There were 395 differentially expressed geness between cirrhotic samples and HCC samples. Of these, 125 genes were up-regulated and 270 genes were down-regulated. We performed pathway enrichment analysis and screened as described previously. Conclusions: The differentially expressed genes might be involved in hepatocarcinogenesis through upregulating the pathways of ECM-receptor interaction, focal adhesion, cell adhesion molecules and other cancer-related pathways, and downregulating the pathways of "complement and coagulation cascades". We hope our results could aid in seeking of therapeutic targets for HCV-induced hepatocellular carcinoma.

Comparison of the Gene Expression Profiles Between Smokers With and Without Lung Cancer Using RNA-Seq

Cheng, Peng,Cheng, You,Li, Yan,Zhao, Zhenguo,Gao, Hui,Li, Dong,Li, Hua,Zhang, Tao Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.8

Lung cancer seriously threatens human health, so it is important to investigate gene expression changes in affected individuals in comparison with healthy people. Here we compared the gene expression profiles between smokers with and without lung cancer. We found that the majority of the expressed genes (threshold was set as 0.1 RPKM) were the same in the two samples, with a small portion of the remainder being unique to smokers with and without lung cancer. Expression distribution patterns showed that most of the genes in smokers with and without lung cancer are expressed at low or moderate levels. We also found that the expression levels of the genes in smokers with lung cancer were lower than in smokers without lung cancer in general. Then we detected 27 differentially expressed genes in smokers with versus without lung cancer, and these differentially expressed genes were foudn to be involved in diverse processes. Our study provided detail expression profiles and expression changes between smokers with and without lung cancer.

Breastfeeding and Ovarian Cancer Risk: a Systematic Review and Meta-analysis of 40 Epidemiological Studies

Li, Da-Peng,Du, Chen,Zhang, Zuo-Ming,Li, Guang-Xiao,Yu, Zhi-Fu,Wang, Xin,Li, Peng-Fei,Cheng, Cheng,Liu, Yu-Peng,Zhao, Ya-Shuang Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.12

The present systematic review and meta-analysis was conducted to assess any association between breastfeeding and the risk of ovarian cancer. A systematic search of published studies was performed in PUBMED and EMBASE and by reviewing reference lists from retrieved articles through March 2013. Data extraction was conducted independently by two authors. Pooled relative risk ratios were calculated using random-effect models. Totals of 5 cohort studies and 35 case-control studies including 17,139 women with ovarian cancer showed a 30% reduced risk of ovarian cancer when comparing the women who had breastfed with those who had never breastfed (pooled RR = 0.70, 95% CI: 0.64-0.76; p = 0.00), with significant heterogeneity in the studies (p = 0.00; I2 = 76.29%). A significant decreasd in risk of epithelial ovarian cancer was also observed (pooled RR = 0.68, 95% CI: 0.61-0.76). When the participants were restricted to only parous women, there was a slightly attenuated but still significant risk reduction of ovarian cancer (pooled RR = 0.76, 95% CI: 0.69-0.83). For total breastfeeding duration, the pooled RRs in the < 6 months, 6-12 months and > 12 months of breastfeeding subgroups were 0.85 (95% CI: 0.77-0.93), 0.73 (95% CI: 0.65-0.82) and 0.64 (95%CI: 0.56-0.73), respectively. Meta-regression of total breastfeeding duration indicated an increasing linear trend of risk reduction of ovarian cancer with the increasing total breastfeeding duration (p = 0.00). Breastfeeding was inversely associated with the risk of ovarian cancer, especially long-term breastfeeding duration that demonstrated a stronger protective effect.

Stability analysis of homogeneous slopes with benches

Zhao, Lianheng,Xia, Peng,Xie, Rongfu,Li, Liang,Zhang, Yingbin,Cheng, Xiao Techno-Press 2017 Geomechanics & engineering Vol.13 No.3

In this paper, with a graphical approach, a series of stability charts for homogeneous slopes with benches are presented based on the upper bound limit analysis theory and strength reduction technique. The objective function of the slope safety factor $F_s$ is optimized by the nonlinear sequential quadratic programming, and a substantial number of examples are illustrated to use the stability charts for homogeneous slopes with benches driven by only the action of the soil weight. These charts can be applied to quick and accurate estimations of the stability status of homogeneous slopes with benches. Moreover, the failure modes and the formula for safety factor Fs of homogeneous slopes with benches are provided to illustrate the stability analysis of slopes with benches, which is validated by samples.

Two New Phenolic Glycosides from Hypoxis aurea Lour

Cheng, Zhong-Quan,Yang, Dan,Liu, Yu-Qing,Hu, Jiang-Miao,Jiang, He-Zhong,Wang, Peng-Cheng,Li, Ning,Zhou, Jun,Zhao, You-Xing Korean Chemical Society 2009 Bulletin of the Korean Chemical Society Vol.30 No.10

Potential Serum Markers for Monitoring the Progression of Hepatitis B Virus-Associated Chronic Hepatic Lesions to Liver Cirrhosis

( Cheng Wu ),( Lijie Liu ),( Peng Zhao ),( Dan Tang ),( Dingkang Yao ),( Liang Zhu ),( Zhiqiang Wang ) 대한소화기학회 2015 Gut and Liver Vol.9 No.5

Background/Aims: To screen for serum protein/peptide biomarkers of hepatitis B virus (HBV)-associated chronic hepatic lesions in an attempt to profile the progression of HBV-associated chronic hepatic lesions using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) techniques. Methods: Using SELDI-TOF MS, serum protein/peptide profiles on the CM10 ProteinChip arrays were obtained from a training group including 26 HBV-associated hepatocellular carcinoma patients with liver cirrhosis (LC), 30 HBV-associated LC patients, 85 patients at different stages of liver fibrosis, and 30 asymptomatic HBV carriers. The most valuable SELDI peak for predicting the progression to LC in HBV-infected patients was identified. Results: A SELDI peak of M/Z 5805 with value for predicting LC in HBV-infected patients was found and was identified as a peptide of the C-terminal fraction of the fibrinogen a-chain precursor, isoform 1. Conclusions: The peptide of the C-terminal fraction of the fibrinogen α-chain precursor, isoform 1 with M/Z 5805, may be a serological biomarker for progression to LC in HBV-infected patients. (Gut Liver 2015;9:665-671)

Transcriptome analysis reveals critical genes and key pathways involved in early phyllotaxy development in maize

Yang Zhao,Xiaojian Peng,Wenbo Chai,Yingquan Tan,Qing Dong,Haiyang Jiang,Beijiu Cheng 한국유전학회 2017 Genes & Genomics Vol.39 No.1

Integrated networks of gene expression, hormonal signaling and metabolite sensing regulate phyllotaxy pattern development. In this study, we characterized differentially expressed genes (DEGs) between maize plants with alternate and opposite phyllotaxies. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that 2432 DEGs were involved in biological processes, molecular functions, cellular components and many pathways. Importantly, we identified 19 DEGs related to plant hormone signal transduction. Additionally, we identified four main alternative splicing types: skipped exons, retained introns, alternative 50-splice sites, and alternative 30-splice sites, which exhibited different characteristics in the alternate and opposite phyllotaxy libraries. The reliability of the sequencing data was verified through using quantitative real-time reverse transcription PCR analysis of the 19 genes: 15 were validated to play a role in phytohormone signal transduction pathways. Taken together, our data provide new insight into the mechanisms of phyllotaxy pattern development, and will increase our understanding of how relative changes in gene expression determine alternate/opposite phyllotaxy in maize.

Map-based cloning and functional analysis of the chromogen gene C in rice (Oryza sativa L.)

Shasha Zhao,Cuihong Wang,Jian Ma,Shuai Wang,Peng Tian,Jiulin Wang,Zhijun Cheng,Xin Zhang,Xiuping Guo,Cailin Lei 한국식물학회 2016 Journal of Plant Biology Vol.59 No.5

The chromogen gene C is critical for anthocyanin regulation in rice, and apiculus color is an important agronomic trait in selective breeding and variety purification. Mapbased cloning and in-depth functional analysis of the C gene will be useful for understanding the molecular mechanism of anthocyanin biosynthesis and for rice breeding. Japonica landrace Lijiangxintuanheigu (LTH) has red apiculi and purple stigmas. Genetic analysis showed that red apiculus and purple stigma in LTH co-segregated indicating control by a single dominant gene, or by two completely linked genes. Using 1,851 recessive individuals from two F2 populations, the target gene OsC was delimited to a 70.8 kb interval on chromosome 6 that contains the rice homologue of the maize anthocyanin regulatory gene C1. When the entire OsC gene and its full-length cDNA cloned from LTH were transformed into japonica cultivar Kitaake with colorless apiculi and stigmas all positive transformants had red apiculi but non-colored stigmas, validating that OsC alone was responsible for the apiculus color and represented the functional C gene. OsC was constitutively expressed in all tissues examined, with strongest expression in leaf blades. These results set a foundation to clarify the regulatory mechanisms of OsC in the anthocyanin biosynthetic pathway.

Oviposition decisions in an endoparasitoid under self-superparasitism conditions

Liu Peng-Cheng,Zhao Bin,Cao Dan-Dan,Wei Jian-Rong 한국응용곤충학회 2021 Journal of Asia-Pacific Entomology Vol.24 No.1

Superparasitism is a widespread phenomenon. Having accepted superparasitism, mated female parasitoids must decide on the sex of each egg they subsequently lay into the same host. Theory predicts that this decision is either based on host quality, when more male eggs are laid in hosts that are already parasitized because they are perceived to be of poorer quality; or more eggs are laid of the sex that is most likely to be a strong larval competitor, i.e. generally females. Anastatus disparis is a facultative endoparasitic egg parasitoid. We used ‘artificial’ hosts to explore outcomes of decision making by A. disparis during superparasitism under a manipulated absence of larval competition. When only one egg was laid it was always female. As the number of eggs laid increased, so more of them were male. This supports the theory that oviposition decisions are based on host quality; more male eggs were laid in hosts that were already parasitized and thus of poorer quality. In a second experiment, eggs were exposed to parasitoids for different periods of time. Half the eggs were dissected to determine the number of parasitoid eggs that had been laid. The remaining eggs were incubated and the number and sex of offspring that ultimately emerged, following larval competition, were recorded. Under superparasitism conditions fierce larval competition ensued; only one offspring survived and they were pre dominantly female. In conclusion, oviposition decisions by female A. disparis accepting self-superparasitism were made based on host quality.

Soil fungal communities of montane natural secondary forest types in China

Fei Cheng,Xin Wei,Lin Hou,Zhengchun Shang,Xiaobang Peng,Peng Zhao,Zhaoxue Fei,Shuoxin Zhang 한국미생물학회 2015 The journal of microbiology Vol.53 No.6

Distinctive plant communities may provide specific physical and chemical properties with soils by specific litters and root exudates to exert effects on soil microorganisms. Past logging activities in the Qinling Mountains induced diverse natural secondary forest types (NSFTs). How these recovered NSFTs regulate patterns of soil microbial communities remain limited. In the study, we used terminal-restriction fragment length polymorphism (T-RFLP) to precisely determine forest type-specific soil fungal diversity and composition in five NSFTs. Our results indicated that NSFTs had significant impacts on the soil fungal communities. The most diverse fungal species were found in the Armand pine (Pinus armandi) and Chinese pine (Pinus tabulaeformis) forest soils, followed by sharptooth oak (Quercus aliena var. acuteserrata) and Chinese pine-sharptooth oak forest soils, the wilson spruce (Picea wilsonii) forests had the lowest soil fungal diversity. The analyses of community composition suggested that the fungal communities of Armand pine forest soils were similar to those of Chinese pine forest soils, while other communities prominently differed from each other. Stepwise multiple regression analysis revealed that soil silt, clay, pH, and ammonium nitrogen had intimate linkages with soil fungal diversity. Furthermore, the patterns of soil fungal communites were strongly governed by the specific soil environments of the tested NSFTs, as described by canonical correspondence analysis (CCA). Finally, our study showed that soil fungal communities may be mediated by NSFTs via specific soil edaphic status. Hence, such a comparable study may provide fundamental information for fungal diversity and community structure of natural forests and assist with better prediction and understanding how soil fungal composition and function alter with forest type transformation.