Comprehensive Bioinformation Analysis of the MRNA Profile of Fascin Knockdown in Esophageal Squamous Cell Carcinoma

Wu, Bing-Li,Luo, Lie-Wei,Li, Chun-Quan,Xie, Jian-Jun,Du, Ze-Peng,Wu, Jian-Yi,Zhang, Pi-Xian,Xu, Li-Yan,Li, En-Min Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12

Background: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. Method: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. Results: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. Conclusions: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

Protein-protein Interaction Network Analyses for Elucidating the Roles of LOXL2-delta72 in Esophageal Squamous Cell Carcinoma

Wu, Bing-Li,Zou, Hai-Ying,Lv, Guo-Qing,Du, Ze-Peng,Wu, Jian-Yi,Zhang, Pi-Xian,Xu, Li-Yan,Li, En-Min Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.5

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2- delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.

Prognostic Evaluation of Categorical Platelet-based Indices Using Clustering Methods Based on the Monte Carlo Comparison for Hepatocellular Carcinoma

Guo, Pi,Shen, Shun-Li,Zhang, Qin,Zeng, Fang-Fang,Zhang, Wang-Jian,Hu, Xiao-Min,Zhang, Ding-Mei,Peng, Bao-Gang,Hao, Yuan-Tao Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Objectives: To evaluate the performance of clustering methods used in the prognostic assessment of categorical clinical data for hepatocellular carcinoma (HCC) patients in China, and establish a predictable prognostic nomogram for clinical decisions. Materials and Methods: A total of 332 newly diagnosed HCC patients treated with hepatic resection during 2006-2009 were enrolled. Patients were regularly followed up at outpatient clinics. Clustering methods including the Average linkage, k-modes, fuzzy k-modes, PAM, CLARA, protocluster, and ROCK were compared by Monte Carlo simulation, and the optimal method was applied to investigate the clustering pattern of the indices including platelet count, platelet/lymphocyte ratio (PLR) and serum aspartate aminotransferase activity/platelet count ratio index (APRI). Then the clustering variable, age group, tumor size, number of tumor and vascular invasion were studied in a multivariable Cox regression model. A prognostic nomogram was constructed for clinical decisions. Results: The ROCK was best in both the overlapping and non-overlapping cases performed to assess the prognostic value of platelet-based indices. Patients with categorical platelet-based indices significantly split across two clusters, and those with high values, had a high risk of HCC recurrence (hazard ratio [HR] 1.42, 95% CI 1.09-1.86; p<0.01). Tumor size, number of tumor and blood vessel invasion were also associated with high risk of HCC recurrence (all p< 0.01). The nomogram well predicted HCC patient survival at 3 and 5 years. Conclusions: A cluster of platelet-based indices combined with other clinical covariates could be used for prognosis evaluation in HCC.

EFFECTS OF CATALYST STRUCTURAL PARAMETERS ON THE PERFORMANCE OF EXHAUST GAS AFTERTREATMENT SYSTEM OF DIESEL ENGINES

Tan Pi Qiang,Li Yun Peng,Wang De Yuan,Hu Zhi Yuan,Lou Di Ming 한국자동차공학회 2022 International journal of automotive technology Vol.23 No.4

To meet increasingly stringent emission regulations, diesel engines must be equipped with DOC, DPF and SCR. Five performance parameters including system back pressure, HC conversion efficiency, conversion efficiency of NO to NO2, passive regeneration rate, and conversion efficiency of NO to N2 are very important for DOC+DPF+SCR system. Nine structural parameters including rDOC, rDPF, rSCR, σDOC, σDPF, σSCR, δDOC, δDPF, and δSCR di rectly a ffect t he f i ve performance parameters, this paper has carried out a detailed study on it. First, a simulation model of DOC+DPF+SCR system was established, and calibrated by experiment. Then, simulation was performed on the five performance parameters under different values of the nine structural parameters. Subsequently, a novel model using random forest algorithm was established to analyze the correlation between the performance parameters and the structural parameters. The results show that σDPF has the greatest influence on system backpressure, followed by rDPF. The rDOC has the greatest influence on HC conversion, followed by σDOC. The rDOC has the greatest influence on conversion of NO to NO2, followed by σDOC. The rDPF has the greatest influence on DPF passive regeneration rate, followed by rDOC. The rSCR has the greatest influence on conversion of NO to N2, followed by rDOC.

Four new compounds from the bulbs of Lycoris aurea with neuroprotective effects against $CoCl_2$ and $H_2O_2$-induced SH-SY5Y cell injuries

Jin, An,Li, Xue,Zhu, Yun-Yun,Yu, Heng-Yi,Pi, Hui-Fang,Zhang, Peng,Ruan, Han-Li 대한약학회 2014 Archives of Pharmacal Research Vol.37 No.3

Three new alkaloids, $2{\alpha}$-hydroxy-6-O-n-butyloduline, O-n-butyllycorenine, (-)-N-(chloromethyl)lycoramine (1-3), and a new phenolic compound, ((7S)-7-(4-hydroxyphenyl)-7-hydroxypropyl)-2'-methylbenzene-3',6'-diol (14), along with ten known alkaloids (4-13), were isolated from the bulbs of Lycoris aurea collected from Huaihua County of Hunan Province, China. Their structures were elucidated by spectroscopic methods including HRESIMS, UV, IR, and NMR. All the isolated compounds were tested for their neuroprotective effects against $CoCl_2$ and $H_2O_2$-induced SH-SY5Y cell death. Compounds 1-7 and 10 exhibited significant neuroprotective effects against $CoCl_2$-induced SH-SY5Y cell injury, while compounds 1-5, 7, 10 and 12 showed obvious neuroprotective effects against $H_2O_2$-induced SH-SY5Y cell death.

Cloning and Functional Analysis of a cDNA Encoding Ginkgo biloba Farnesyl Diphosphate Synthase

Kexuan Tang,Peng Wang,Zhihua Liao,Liang Guo,Wenchao Li,Min Chen,Yan Pi,Yifu Gong,Xiaofen Sun 한국분자세포생물학회 2004 Molecules and cells Vol.18 No.2

Farnesyl diphosphate synthase (FPS; EC2.5.1.1/EC2. 5.1.10) catalyzes the synthesis of farnesyl diphosphate, and provides precursor for biosynthesis of sesquiterpene and isoprenoids containing more than 15 isoprene units in Ginkgo biloba. Here we report the cloning, characterization and functional analysis of a new cDNA encoding FPS from G. biloba. The full-length cDNA (designated GbFPS) had 1731 bp with an open reading frame of 1170 bp encoding a polypeptide of 390 amino acids. The deduced GbFPS was similar to other known FPSs and contained all the conserved regions of trans-prenyl chain-elongating enzymes. Structural modeling showed that GbFPS had the typical structure of FPS, the most prominent feature of which is the arrangement of 13 core helices around a large central cavity. Southern blot analysis revealed a small FPS gene family in G. biloba. Expression analysis indicated that GbFPS expression was high in roots and leaves, and low in stems. Functional complementation of GbFPS in an FPS-deficient strain confirmed that GbFPS mediates farnesyl diphosphate biosynthesis.

Neoadjuvant Chemotherapy for Resectable Esophageal Carcinoma: A Meta-analysis of Randomized Clinical Trials

Xu, Xiao-Hua,Peng, Xue-Hong,Yu, Ping,Xu, Xiao-Yuan,Cai, Er-Hui,Guo, Pi,Li, Ke Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.1

Neoadjuvant chemotherapy for resectable esophageal carcinoma has been a focus of study, but no agreement has been reached on clinical randomized controlled trials and relevant systematic evaluation. The purpose of this study was to perform a meta-analysis on published randomized controlled trials (RCTs) that compared neoadjuvant chemotherapy and surgery with surgery alone for resectable esophageal carcinoma. Medline and manual searches was conducted in PubMed, ASCO (American Society of Clinical Oncology) meeting summary, Embase, the Cochrane Library (up to October 2010), Chinese Biomedical Literature Database, China National Knowledge Infrastructure, VIP Database, Wanfang Database. The selection contents were to identify all published and unpublished RCTs that compared neoadjuvant chemotherapy and surgery with surgery alone for resectable esophageal carcinoma. Sixteen RCTs which included 2,594 patients were selected. The risk ratio (RR) (95% confidence interval [CI]; P value), expressed as neoadjuvant chemotherapy and surgery versus surgery alone (treatment versus control), was 1.02 (0.95, 1.10; P=0.54) for 1-year survival, 1.29 (1.13, 1.47; P=0.0001) for 3-year survival, 1.31 (1.13, 1.51; P=0.0003) for 5-year survival, 1.00 (0.95, 1.04; P= 0.85) for rate of resection and 0.89 (0.64, 1.23; P=0.48) for operative mortality. The results showed that neoadjuvant chemotherapy for resectable esophageal carcinoma can raise the overall survival rate of patients with esophageal carcinoma, but it does not affect treatment-related mortality.

Alkaloids from the bulbs of Lycoris longituba and their neuroprotective and acetylcholinesterase inhibitory activities

Yun-Yun Zhu,Xue Li,Heng-Yi Yu,Yu-Fang Xiong,Peng Zhang,Hui-Fang Pi,Han-Li Ruan 대한약학회 2015 Archives of Pharmacal Research Vol.38 No.5

Three novel alkaloids (1–3), together withnineteen known ones (4–22), were isolated from the bulbsof Lycoris longituba. Their structures were elucidated onthe basis of extensive spectroscopic analyses, which belongto several Amaryllidaceae alkaloid skeletons. Amongthem, the harmane-type alkaloids (the new compound 1and the known compounds 5, 6 and 7) were found for thefirst time from Lycoris genus. The isolates were tested fortheir neuroprotective activities against CoCl2, H2O2 andAb25–35-induced SH-SY5Y cell injuries, and the majorityof them exhibited neuroprotective activities of differentdegrees. The acetylcholinesterase (AChE) inhibitoryactivities of the isolated alkaloids were also evaluated,while compounds 12, 14–20 and 22 exhibited extremelysignificant AChE inhibitory activities.

The effect of light on follicular development in laying hens

Cheng, Shi Bin,Li, Xian Qiang,Wang, Jia Xiang,Wu, Yan,Li, Peng,Pi, Jin Song Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.11

Objective: The oxidative stress status and changes of chicken ovary tissue after shading were studied, to determine the mechanism of the effect of shading on follicular development. Methods: Twenty healthy laying hens (40 weeks old) with uniform body weight and the same laying rate were randomly divided into two groups (the shading group and normal light group). In the shading group, the cage was covered to reduce the light intensity inside the cage to 0 without affecting ventilation or food intake. The normal lighting group received no additional treatment. After 7 days of shading, oxidative stress related indicators and gene expression were detected. Results: Analysis of paraffin and ultrathin sections showed that apoptosis of ovarian granulosa cells (GCs) increased significantly after light shading. Enzyme linked immunosorbent assay results revealed that the levels of total antioxidant capacity, malondialdehyde, superoxide dismutase (SOD), glutathione, catalase (CAT), and other substances in the sera, livers, ovaries, and follicular GCs of laying hens increased significantly after shading for 7 days; and reactive oxygen species (ROS) levels in the livers of laying hens also increased significantly. ROS in the serum, ovarian and GCs also increased. After shading for 7 days, the levels of 8-hydroxy-2 deoxyguanosine in the sera and ovarian tissues of laying hens increased significantly. Cell counting kit-8 detection showed that the proliferation activity of GCs in layer follicles decreased after shading for 7 days; the expression level of the anti-apoptotic gene B-cell lymphoma-2 in ovarian tissue and follicular GCs was significantly reduced, and the expression levels of pro-apoptotic caspase 3 (casp3), and SOD, glutathione peroxidase 2 (GPX2), and CAT were all significantly increased. Conclusion: Oxidative stress induced by shading light has a serious inhibitory effect on follicular development during reproduction in laying hens.

Phylogeographic study of the Bufo gargarizans species complex, with emphasis on Northeast Asia

이창훈,Jonathan J. Fong,Jian-Ping Jiang,Pi-Peng Li,Bruce Waldman,Jong Ryol Chong,이항,민미숙 한국통합생물학회 2021 Animal cells and systems Vol.25 No.6

We conduct a phylogeographic and population genetic study of the Asiatic toad (Bufo gargarizans) to understand its evolutionary history, and the influence of geology and climate. A total of 292 individuals from 94 locations were genotyped for two mitochondrial loci (cytb, ND2) and five nuclear introns (Sox9-2, Rho-3, CCNB2-3, UCH-2, and DBI-2), and we performed a suite of phylogenetic, population genetic, and divergence dating analyses. The phylogenetic trees constructed using mitochondrial loci inferred B. gargarizans being divided into two major groups: China mainland and Northeast Asia (Northeast China, Russia, and Korean Peninsula). As with previous studies of this species, we recover population genetic structure not tied to geographic region. Additionally, we discover a new genetic clade restricted to Northeast Asia that points towards the Korean Peninsula being a glacial refugium during the Pleistocene. The weak phylogeographic pattern of B. gargarizans is likely the result of multiple biological, anthropogenic, and historical factors – robust dispersal abilities as a consequence of physiological adaptations, human translocation, geologic activity, and glacial cycles of the Pleistocene. We highlight the complex geologic and climatic history of Northeast Asia and encourage further research to understand its impact on the biodiversity in the region.