Comparative Genomics Profiling of Clinical Isolates of Helicobacter pylori in Chinese Populations Using DNA Microarray

Yue-Hua Han,Wen-Zhong Liu,Yao-Zhou Shi,Li-Qiong Lu,Shudong Xiao,Qing-Hua Zhang,Guo-Ping Zhao 한국미생물학회 2007 The journal of microbiology Vol.45 No.1

In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China.The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on ln(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori’s growth and colonization in its host. In contrast, 522(31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strainspecific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.

Ginsengenin derivatives synthesized from 20(R)-panaxotriol: Synthesis, characterization, and antitumor activity targeting HIF-1 pathway

Guo, Hong-Yan,Xing, Yue,Sun, Yu-Qiao,Liu, Can,Xu, Qian,Shang, Fan-Fan,Zhang, Run-Hui,Jin, Xue-Jun,Chen, Fener,Lee, Jung Joon,Kang, Dongzhou,Shen, Qing-Kun,Quan, Zhe-Shan The Korean Society of Ginseng 2022 Journal of Ginseng Research Vol.46 No.6

Background: Ginseng possesses antitumor effects, and ginsenosides are considered to be one of its main active chemical components. Ginsenosides can further be hydrolyzed to generate secondary saponins, and 20(R)-panaxotriol is an important sapogenin of ginsenosides. We aimed to synthesize a new ginsengenin derivative from 20(R)-panaxotriol and investigate its antitumor activity in vivo and in vitro. Methods: Here, 20(R)-panaxotriol was selected as a precursor and was modified into its derivatives. The new products were characterized by ¹H-NMR, ¹³C-NMR and HR-MS and evaluated by molecular docking, MTT, luciferase reporter assay, western blotting, immunofluorescent staining, colony formation assay, EdU labeling and immunofluorescence, apoptosis assay, cells migration assay, transwell assay and in vivo antitumor activity assay. Results: The derivative with the best antitumor activity was identified as 6,12-dihydroxy-4,4,8,10,14-pentamethyl-17-(2,6,6-trimethyltetrahydro-2H-pyran-2-yl)hexadecahydro-1H-cyclopenta[a]phenanthren-3-yl(tert-butoxycarbonyl)glycinate (A11). The focus of this research was on the antitumor activity of the derivatives. The efficacy of the derivative A11 (IC₅₀ < 0.3 µM) was more than 100 times higher than that of 20(R)- panaxotriol (IC₅₀ > 30 µM). In addition, A11 inhibited the protein expression and nuclear accumulation of the hypoxia-inducible factor HIF-1α in HeLa cells under hypoxic conditions in a dose-dependent manner. Moreover, A11 dose-dependently inhibited the proliferation, migration, and invasion of HeLa cells, while promoting their apoptosis. Notably, the inhibition by A11 was more significant than that by 20(R)-panaxotriol (p < 0.01) in vivo. Conclusion: To our knowledge, this is the first study to report the production of derivative A11 from 20(R)-panaxotriol and its superior antitumor activity compared to its precursor. Moreover, derivative A11 can be used to further study and develop novel antitumor drugs.

Resistance selection with cadmium and changes in the activities of antioxidases in Boettcherisca peregrina (Diptera: Sarcophagidae)

Guo-Xing Wu,Xi Gao,Qing Tan,Zheng-Yue Li,Cui Hu,Gong-yin Ye 한국응용곤충학회 2014 Journal of Asia-Pacific Entomology Vol.17 No.2

In order to establish a physiological link between antioxidases and the resistance level of insects to cadmium(Cd), natural populations of Boettcherisca peregrina (Diptera: Sarcophagidae)weremaintained for 20 generationsand reared either on an uncontaminated diet or on a diet contaminated with cadmium (Cd) at a concentrationequivalent to the median lethal concentration (LC50) as determined every five generations. A relatively susceptiblestrain (S) and a Cd-resistant strain (R) were selected. Themetal accumulation, growth and development, reproduction,and antioxidant enzyme activities in these strains were analyzed. The results showed that R-strain organismshad enhanced juvenile survivorship, increased Cd accumulation, and increased adult female fecundity whencompared with S-strain. The larval enzyme activities of superoxide dismutase (SOD), catalase (CAT), glutathionereductase (GR), and glutathione S-transferase (GST) in R-strain larvae were higher than those in S-strain larvaewhen fed diets with or without Cd. This indicates that Cd resistance in B. peregrina larvae is mediated by SOD,CAT, GR, and GST.

Pig Large tumor suppressor2 (Lats2), a novel gene that may regulate the fat reduction in adipocyte

( Qiu Yue Liu ),( Xiao Rong Gu ),( Yi Qiang Zhao ),( Jin Zhang ),( Yao Feng Zhao ),( Qing Yong Meng ),( Guo Heng Xu ),( Xiao Xiang Hu ),( Ning Li ) 생화학분자생물학회 2010 BMB Reports Vol.43 No.2

Comparative Genomics Profiling of Clinical Isolates of Helicobacter pylori in Chinese Populations Using DNA Microarray

Han, Yue-Hua,Liu, Wen-Zhong,Shi, Yao-Zhou,Lu, Li-Qiong,Xiao, Shudong,Zhang, Qing-Hua,Zhao, Guo-Ping The Microbiological Society of Korea 2007 The journal of microbiology Vol.45 No.1

In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on In(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori's growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strain-specific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.

Apoptotic Effects of psiRNA-STAT3 on 4T1 Breast Cancer Cells in Vitro

Zhou, Yue,Tian, Lin,Zhang, Ying-Chao,Guo, Bao-Feng,Zhou, Qing-Wei Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.16

Background: The aim of this study was to investigate the effect of a Lipofectamine2000 (Life2000) Transfection Reagent transfected psiRNA-STAT3 plasmid on 4T1 breast cancer cells. Materials and Methods: MTT was used to detect the cell proliferation of breast cancer 4T1 cells at different periods (0h, 6h, 8h, 10h); the cell cycle was assessed by flow cytometry; variation of apoptosis and mitochondrial membrane potential was observed under a fluorescence microscope; immunohistochemical staining was used to determine the expression of caspase-3 and cyclin-D1 protein. Results: An obvious effect of inhibition to 4T1 cancer cells could be observed at 8h after the psiRNA-STAT3 was transfected. Typical alterations of apoptotic morphological features were visible in the psiRNA-STAT3 treatment group. Mitochondrial membrane potential decreased significantly, the number of cells was increased in G0/G1 phase, and the number of cells was decreased in S phase, and the data were statistically significant (p<0.05), compared with the Scramble and Mock groups. Expression of caspase-3 protein was increased significantly, while that of cyclin D1 was significantly decreased. Conclusions: Life2000 transfected psiRNA-STAT3 plasmid can inhibit 4T1 tumor cell proliferation and promote apoptosis of 4T1 tumor cells, which process depends on the regulation of expression of cyclin D1 and caspase-3 protein.

Electronic Structures and Optical Properties of CuSCN with Cu Vacancies

Wei Jin,Guo-Qing Yue,Fu-Shun Ke,Song Wu,Hai-Bin Zhao,Liang-Yao Chen,Song-You Wang,Yu Jia 한국물리학회 2012 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.60 No.8

Based on density functional theory (DFT) within the generalized gradient approximation (GGA) using the CASTEP code, we calculated the formation energy of a Cu vacancy, as well as the band structure and the optical properties of β-CuSCN with Cu vacancies. Removal a Cu atom from the 32-site and the 72-site supercell results in an enlargement of the band-gap and a slight relaxation in the lattice parameter. An accepter level above the valence band maximum is observed in the 32-site supercell with a Cu vacancy, which results in the onset of a small absorption pre-peak at 0.65 eV.

Short Low Concentration Cisplatin Treatment Leads to an Epithelial Mesenchymal Transition-like Response in DU145 Prostate Cancer Cells

Liu, Yi-Qing,Zhang, Guo-An,Zhang, Bing-Chang,Wang, Yong,Liu, Zheng,Jiao, Yu-Lian,Liu, Ning,Zhao, Yue-Ran Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.3

Background: Prostate cancer is one of the main causes of cancer death, and drug resistance is the leading reason for therapy failure. However, how this occurs is largely unknown. We therrfore aimed to study the response of DU145 cells to cisplatin. Materials and Methods: Du145 prostate cancer cells were treated with a low dose of cisplatin for 24 h and cell viability and number were determined by MTT assay and trypan blue exclusion assay, respectively. The real time polymerase chain reaction (PCR) was used to assess responses to cisplatin treatment. Results: After 24h $2{\mu}g/ml$ treatment did not result in significant reduction in cell viability or number. However, it led to enhanced cancer cell invasiveness. E-cadherin mRNA was reduced, and vimentin, Snail, Slug, metalloproteinase 9 (MMP9) mRNA expression increased significantly, a feature of epithelial-mesenchymal transition (EMT). Conclusions: Short time low concentration cisplatin treatment leads to elevated invasiveness of DU145 cancer cells and this is possibly due to EMT.

Study on molten salt oxidation process of simulated Co doped cation exchange resins

Yun Xue,Yue-Lin Wang,Yu Li,Wen-Da Xu,Fu-Qiu Ma,Yang-Hai Zheng,Qing-Guo Zhang,Zhi Zhang,Mi-lin Zhang,Yong-De Yan 한국공업화학회 2023 Journal of Industrial and Engineering Chemistry Vol.126 No.-

Cation exchange resins (CERs) are widely applied to purify waste liquids generated during the operationof nuclear reactors. The radioactive nuclides 60Co and 58Co are important corrosion activation products inreactor cooling water. In this study, the simulated Co doped CERs were oxidized with ternary carbonate. According to the thermogravimetric analysis (TG), the decomposition of Co doped CERs includes threeprocesses: 1. Elimination of the osmotic water; 2. Pyrolysis of sulfonic acid group; 3. Destruction of styrene–divinylbenzene copolymer. The X-Ray Diffraction (XRD) patterns indicate that sulfur mainly exists inthe form of sulfate in waste salt. The Co2+ undergoes the path of CoS2 ? Co3O4 with the increase of temperatureand the transition point is 650 C. Combined with Fourier Transform Infrared Spectrometer (FTIR)spectra and X-ray Photoelectron Spectroscopy (XPS) analysis, sulfonic acid groups begin to decomposeat 350 C. During the molten salt oxidation process, most of the sulfur in sulfonic acid groups is entrappedby carbonate as the form of sulfate, and a little of which remains as sulfone group, sulfoxide group andsulfur bridge in residue. When the resins are oxidized at 800 C, the retention rate of Co2+ is 97.3%, indicatingthat the molten salt oxidation can effectively remain Co2+ and convert it into a more stablesubstance.

A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

Jia-Feng Yu,Jing Guo,Qing-Bin Liu,Yue Hou,Ke Xiao,Qing-Li Chen,Ji-Hua Wang,Xiao Sun 한국유전학회 2015 Genes & Genomics Vol.37 No.4

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.