A Review on DNA Methylation Occurring in Tissue Culture

Zhen Wang,Xin-Qiang Zheng,Yue-Rong Liang,Kwan-Jeong Song,Jian-Liang Lu 한국차학회 2015 한국차학회지 Vol.- No.S

Tissue culture is an important practice for industrial seedling production and germplasm conservation as well as transgenic operation. More and more evidences proved that DNA methylation change is usually involved in dedifferentiation, continuous cultivation and redifferentiation during tissue culture. DNA methylation variation increases with prolonging culture duration and increasing subculture times which might induce abnormal phenotype of propagules. The pattern and level of DNA methylation are significantly influenced by explants, growth regulators ents. DNA methylation change might reflect the growth and development processes and stress response of cells or tissues during tissue culture. Elucidation of epigenetic variation mechanism might help to improve tissue culture and transgene technology especially for the woody plant with high regeneration difficulty and low transformation frequency.

Predictive Role of ERCC1 and XPD Genetic Polymorphisms in Survival of Chinese Non-small Cell Lung Cancer Patients Receiving Chemotherapy

Zhang, Zhen-Yong,Tian, Xin,Wu, Rong,Liang, Yuan,Jin, Xue-Ying Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.6

Aim: There is increasing evidence that ERCC1 and XPD have roles in response to chemotherapy among patients with NSCLC, but the results are conflicting. Therefore, we conducted the present prospective study in a Chinese population. Methods: A total of 632 primary NSCLC patients were included, followed-up from May 2006 to May 2011. Polymorphisms were detected by real time PCR with TaqMan probse, using genomic DNA extracted from peripheral blood samples. The Cox regression model was used to analyze the hazard ratios (HR) for ERCC1 and XPD. Results: The median time of follow-up was 31.6 months. Our results showed the ERCC1 118 T/T(HR=1.65, 95% CI=1.17-2.43) and XPD 751 Gln/Gln genotypes (HR=1.52, 95%CI=1.04-2.08) were associated with an increased risk of death from NSCLC. Moreover, the ERCC118 T allele and XPD 751 Gln allele genotypes had a more higher risk of death from NSCLC among both ex-smokers and current smokers. Conclusion: In summary, ERCC1 and XPD gene polymorphisms might provide better prognostic predictive information for NSCLC patients in Chinese populations, with smoking possibly interacting with the genotypes.

Surrounding rock pressure of shallow-buried bilateral bias tunnels under earthquake

Liu, Xin-Rong,Li, Dong-Liang,Wang, Jun-Bao,Wang, Zhen Techno-Press 2015 Geomechanics & engineering Vol.9 No.4

By means of finite element numerical simulation and pseudo-static method, the shallow-buried bilateral bias twin-tube tunnel subject to horizontal and vertical seismic forces are researched. The research includes rupture angles, the failure mode of the tunnel and the distribution of surrounding rock relaxation pressure. And the analytical solution for surrounding rock relaxation pressure is derived. For such tunnels, their surrounding rock has sliding rupture planes that generally follow a "W" shape. The failure area is determined by the rupture angles. Research shows that for shallow-buried bilateral bias twin-tube tunnel under the action of seismic force, the load effect on the tunnel structure shall be studied based on the relaxation pressure induced by surrounding rock failure. The rupture angles between the left tube and the right tube are independent of the surface slope. For tunnels with surrounding rock of Grade IV, V and VI, which is of poor quality, the recommended reinforcement range for the rupture angles is provided when the seismic fortification intensity is VI, VII, VIII and IX respectively. This study is expected to provide theoretical support regarding the ground reinforcement range for the shallow-buried bilateral bias twin-tube tunnel under seismic force.

Cryptotanshinone Induces Inhibition of Breast Tumor Growth by Cytotoxic CD4+ T Cells through the JAK2/STAT4/ Perforin Pathway

Zhou, Jun,Xu, Xiao-Zhen,Hu, Yao-Ren,Hu, Ai-Rong,Zhu, Cheng-Liang,Gao, Guo-Sheng Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.6

Cryptotanshinone (CPT), is a quinoid diterpene isolated from the root of the Asian medicinal plant, Salvia miotiorrhiza bunge. Numerous researchers have found that it could work as a potent antitumor agent to inhibit tumor growth in vitro, buith there has been much less emphasis on its in vivo role against breast tumors. Using a mouse tumor model of MCF7 cells, we showed that CPT strongly inhibited MCF7 cell growth in vivo with polarization of immune reactions toward Th1-type responses, stimulation of naive CD4+ T cell proliferation, and also increased IFN-${\gamma}$ and perforin production of CD4+ T cells in response to tumor-activated splenocytes. Furthermore, data revealed that the cytotoxic activity of CD4+ T cells induced by CPT was markedly abrogated by concanamycin A(CMA), a perforin inhibitor, but not IFN-${\gamma}$ Ab. On the other hand, after depletion of CD4+ T cells or blocked perforin with CMA in a tumor-bearing model, CPT could not effectively suppress tumor growth, but this phenomenon could be reversed by injecting naive CD4+ T cells. Thus, our results suggested that CPT mainly inhibited breast tumor growth through inducing cytotoxic CD4+ T cells to secrete perforin. We further found that CPT enhanced perforin production of CD4+ T cells by up-regulating JAK2 and STAT4 phosphorylation. These findings suggest a novel potential therapeutic role for CPT in tumor therapy, and demonstrate that CPT performs its antitumor functions through cytotoxic CD4+ T cells.

Hsp90 Inhibitor Geldanamycin Enhances the Antitumor Efficacy of Enediyne Lidamycin in Association with Reduced DNA Damage Repair

Han, Fei-Fei,Li, Liang,Shang, Bo-Yang,Shao, Rong-Guang,Zhen, Yong-Su Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.17

Inhibition of heat shock protein 90 (Hsp90) leads to inappropriate processing of proteins involved in DNA damage repair pathways after DNA damage and may enhance tumor cell radio- and chemotherapy sensitivity. To investigate the potentiation of antitumor efficacy of lidamycin (LDM), an enediyne agent by the Hsp90 inhibitorgeldanamycin (GDM), and possible mechanisms, we have determined effects on ovarian cancer SKOV-3, hepatoma Bel-7402 and HepG2 cells by MTT assay, apoptosis assay, and cell cycle analysis. DNA damage was investigated with H2AX C-terminal phosphorylation (${\gamma}H2AX$) assays. We found that GDM synergistically sensitized SKOV-3 and Bel-7402 cells to the enediyne LDM, and this was accompanied by increased apoptosis. GDM pretreatment resulted in a greater LDM-induced DNA damage and reduced DNA repair as compared with LDM alone. However, in HepG2 cells GDM did not show significant sensitizing effects both in MTT assay and in DNA damage repair. Abrogation of LDM-induced $G_2/M$ arrest by GDM was found in SKOV-3 but not in HepG2 cells. Furthermore, the expression of ATM, related to DNA damage repair responses, was also decreased by GDM in SKOV-3 and Bel-7402 cells but not in HepG2 cells. These results demonstrate that Hsp90 inhibitors may potentiate the antitumor efficacy of LDM, possibly by reducing the repair of LDM-induced DNA damage.

DNA methylation levels in different tissues in tea plant via an optimized HPLC method

Ying Gao,Jia-Li Hao,Zhen Wang,Kwan-Jeong Song,Jian-Hui Ye,Xin-Qiang Zheng,Yue-Rong Liang,Jian-Liang Lu 한국원예학회 2019 Horticulture, Environment, and Biotechnology Vol.60 No.6

DNA methylation is one of the most important events in epigenetics and significantly influences plant growth and development. In the present study, we established and optimized a high-performance liquid chromatography method for detecting the base composition in DNA in tea plant (Camellia sinensis L.) tissues by using saline buffers-free mobile phases. The DNA methylation level varied with tea plant tissue, cultivar, and growth stage. A relatively higher DNA methylation level was observed in tender leaf (38.34%) and pistil (38.19%) tissues, while a relatively low level was detected in capillary root (19.45%), stamen (19.61%), and old leaf (20.70%) tissues. The pattern of the methylation level formed a saddle curve during the growth of dormant buds in spring; the lowest point appeared at the stage of one leaf and a bud. The methylation level in the adventitious buds regenerated from the branch after pruning seemed to decrease with an increase in the degree of pruning. These DNA methylation levels might be associated with the development of tea plant.

Biochemical Characterization of a GDSL-Motif Esterase from Bacillus sp. K91 with a New Putative Catalytic Mechanism

( Jun Mei Ding ),( Ting Ting Yu ),( Lian Ming Liang ),( Zhen Rong Xie ),( Yun Juan Yang ),( Jun Pei Zhou ),( Bo Xu ),( Jun Jun Li ),( Zun Xi Huang ) 한국미생물 · 생명공학회 2014 Journal of microbiology and biotechnology Vol.24 No.11

The esterase gene Est8 from the thermophilic bacterium Bacillus sp. K91 was cloned and expressed in Escherichia coli. The monomeric enzyme exhibited a theoretical molecular mass of 24.5 kDa and an optimal activity around 50°C at pH 9.0. A model of Est8 was constructed using a hypothetical YxiM precursor structure (2O14_A) from Bacillus subtilis as template. The structure showed an α/β-hydrolase fold and indicated the presence of a typical catalytic triad consisting of Ser-11, Asp-182, and His-185, which were investigated by site directed replacements coupled with kinetic characterization. Asp-182 and His-185 residues were more critical than the Ser-11 residue in the catalytic activity of Est8. A comparison of the amino acid sequence showed that Est8 could be grouped into the GDSL family and further classified as an SGNH hydrolase. Est8 is a new member of the SGNH hydrolase subfamily and may employ a different catalytic mechanism.

Metastasis associated genomic aberrations in stage II rectal cancer

Hong Zhao,Zhi-Zhou Shi,Rui Jiang,Dong-Bing Zhao,Hai-Tao Zhou,Jian-Wei Liang,Xin-Yu Bi,Jian-Jun Zhao,Zhi-Yu Li,Jian-Guo Zhou,Zhen Huang,Ye-Fan Zhang,Jian Wang,Xin Xu,Yan Cai,Ming-Rong Wang,Yu Zhang 한국유전학회 2016 Genes & Genomics Vol.38 No.11

Genomic aberrations of rectal carcinoma, especially DNA copy number changes associated with metastasis were largely unclear. We aim to identify the metastasis associated biomarkers in stage II rectal cancer. Formalin-fixed, paraffin-embedded primary tumor tissues of stage II rectal carcinoma were analyzed by array-based comparative genomic hybridization, and genomic aberrations were identified by Genomic Workbench and SAM software. Copy number changes and mRNA expressions were validated by Real-time PCR in an independent rectal cancer samples. The results showed that the most frequent gains in stage II rectal cancer were at 1q21.2-q23.1, 3p21.31, 11q12.2-q23.3, 12q24.11-q24.31, 12q13.11-q14.1 and losses in 18q11.2-q23, 17q21.33-q22, 13q31.1-q31.3, 21q21.1-q21.3, 8p23.3-p23.1 and 4q22.1-q23. Twenty-two amplifications and five homozygous deletions were also identified. We further found that S100A1 (1q21.3-q23.1), MCM7 (7q22.1) and JUND (19p13.11) were amplified and overexpressed in stage II rectal cancer. Interestingly, the genomic aberrations affected 14 signaling pathways including VEGF signaling pathway and fatty acid metabolism. Most importantly, loss of 13q31.1-q34 and gain of 1q44 were associated with distant metastasis. Our results indicated that these metastasis associated genomic changes may be useful to reveal the pathogenesis of rectal cancer metastasis and identify candidate biomarkers.

Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China

Wang Ju-Wei,Han Pei-Jie,Han Da-Yong,Zhou Sen,Li Kuan,He Peng-Yu,Zhen Pan,Yu Hui-Xin,Liang Zhen-Rong,Wang Xue-Wei,Bai Feng-Yan 한국미생물학회 2021 The journal of microbiology Vol.59 No.8

The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55–18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85–23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.