Efficient Mining Maximal Subspace Differential Co-expression Patterns in Matrix Datasets : a General Earthquake Analysis Approach

Miao Wang,Zhiyong Xiong,Liang Xu,Lihua Zhang,Cheng Gong,Yi Hu,Yi Lin 보안공학연구지원센터 2015 International Journal of Database Theory and Appli Vol.8 No.3

The electromagnetic anomaly observations before earthquake, have been confirmed by many cases of strong earthquakes. The analysis of earthquake magnetic anomaly is an effective approach for seismo-precursor detection. Traditional frequent mining methods for electromagnetic matrix datasets analysis often find the co-related items. However, these methods may miss the items which are differential co-related patters under different datasets. Mining these differential co-related patterns is more valuable for inferring potential knowledge. In this paper, we develop an algorithm, MSPattern, to mine maximal subspace differential co-expression patterns. MSPattern constructs a weighted undirected item-item relational graph firstly. Then all the maximal co-related patterns would be mined using item-growth method in above graph. MSPattern also utilizes several techniques for producing maximal patterns without candidate patterns maintenance. Evaluated by real electromagnetic matrix datasets and the gene expression datasets, the experimental results show our algorithm can find some potential knowledge for earthquake analysis, and MSPattern algorithm is more efficient than traditional ones. The performance of MSPattern is also evaluated by empirical p-value and gene ontology, the results show our algorithm can find statistical significant and biological differential co-expression patterns.

Telomere-Mitochondrion Links Contribute to Induction of Senescence in MCF-7 Cells after Carbon-Ion Irradiation

Miao, Guo-Ying,Zhou, Xin,Zhang, Xin,Xie, Yi,Sun, Chao,Liu, Yang,Gan, Lu,Zhang, Hong Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.4

The effects of carbon-ion irradiation on cancer cell telomere function have not been comprehensively studied. In our previous report cancer cells with telomere dysfunction were more sensitive to carbon-ion irradiation, but the underlying mechanisms remained unclear. Here we found that telomerase activity was suppressed by carbon-ion irradiation via hTERT down-regulation. Inhibition of telomere activity by MST-312 further increased cancer cell radiosensitivity to carbon-ion radiation. hTERT suppression caused by either carbon-ion irradiation or MST-312 impaired mitochondrial function, as indicated by decreased membrane potential, mtDNA copy number, mitochondrial mass, total ATP levels and elevated reactive oxygen species (ROS). PGC-$1{\alpha}$ expression was repressed after carbion-ion irradiation, and hTERT inhibition by MST-312 could further exacerbate this effect. Lowering the mitochondrial ROS level by MitoTEMPO could partially counteract the induction of cellular senescence induced by carbon-ion radiation and MST-312 incubation. Taken together, the current data suggest that telomere-mitochondrion links play a role in the induction of senescence in MCF-7 cells after carbon-ion irradiation.

Protective Effect of Nitric Oxide against Oxidative Damage in Arabidopsis Leaves under Ultraviolet-B Irradiation

Lingang Zhang,Shuo Zhou,Yi Xuan,Miao Sun,Liqun Zhao 한국식물학회 2009 Journal of Plant Biology Vol.52 No.2

Nitric oxide (NO) is a key molecule involved in many physiological processes. To characterize its roles in the tolerance of Arabidopsis thaliana to ultraviolet-B (UV-B), we investigated the effect of a reduced endogenous NO level on oxidative damage to wild-type and mutant (Atnoa1) plants. Under irradiation, hydrogen peroxide was accumulated more in mutant leaves than in the wild type. However, the amounts of UV-B-absorbing compounds (flavonoids and anthocyanin) and the activities of two antioxidant enzymes—catalase (CAT, EC 1.11.1.6) and ascorbate peroxidase (APX, EC 1.11.1.11)—were lower in leaves of the former. Supplementing with sodium nitroprusside, an NO donor, could alleviate the oxidative damage to mutant leaves by increasing flavonoid and anthocyanin contents and enzyme activities. In comparison, Nw ? nitro ? l ? arginine, an inhibitor of nitric oxide synthase, had the opposite effects on oxidation resistance in wild-type leaves. All these results suggest that nitric oxide acts as a signal for an active oxygen-scavenging system that protects plants from oxidative stress induced by UV-B irradiation.

High-Level Expression of an Aspergillus niger Endo-β-1,4-Glucanase in Pichia Pastoris Through Gene Codon Optimization and Synthesis

( Shu Miao Zhao ),( Jun Huang ),( Chang Yi Zhang ),( Ling Deng ),( Nan Hu ),( Yun Xiang Liang ) 한국미생물 · 생명공학회 2010 Journal of microbiology and biotechnology Vol.20 No.3

Elevated Expression of Nuclear Protein Kinase CK2α as a Poor Prognosis Indicator in Lymph Node Cancerous Metastases of Human Thyroid Cancers

Guo, Miao,Liu, Chao,Qi, Feng-Jie,Zhang, Xiu-Mei,Ren, Li-Li,Liu, Yi-Meng,Meng, Zhi-Chao,Zhu, Zhi-Tu,Xiao, Jian-Ying Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.17

Aim: To investigate the expression of protein kinase $CK2{\alpha}$ ($CK2{\alpha}$) in human thyroid disease and its relationship with thyroid cancer metastasis. Materials and Methods: Using immunohistochemistry we measured the expression of $CK2{\alpha}$ in 76 benign and malignant human thyroid cancer tissues, including 10 pairs of papillary carcinoma tissues with or without lymph node cancerous metastasis and similarly 10 pairs of lymph nodes. Results: The expression of $CK2{\alpha}$ was found to be higher in thyroid carcinoma cases (papillary carcinoma, follicular carcinoma, anaplastic carcinoma and medullary carcinoma) than in ones such as chronic lymphocytic thyroiditis, nodular goiter and adenoma. These findings were also confirmed by RT-PCR and Western blotting. More strikingly, elevated expression of $CK2{\alpha}$ in thyroid papillary carcinoma tissues was not only significantly associated with lymph node cancerous metastasis and clinical stage of thyroid cancers; but also correlated with epithelial-mesenchymal transition (EMT) and high tenascin C (TNC) expression. In addition, EMT and high TNC expression in thyroid carcinoma tissues was significantly associated with lymph node cancerous metastasis. Conclusions: Elevated expression of nuclear $CK2{\alpha}$ is a poor prognosis indicator in lymph node cancerous metastasis of human thyroid cancers.

Simple and green fabrication of a biomass-derived N and O self-doped hierarchical porous carbon via a self-activation route for supercapacitor application

Yang Binbin,Zhang Deyi,He Jingjing,Wang Yuling,Wang Kunjie,Li Hongxia,Wang Yi,Miao Lei,Ren Ruiye,Xie Mei 한국탄소학회 2020 Carbon Letters Vol.30 No.6

To meet the increased performance and cost requirements of commercial supercapacitor, a N and O self-doped hierarchical porous carbon is fabricated via a green and simple self-activation route utilizing leaves of wild hollyhock as raw materials. Comparing to commercial activated carbon, the reported material exhibits some marked merits, such as simple and green fabrication process, low cost, and superior capacitance performance. The specifc surface area of the obtained N and O co�doped hierarchical porous carbon arrives 954 m2 g−1, and the content of the self-doped nitrogen and oxygen reaches 2.64 at.% and 7.38 at.%, respectively. The specifc capacitance of the obtained material reaches 226 F g−1 while the specifc capacitance of the symmetric supercapacitor arrives 47.3 F g−1. Meanwhile, more than 90.3% of initial specifc capacitance is kept under a current density of 20 A g−1, and no arresting degradation is observed for capacitance after 5000 times cycle, perfectly demonstrating the excellent cycle and rate capability of the obtained material. The obtained N and O co-doped hierarchical porous carbon are expected to be an ideal substitution for commercial activated carbon.

Molecular Epidemiology and Prevalence of Echovirus 30 in Zhejiang Province, China, from 2002 to 2015

( Yin Chen ),( Yi Sun ),( Juying Yan ),( Ziping Miao ),( Changping Xu ),( Yanjun Zhang ),( Haiyan Mao ),( Liming Gong ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.12

Echovirus serotype 30 (ECHO30) has been responsible for several recent worldwide outbreaks of viral meningitis. In Zhejiang Province, China, ECHO30 has been one of the main causes of viral meningitis for years. This study, using phylogenetic analysis of the VP1 gene, was performed to investigate the general molecular epidemiology and genetic patterns of ECHO30 circulating in Zhejiang Province between the years 2002 and 2015. The nucleotide sequences of ECHO30 VP1 showed that they were 64.8% identical with the prototype strain, Bastianni, while the amino acids were 84.9% identical. Phylogenetic analyses showed that ECHO30 in the Zhejiang area has diverged into two genotypes. Genotype I consists of strains isolated since 2002, whereas genotype II includes strains that were mainly isolated during the 2002 to 2004 outbreak. ECHO30 has been endemically circulating in both humans and the environment for a long period of time. Additionally, we evaluated the significance of recombination presented during the years 2005 to 2007 to demonstrate that recombination plays an important role in the prevalence of ECHO30 in the Zhejiang area.

Transcript Profiling of Toll-Like Receptor mRNAs in Selected Tissues of Mink (Neovison vison)

( Mingwei Tong ),( Li Yi ),( Yuening Cheng ),( Miao Zhang ),( Zhigang Cao ),( Jianke Wang ),( Hang Zhao ),( Peng Lin ),( Yong Yang ),( Shipeng Cheng ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.12

Toll-like receptors (TLRs) can recognize conserved molecular patterns and initiate a wide range of innate and adaptive immune responses against invading infectious agents. The aim of this study was to assess the transcript profile of mink TLRs (mTLRs) in mink peripheral blood mononuclear cells (PBMCs) and a range of tissues, and to explore the potential role of mTLRs in the antiviral immune response process. The results indicated that the mTLR partial nucleotide sequences had a high degree of nucleotide identity with ferret sequences (95-98%). Phylogenetic analysis showed that mammalian TLRs grouped into five TLR families, with a closer relationship of the mTLRs with those of ferret than the other mammalian sequences. Moreover, all the mTLRs were ubiquitously expressed in lymphoid organs (spleen and lymph nodes) and PBMCs. Interestingly, the mTLR expression patterns in lung, uterus, and heart showed quite a lot of similarity. Another remarkable observation was the wide expression of mTLR1-3 mRNAs in all tissues. Among the analyzed tissues, skeletal muscle was revealed to being the lowest repertoire of mTLR expression. Additionally, mink PBMCs exposed to the canine distemper virus revealed significant upregulation of mTLR2, mTLR4, mTLR7, and mTLR8 mRNAs, indicating that mTLRs have a role in innate immunity in the mink. Collectively, our results are the first to establish the basic expression patterns of mTLRs and the relationship between mTLRs and a virus, which will contribute to better understanding of the evolution and the functions of mTLRs in the innate immune system in minks.

Clinical Implications of p57^KIP2 Expression in Breast Cancer

Xu, Xiao-Yin,Wang, Wen-Qian,Zhang, Lei,Li, Yi-Ming,Tang, Miao,Jiang, Nan,Cai, Shou-Liang,Wei, Liang,Jin, Feng,Chen, Bo Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.10

Objective: To study the relationship between expression of $p57^{KIP2}$ and prognosis and other clinicopathological parameters in invasive breast cancers. Methods: We assessed the expression of $p57^{KIP2}$ in 89 cases of invasive breast cancer and 20 cases of normal breast tissue by immunohistochemical methods and analyzed the results with SPSS software (ver. 16.0). Result: The positive expression rates of $p57^{KIP2}$ protein in the invasive breast cancers and surrounding normal tissue were 30.3% (27/89) and 65% (13/20), respectively. Cases with no $p57^{KIP2}$ expression exhibited a significantly higher post-operative distant metastasis rate than those with $p57^{KIP2}$ expression (37.9% vs. 14.8%; P = 0.01). DFS analysis showed that $p57^{KIP2}$-/C-erbB-2+ tumors also exhibited a significantly higher post-operative distant metastasis rate than the other groups (66.7% vs. 29.2%; P = 0.007), as did $p57^{KIP2}$-/p53+ tumors (64.3% vs. 22.7%; P = 0.001). Survival analysis revealed that $p57^{KIP2}$ was associated with breast cancer-specific survival overall (P = 0.045, log-rank test). Subgroup analysis demonstrated that individuals with $p57^{KIP2}$-/C-erbB-2+tumors experienced significantly worse post-operative survival than those with $p57^{KIP2}$-/C-erbB-2- or other tumors (P = 0.006, log-rank test). $p57^{KIP2}$-/p53+ tumors were associated with significantly worse post-operative survival than $p57^{KIP2}$-/p53- or other tumors (P = 0.001, log-rank test). Cox regression analysis showed that $p57^{KIP2}$ was a non-independent prognostic factor for breast cancer (P = 0.303). Conclusions: $p57^{KIP2}$ is expressed at low levels in invasive breast cancer and is associated with better overall survival rate and disease-free survival in breast cancer patients, but it was a non-independent prognostic factor for breast cancer. Thus, the connection between $p57^{KIP2}$/p53 and $p57^{KIP2}$/C-erbB-2 may provide biomarkers for breast cancer.

Nucleomodulin BspJ as an effector promotes the colonization of Brucella abortus in the host

Zhongchen Ma,Shuifa Yu,Kejian Cheng,Yuhe Miao,Yimei Xu,Ruirui Hu,Wei Zheng,Jihai Yi,Huan Zhang,Ruirui Li,Zhiqiang Li,Yong Wang,Chuangfu Chen 대한수의학회 2022 Journal of Veterinary Science Vol.23 No.1

Background: Brucella infection induces brucellosis, a zoonotic disease. The intracellular circulation process and virulence of Brucella mainly depend on its type IV secretion system (T4SS) expressing secretory effectors. Secreted protein BspJ is a nucleomodulin of Brucella that invades the host cell nucleus. BspJ mediates host energy synthesis and apoptosis through interaction with proteins. However, the mechanism of BspJ as it affects the intracellular survival of Brucella remains to be clarified. Objectives: To verify the functions of nucleomodulin BspJ in Brucella's intracellular infection cycles. Methods: Constructed Brucella abortus BspJ gene deletion strain (B. abortus ΔBspJ) and complement strain (B. abortus pBspJ) and studied their roles in the proliferation of Brucella both in vivo and in vitro. Results: BspJ gene deletion reduced the survival and intracellular proliferation of Brucella at the replicating Brucella-containing vacuoles (rBCV) stage. Compared with the parent strain, the colonization ability of the bacteria in mice was significantly reduced, causing less inflammatory infiltration and pathological damage. We also found that the knockout of BspJ altered the secretion of cytokines (interleukin [IL]-6, IL-1β, IL-10, tumor necrosis factor-α, interferon-γ) in host cells and in mice to affect the intracellular survival of Brucella. Conclusions: BspJ is extremely important for the circulatory proliferation of Brucella in the host, and it may be involved in a previously unknown mechanism of Brucella's intracellular survival.