Gene Expression Profile of Helicobacter pylori in Response to Growth Temperature Variation

Yue-hua Han,Wen-zhong Liu,Yao-zhou Shi,Li-qiong Lu,Shu-dong Xiao,Qing-hua Zhang 한국미생물학회 2009 The journal of microbiology Vol.47 No.4

A Helicobacter pylori whole-genome DNA microarray was constructed to study expression profiles of H. pylori in response to a sudden temperature transfer from 37°C to 20°C. The expression level of the genome at each of four time points (15, 30, 60, and 120 min) after temperature downshift was compared with that just before cold treatment. Globally, 10.2% (n=167) of the total predicted H. pylori genes (n=1636) represented on the microarray were significantly differentially expressed (p<0.05) over a 120 min period after shift to low temperature. The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative real-time PCR. Up-regulated genes mainly included genes involved in energy metabolism and substance metabolism, cellular processes, protein fate, ribosomal protein genes, and hypothetical protein genes, which indicate the compensational responses of H. pylori to temperature downshift. Those genes play important roles in adaption to temperature downshift of H. pylori. Down-regulation of DNA metabolism genes and cell envelope genes and cellular processes genes may reflect damaged functions under low temperature, which is unfavorable to bacterial infection and propagation. Overall, this time-course study provides new insights into the primary response of H. pylori to a sudden temperature downshift, which allow the bacteria to survive and adapt to the new host environment.

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.

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.

Preparation and characteristics of carboplatin-Fe@C-loaded chitosan nanoparticles with dual physical drug-loaded mechanisms

Yue-Hua Guo,Fu-Rong Li,Shi-Yun Bao,Tao Han,Jun-Jian Cao,Han-Xin Zhou 한국물리학회 2007 Current Applied Physics Vol.7 No.s1

The present work is intended to set up the optimal carboplatin-Fe@C-loaded chitosan nanoparticles method and to compare andassess carboplatin-Fe@C-loaded with carboplatin-Fe-loaded chitosan nanoparticles. Both kinds of nanoparticles were prepared by areverse microemulsion method. The carboplatin-Fe@C-loaded chitosan nanoparticles consisted of Fe@C nanopowder with the adsorbeddrug as the magnetic core, chitosan as the matrix and carboplatin as the model drug. The core of the carboplatin-Fe-loaded chitosannanoparticles was pure iron nanopowder, which was unable to adsorb a drug. The characteristics of both kinds of nanoparticles weredetermined and compared. The results showed that both kinds of nanoparticles were spherical in shape with an average size of210 nm ± 26 nm (size range 150300 nm) and a good magnetic responsivity. The drug content of the nanoparticles wasrespectively. The cumulative release percentages of carboplatin-Fe@C-loaded chitosan nanoparticles in vitro in 1d, 2d, 3d, 4d were60%, 74%, 84%, and 92%, respectively, and those of carboplatin-Fe-loaded chitosan nanoparticles in 1d, 2d were 81% and 91%. Thus,the carboplatin-Fe@C-loaded chitosan nanoparticles with dual physical drug-loaded mechanisms (physical encapsulation and adsorp-tion of active carbon) possessed a higher drug content and showed more sustained releasing. The cooperation of multiple mechanismswas a promising feature to improve the properties of nanoparticles.

On-orbit Reconfiguration Using Adaptive Dynamic Programming for Multi-mission-constrained Spacecraft Attitude Control System

Yue-Hua Cheng,Bin Jiang,Huan Li,Xiao-dong Han 제어·로봇·시스템학회 2019 International Journal of Control, Automation, and Vol.17 No.4

For the on-orbit reconfiguration problem of spacecraft attitude control systems under multi-mission constraints, the idea of a reinforcement-learning algorithm is adopted, and an adaptive dynamic programming algorithm for on-orbit reconfiguration decision-making that is based on a dual optimization index is proposed. Two optimization objectives, total mission reward and total control cost (energy consumption), are defined to obtain the optimal reconfiguration policy of the spacecraft attitude control system reconfiguration, and the on-orbit reconfiguration model for multi-mission constraints is established. Then, based on the Bellman optimality principle, the optimal reconfiguration policy formulated by the discrete HJB equation is obtained. Since the HJB equation is difficult to solve accurately, a method of bi-objective adaptive dynamic programming is proposed to obtain the optimal reconfiguration policy. This method constructs a mission network and an energy network. The method then adopts a Q-learning-based algorithm to train the networks to estimate the values of total mission reward and total control cost to achieve the on-orbit optimal reconfiguration decision under multi-mission constraints. Simulation results for different cases demonstrate the validity and rationality of the proposed method.

Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

Haoyuan Han,Qin Zhang,Kexin Gao,Xiangpeng Yue,Tao Zhang,Rui-Hua Dang,Xianyong Lan,Hong Chen,Chuzhao Lei 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.8

In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10‒4) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

Association of TNF-α-308 and -238 Polymorphisms with Risk of Cervical Cancer: A Meta-analysis

Pan, Feng,Tian, Jing,Ji, Chu-Shu,He, Yi-Fu,Han, Xing-Hua,Wang, Yong,Du, Jian-Ping,Jiang, Feng-Shou,Zhang, Ying,Pan, Yue-Yin,Hu, Bing Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.11

Published data on the associations between tumor necrosis factor-alpha (TNF-${\alpha}$) promoter -308G>A and -238G>A polymorphisms and cervical cancer risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was performed. Data were collected from MEDLINE and PubMed databases. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated in a fixed/random effect model. 13 separate studies including 3294 cases and 3468 controls were involved in the meta-analysis. We found no association between TNF-${\alpha}$-308G>A polymorphism and cervical cancer in overall population. In subgroup analysis, significantly elevated risks were found in Caucasian population (A vs. G: OR = 1.43, 95% CI = 1.00-2.03; AA vs. GG: OR = 2.09, 95% CI = 1.34-3.25; Recessive model: OR = 2.09, 95% CI = 1.35-3.25) and African population (GA vs. GG: OR = 1.53, 95% CI = 1.02-2.30). An association of TNF-${\alpha}$-238G>A polymorphism with cervical cancer was found (A vs. G: OR = 0.61, 95% CI = 0.47-0.78; GA vs. GG: OR = 0.59, 95% CI = 0.45-0.77; Dominant model: OR = 0.59, 95% CI = 0.46-0.77). When stratified by ethnicity, similar association was observed in Caucasian population (A vs. G: OR = 0.62, 95% CI = 0.46-0.84; GA vs. GG: OR = 0.59, 95% CI = 0.43-0.82; Dominant model: OR = 0.60, 95% CI = 0.44-0.83). In summary, this meta-analysis suggests that TNF-${\alpha}$-238A allele significantly decreased the cervical cancer risk, and the TNF-${\alpha}$-308G>A polymorphism is associated with the susceptibility to cervical cancer in Caucasian and African population.

Molecular and Biochemical Characterization of a Novel Xylanase from Massilia sp. RBM26 Isolated from the Feces of Rhinopithecus bieti

( Bo Xu ),( Li Ming Dai ),( Jun Jun Li ),( Meng Deng ),( Hua Biao Miao ),( Jun Pei Zhou ),( Yue Lin Mu ),( Qian Wu ),( Xiang Hua Tang ),( Yun Juan Yang ),( Jun Mei Ding ),( Nan Yu Han ),( Zun Xi Huang 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.1

Xylanases sourced from different bacteria have significantly different enzymatic properties. Therefore, studying xylanases from different bacteria is important to their applications in different fields. A potential xylanase degradation gene in Massilia was recently discovered through genomic sequencing. However, its xylanase activity remains unexplored. This paper is the first to report a xylanase (XynRBM26) belonging to the glycosyl hydrolase family (GH10) from the genus Massilia. The gene encodes a 383-residue polypeptide (XynRBM26) with the highest identity of 62% with the endoxylanase from uncultured bacterium BLR13. The XynRBM26 expressed in Escherichia coli BL21 is a monomer with a molecular mass of 45.0 kDa. According to enzymatic characteristic analysis, pH 5.5 is the most appropriate for XynRBM26, which could maintain more than 90% activity between pH 5.0 and 8.0. Moreover, XynRBM26 is stable at 37°C and could maintain at least 96% activity after being placed at 37°C for 1 h. This paper is the first to report that GH10 xylanase in an animal gastrointestinal tract (GIT) has salt tolerance, which could maintain 86% activity in 5 M NaCl. Under the optimum conditions, Km, Vmax, and kcat of XynRBM26 to beechwood xylan are 9.49 mg/ml, 65.79 μmol/min/mg, and 47.34 /sec, respectively. Considering that XynRBM26 comes from an animal GIT, this xylanase has potential application in feedstuff. Moreover, XynRBM26 is applicable to high-salt food and seafood processing, as well as other high-salt environmental biotechnological fields, because of its high catalytic activity in high-concentration NaCl.

20(S)-ginsenoside Rg3 exerts anti-fi brotic effect after myocardial infarction by alleviation of fi broblasts proliferation and collagen deposition through TGFBR1 signaling pathways

Honglin Xu,Haifeng Miao,Guanghong Chen,Guoyong Zhang,Yue Hua,Yuting Wu,Tong Xu,Changlei Hu,Mingjie Pang,Leyi Tan,Xin Han,Bin Liu,Yingchun Zhou 고려인삼학회 2023 Journal of Ginseng Research Vol.47 No.6

Background: Myocardial fibrosis post-myocardial infarction (MI) can induce maladaptive cardiacremodeling as well as heart failure. Although 20(S)-ginsenoside Rg3 (Rg3) has been applied to cardiovasculardiseases, its efficacy and specific molecular mechanism in myocardial fibrosis are largely unknown. Herein, we aimed to explore whether TGFBR1 signaling was involved in Rg3's anti-fibrotic effectpost-MI. Methods: Left anterior descending (LAD) coronary artery ligation-induced MI mice and TGF-b1-stimulated primary cardiac fibroblasts (CFs) were adopted. Echocardiography, hematoxlin-eosin andMasson staining, Western-blot and immunohistochemistry, CCK8 and Edu were used to study the effectsof Rg3 on myocardial fibrosis and TGFBR1 signaling. The combination mechanism of Rg3 and TGFBR1 wasexplored by surface plasmon resonance imaging (SPRi). Moreover, myocardial Tgfbr1-deficient mice andTGFBR1 adenovirus were adopted to confirm the pharmacological mechanism of Rg3. Results: In vivo experiments, Rg3 ameliorated myocardial fibrosis and hypertrophy and enhanced cardiacfunction. Rg3-TGFBR1 had the 1.78 10 7 M equilibrium dissociation constant based on SPRi analysis,and Rg3 inhibited the activation of TGFBR1/Smads signaling dose-dependently. Cardiac-specific Tgfbr1knockdown abolished Rg3's protection against myocardial fibrosis post-MI. In addition, Rg3 downregulatedthe TGF-b1-mediated CFs growth together with collagen production in vitro through TGFBR1signaling. Moreover, TGFBR1 adenovirus partially blocked the inhibitory effect of Rg3. Conclusion: Rg3 improves myocardial fibrosis and cardiac function through suppressing CFs proliferationalong with collagen deposition by inactivation of TGFBR1 pathway.