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.

Laparoscopic left hepatectomy in swine: a safe and feasible technique

Hua Zhang,Tao Liu,Yue Wang,Hai-feng Liu,Jian-tao Zhang,Yan-shuang Wu,Lei Lei,Hong-bin Wang 대한수의학회 2014 JOURNAL OF VETERINARY SCIENCE Vol.15 No.3

A purely laparoscopic four-port approach was created forleft hepatectomy in pigs. A polyethylene loop was placed onthe left two hepatic lobes for traction and lift. Next,penetrating ligation of the lobes using of a double row of silksutures was performed to control bleeding. A direct hepatictransection was completed using a monopolar hook electrodewithout meticulous dissection of the left hepatic vein. Theraw surface of the liver was coagulated and sealed with fibringlue. Lobes were retrieved through an enlarged portal. Laparoscopic hepatic lobectomy was completed in all pigswithout the use of specialized instruments and with a meanoperative time of 179 ± 9 min. No significant perioperativecomplications were observed. The average weight of eachresected lobe was 180 ± 51 g. Complete blood count as well asserum organics and enzyme levels normalized after about 2weeks. During necropsy, adhesion of the hepatic raw surfaceto the gastric wall and omentum were observed. No otherabnormalities were identified. This minimally invasive lefthepatectomy technique in swine could serve as a usefulmodel for investigating liver diseases and regeneration, andoffer preclinical information to improve hepatobiliary surgical procedures.

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.

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.

ACCURACY OF LAMOST DR1 STELLAR PARAMETERS

GAO, HUA,ZHANG, HUA-WEI,XIANG, MAO-SHENG,HUANG, YANG,LIU, XIAO-WEI,LUO, A-LI,ZHANG, HAO-TONG,WU, YUE,ZHANG, YONG,LI, GUANG-WEI,DU, BING The Korean Astronomical Society 2015 天文學論叢 Vol.30 No.2

We adopt the PASTEL catalog combined with SIMBAD radial velocities as a testing standard to validate the stellar parameters (effective temperature $T_{eff}$, surface gravity log g, metallicity [Fe/H] and radial velocity $V_r$) from the first data release (DR1) of The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey. After applying data reduction and temperature constraints to the sample obtained by cross-identification, we compare the stellar parameters from DR1 and PASTEL. The results show that the DR1 results are reliable under certain conditions. We derive a dispersion of 110 K, 0.19 dex, 0.11 dex and $4.91kms^{-1}$ in specified effective temperature ranges, for $T_{eff}$, log g, [Fe/H] and $V_r$ respectively. Systematic errors are negligible except for those of $V_r$. In addition, for stars with PASTEL [Fe/H] < -1:5, the metallicities in DR1 are systematically higher than those in PASTEL.

Roles of Immunohistochemical Staining in Diagnosing Pulmonary Squamous Cell Carcinoma

Yan, Yue,Zhang, Ya-Xiong,Fang, Wen-Feng,Kang, Shi-Yang,Zhan, Jian-Hua,Chen, Nan,Hong, Shao-Dong,Liang, Wen-Hua,Tang, Yan-Na,He, Da-Cheng,Wu, Xuan,Zhang, Li Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.2

Background: Differentiating morphologic features based on hematoxylin-eosin (HE) staining is the most common method to classify pathological subtypes of non-small-cell lung cancer (NSCLC). However, its accuracy and inter-observer reproducibility in pathological diagnosis of poorly differentiated NSCLC remained to be improved. Materials and Methods: We attempted to explore the role of immunohistochemistry (IHC) staining in diagnosing pulmonary squamous cell carcinoma (SQCC) with poorly differentiated features by HE staining or with elevated serum adenocarcinoma-specific tumor markers (AD-TMs). We also compared the difference of epidermal growth factor receptor (EGFR) mutation rate between patients with confirmed SQCC and those with revised pathological subtype. Logistic regression analyses were used to test the association between different factors and diagnostic accuracy. Results: A total of 132 patients who met the eligible criteria and had adequate specimens for IHC confirmation were included. Pathological revised cases in poor differentiated subgroup, biopsy samples and high-level AD-TMs cases were more than those with high/moderate differentiation, surgical specimens and normal-level AD-TMs. Moreover, biopsy sample was a significant factor decreasing diagnostic accuracy of pathological subtype (OR, 4.037; 95% CI 1.446-11.267, p=0.008). Additionally, EGFR mutation rate was higher in patients with pathological diagnostic changes than those with confirmed SQCC (16.7% vs 4.4%, p=0.157). Conclusions: Diagnosis based on HE staining only might cause pathological misinterpretation in NSCLC patients with poor differentiation or high-level AD-TMs, especially those with biopsy samples. HE staining and IHC should be combined as pathological diagnostic standard. The occurrence of EGFR mutations in pulmonary SQCC might be overestimated.

Protective effects of 20,40-dihydroxy-60-methoxy-30,50- dimethylchalcone against hydrogen peroxide-induced oxidative stress in hepatic L02 cell

Yue Lu,Yan-Yan Zhang,Ying-Chun Hu,Yan-Hua Lu 대한약학회 2014 Archives of Pharmacal Research Vol.37 No.9

2',4'-Dihydroxy-6'-methoxy-3',5'-dimethylchalcone(DMC) is a chalcone isolated from the buds of Cleistocalyxoperculatus (Roxb.) Merr. et Perry, and thehepatoprotective effects of DMC on Kunming mice havebeen studied in previous study. However, the effects ofDMC on hepatocyte toxicity and corresponding mechanismremain unclear. The aim of this study was to evaluate thehepatoprotective mechanism of DMC in human hepatocytes(L02) treated with H2O2. The results demonstrated thatpretreatment with DMC effectively protected H2O2-inducedcell viability loss, cell membrane damage (lactate dehydrogenase,nitric oxide production and caspase-3 accumulation. Besides, DMC pretreatment increased the amount ofglutathione, decreased malondialdehyde and the percentageof apoptotic L02 cells compared with only H2O2 treatedgroup. Taken together, these results indicated that DMC hadhepatoprotective effects against H2O2-induced liver injuryby alleviating oxidative stress and apoptosis process in L02cells, and DMC might be a potential candidate for theintervention of liver diseases.

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota

Zhang Dao-Feng,Yao Yu-Fang,Xue Hua-Peng,Fu Zi-Yue,Zhang Xiao-Mei,Shao Zongze 한국미생물학회 2022 The journal of microbiology Vol.60 No.9

A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

"Sandwich" Chemotherapy (CT) with Radiotherapy (RT) Improves Outcomes in Patients with Stage I_E/II_E Extranodal Natural Killer (NK)/T-cell Lymphomas

Zhang, Jing,Zhu, Meng-Yuan,Wang, Liang,Wang, Hua,Wang, Wei-Da,Geng, Qi-Rong,Lu, Yue Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.7

The extranodal natural killer/T-cell lymphoma (ENKTL) shows high local or systemic failure rates when radiotherapy (RT) is taken as the primary treatment, suggesting a role for chemotherapy (CT) added to RT for this disease. However, the appropriate mode of combined modality therapy (CMT) has not been fully defined. A total of one hundred and twenty-one patients with ENKTL receiving sandwich CT with RT were reviewed between January 2003 and August 2012. The primary endpoints were the response rate, progression-free survival (PFS), overall survival (OS), and the relapse rate. After the initial CT, there were 84 (69.4%) patients in CR, 22 (18.2%) patients in PR, 9 (7.4%) patients in SD, and 6 (5%) patients in PD, respectively. At the end of RT, the CR, PR, SD, and PD rates for all patients were 90.9% (n=110), 1.7% (n=2), 4.1% (n=5), and 3.3% (n=4), respectively. After a median follow-up of 42.3 months (3.5~112.3 months), the 5-year PFS was 74.7% (95% CI 70.4%~79.0%), and 5-year OS was 77.3% (95% CI 67.9%~86.7%). Disease progression was documented in 25 (20.7%) patients. The rates of systemic failure, local failure, and regional failure were 18.2%, 5.8%, 1.7%, respectively. Twenty death events (16.5%) were observed for the entire group of patients (18 deaths related to PD). Furthermore, CR to the initial CT and low Korean Prognostic Index (KPI) can independently predict long PFS and OS. The sandwich CMT achieved an excellent outcome for localized ENKTL with acceptable toxicity. We recommend it can be applied as the optimal choice for localized ENKTL.

Two new species of the genus Arboridia Zachvatkin from karst area of southwestern China (Hemiptera: Cicadellidae: Typhlocybinae)

Zhang Ni,Jiang Jia,Song Yue-Hua 한국응용곤충학회 2022 Journal of Asia-Pacific Entomology Vol.25 No.3

Two new species: A. (Arboridia) xiaotungensis sp. nov. and A. (Arboridia) luojiashangensis sp. nov. from Guizhou Province, China are described and illustrated. In addition, the appearances of A. reniformis Song & Li (2013a) and A. anteoculara Song & Li (2013a) are supplementarily described. A key to distinguish all known species of the genus from China is provided. LSID: https://www.zoobank.org/urn:lsid:zoobank.org:pub:3DD14108-ED08-430D-AE8D-CD0 FCC215A4E