Comparison of methods for library construction and short read annotation of shellfish viral metagenomes

Hong‑Ying Wei,Sheng Huang,Jiang‑Yong Wang,Fang Gao,Jing‑Zhe Jiang 한국유전학회 2018 Genes & Genomics Vol.40 No.3

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI’s NR and Uniprot’s Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

Constituents from Zhuyeqing Liquor with hepatoprotective effect on alcohol-induced HepaG 2 toxicity

Hong-Ying Gao,Guo-Yu Li,Hang-Yu Wang,Jian Huang,Xiao-Wei Du,Ying Han,Li-Fei Wang,Jin-Hui Wang 대한약학회 2015 Archives of Pharmacal Research Vol.38 No.5

An unprecedented new skeleton compound (1R,10R, 11S)-10,11-dimethyl-4-formyl-2,9-dioxa-bicyclo [5.4.0]undeca-4,6-dien-3-one (1), monoterpenoids and monoterpeneglycoside picrocrocinic ester (2), epijasminoside B (3) and 60 -O-(3-methoxyl-4-hydroxyl-coumaroyl)-epijasminoside B (4),along with 26 known compounds, were obtained fromZhuyeqing Liquor. These compounds were identified mainlyby analyzing their NMR, HR-ESI–MS and CD data. The isolatedcompounds were screened against alcohol induced HepaG2 toxicity for hepatoprotective assay. Compounds 10, 19,21 and 26 displayed the highest potency against alcoholinduced HepaG 2 toxicity with the cell viability ratio 41.21,56.91, 67.69 and 70.32 % respectively.

Tea Consumption, Alcohol Drinking and Physical Activity Associations with Breast Cancer Risk among Chinese Females: a Systematic Review and Meta-analysis

Gao, Ying,Huang, Yu-Bei,Liu, Xue-Ou,Chen, Chuan,Dai, Hong-Ji,Song, Feng-Ju,Wang, Jing,Chen, Ke-Xin,Wang, Yao-Gang Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12

Objective: To evaluate associations between tea consumption, alcohol drinking and physical activity and breast cancer risk among Chinese females. Methods: Three English databases (PubMed, ScienceDirect and Wiley) and three Chinese databases (CNKI, WanFang and VIP) were independently searched by 2 reviewers up to December 2012, complemented by manual searches. The quality of included studies was assessed with the Newcastle-Ottawa Scale items. Random-effects models were used to estimate the pooled odds ratios (ORs) and 95% confidence intervals (CIs). Potential publication bias was estimated through Egger's and Begg's tests. Heterogeneity between studies was evaluated with $I^2$ statistics. Results: Thirty-nine studies involving 13,204 breast cancer cases and 87,248 controls were identified. Compared with non-drinkers, regular tea drinkers had decreased risk (OR=0.79, 95%CIs: 0.65-0.95; $I^2$=84.9%; N=16). An inverse association was also found between regular physical activity and breast cancer risk (OR=0.73, 95%CIs: 0.63-0.85; $I^2$=77.3%; N=15). However, there was no significant association between alcohol drinking and breast cancer risk (OR=0.85, 95%CIs: 0.72-1.02; $I^2$=63.8%; N=26). Most of the results from the subgroup analysis were consistent with the main results. Conclusion: Tea consumption and physical activity are significantly associated with a decreased risk of breast cancer in Chinese females. However, alcohol drinking may not be associated with any elevation of risk.

Decitabine in the Treatment of Acute Myeloid Leukemia and Myelodysplastic Syndromes, Which Combined with Complex Karyotype Respectively

Gao, Su,Li, Zheng,Fu, Jian-Hong,Hu, Xiao-Hui,Xu, Yang,Jin, Zheng-Ming,Tang, Xiao-Wen,Han, Yue,Chen, Su-Ning,Sun, Ai-Ning,Wu, De-Pei,Qiu, Hui-Ying Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.15

Background: We conducted a study exploring the clinical safety and efficacy of decitabine in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), combined with a complex karyotype. Materials and Methods: From April 2009 to September 2013, a total of 35 patients with AML/MDS combined with a complex karyotype diagnosed in the First Affiliated Hospital of Soochow University were included for retrospective analysis. All patients were treated with decitabine alone ($20mg/m^2$ daily for 5 days) or combination AAG chemotherapy (Acla 20mg qod*4d, Ara-C $10mg/m^2$ q12h*7d, G-CSF $300{\mu}g$ qd, the dose of G-CSF adjusted to the amount in blood routinely). Results: In 35 patients, 15 exhibited a complete response (CR), and 6 a partial response (PR), the overall response rate (CR+PR) being 60% (21 of 35). Median disease-free survival was 18 months and overall survival was 14 months. In the 15 MDS patients with a complex karyotype, the CR rate was 53.3% (8 of 15); in 20 AML patients with complex karyotype, the overall response rate was 65% (13 of 20). The response rate of decitabine alone (22 cases) was 56.5% (13 of 22), while in the combination chemotherapy group (13 cases), the effective rate was 61.5% (8 of 13)(P>0.05). There are 15 patients with chromosome 7 aberration, after treatment with decitabine, 7 CR, 3 PR, overall response rate was 66.7% (10 of 15). Of 18 patients with 3 to 5 kinds of chromosomal abnormalities, 66.7% demonstrated a response; of 17 with more than 5 chromosomal abnormalities, 52.9% had a response. In the total of 35 patients, with one course (23 patients) and ${\geq}$two courses (12 patients), the overall response rate was 40.9% and 92.3% (P<0.05). Grade III to IV hematological toxicity was observed in 27 cases (75%). Grade III to IV infections were clinically documented in 7 (20%). Grades I to II non-hematological toxicity were infections (18 patients), haematuria (2 patients), and bleeding (3 patients). With follow-up until September 2013, 7 patients were surviving, 18 had died and 10 were lost to follow-up. In the 6 cases who underwent allogeneic hematopoietic stem cell transplantation (HSCT) all were still relapse-free survivors. Conclusions: Decitabine alone or combination with AAG can improve outcome of AML/MDS with a complex karyotype, there being no significant difference decitabine in inducing remission rates in patients with different karyotype. Increasing the number of courses can improve efficiency. This approach with fewer treatment side effects in patients with a better tolerance should be employed in order to create an improved subsequent chance for HSCT.

The Cyclic Peptide Ecumicin Targeting ClpC1 Is Active against <i>Mycobacterium tuberculosis In Vivo</i>

Gao, Wei,Kim, Jin-Yong,Anderson, Jeffrey R.,Akopian, Tatos,Hong, Seungpyo,Jin, Ying-Yu,Kandror, Olga,Kim, Jong-Woo,Lee, In-Ae,Lee, Sun-Young,McAlpine, James B.,Mulugeta, Surafel,Sunoqrot, Suhair,Wang, American Society for Microbiology 2015 Antimicrobial Agents and Chemotherapy Vol.59 No.2

<P>Drug-resistant tuberculosis (TB) has lent urgency to finding new drug leads with novel modes of action. A high-throughput screening campaign of >65,000 actinomycete extracts for inhibition of <I>Mycobacterium tuberculosis</I> viability identified ecumicin, a macrocyclic tridecapeptide that exerts potent, selective bactericidal activity against <I>M. tuberculosis</I> <I>in vitro</I>, including nonreplicating cells. Ecumicin retains activity against isolated multiple-drug-resistant (MDR) and extensively drug-resistant (XDR) strains of <I>M. tuberculosis</I>. The subcutaneous administration to mice of ecumicin in a micellar formulation at 20 mg/kg body weight resulted in plasma and lung exposures exceeding the MIC. Complete inhibition of <I>M. tuberculosis</I> growth in the lungs of mice was achieved following 12 doses at 20 or 32 mg/kg. Genome mining of lab-generated, spontaneous ecumicin-resistant <I>M. tuberculosis</I> strains identified the ClpC1 ATPase complex as the putative target, and this was confirmed by a drug affinity response test. ClpC1 functions in protein breakdown with the ClpP1P2 protease complex. Ecumicin markedly enhanced the ATPase activity of wild-type (WT) ClpC1 but prevented activation of proteolysis by ClpC1. Less stimulation was observed with ClpC1 from ecumicin-resistant mutants. Thus, ClpC1 is a valid drug target against <I>M. tuberculosis</I>, and ecumicin may serve as a lead compound for anti-TB drug development.</P>

An international Comparison Measurement of Silicon Wafer Sheet Resistance using the Four-point Probe Method

Jeon-Hong Kang,Gao-Ying,Yuh-Chuan Cheng,Chang-Soo Kim,Sang-Hwa Lee,Kwang-Min Yu 대한전기학회 2015 Journal of Electrical Engineering & Technology Vol.10 No.1

With approval from the Asia Pacific Metrology Program Working Group on Materials Metrology (APMP WGMM), an international comparison for sheet resistance standards for silicon wafers was firstly conducted among Korea Research Institute of Standards and Science (KRISS) in Korea, CMS/ITRI in Taiwan, and NIM in China, which are national metrology institutes (NMIs), from August 2011 to January 2012. The sheet resistance values of the standards are 10 Ω, 100Ω, and 1000 Ω; the measurement was conducted in sequence at KRISS, CMS/ITRI, NIM, and KRISS again using the four-point probe method with single and dual configuration techniques. The reference value for the measurement results of the three NMIs was obtained through averaging the values of the three results for each sheet resistance range. The differences between the reference value and the measured values is within 0.22% for 10Ω, 0.17% for 100Ω, and 0.12% for 1000Ω. Therefore, the international consistency for conducting sheet resistance measurements is confirmed within 0.22% through the APMP WGMM approved comparison.

Disorders of Small and Large Intestine : Colorectal Cancer In Guangdong Province: A Demographic And Anatomic Survey

( An Gao Xu ),( Bo Jiang ),( Zhi Jin Yu ),( Xin Ying Wang ),( Xu Hui Zhong ),( Ji Hong Liu ),( Li Shou Xiong ),( Qiu Yun Luo ),( Ai Hua Gan ) 대한소화기학회 2007 SIDDS Vol.9 No.-

Background/Aims: Colorectal cancer is the third leading incidence of malignant tumour in the world and the incidence of colorectal cancer has steadily been increasing in Asia in recently years. The aim of our study is to determine the basic demographic features of patients with colorectal cancer and the anatomic distribution and characteristics of the tumour in Guangdong population. Methods: A review of patients from 1990 to 2004 at five hospitals was conducted, including Peal Triangle Area in Guangdong (Nanfang Hospital and Huizhou Central People`s Hospital), North area of Guangdong (Shaoguan North-Guangdong People`s Hospital), West area of Guangdong (Affiliated Hospital Guangdong Medical Institute) and East area of Guangdong (Meizhou People`s Hospital). Results: Analysis was carried out on 6,501 patents, only 6,488 cases provided age. The age ranged from 5 years old to 91 years old and the mean age of 6,488 cases is 59. 5.2% (340/6,488) of the patients was young CRC patients. The peak incidence was between the ages 61 and 70 years old (29.5%). The mean age increases from 55 years old (1990-1992) to 61 years old (2002-2004) and the proportion of young CRC patients descends from 7.1% to 3.5%. The make to female ratio is 1.5:1 and the ratio increased with age increasing. Of 6,501 lesions, 3,423 (52.7%) were located in rectum and 3,078 (47.3%) in colon, the ratio of rectum cancer to colon cancer is 1.1:1. The proportion of rectum cancer decreased significantly from 74.5% (1990-1992) to 64.9% (2002-2004) and that of the right sides colon cancer increased from 25.5% to 35.1%. In four different areas, the mean age of CRC increasing and East area of Guangdong ranked the fist. There was no significant difference in the ratio of male to female. Conclusions: The demography of colorectal cancer in Guangdong is different from before and further study should be pursued to find the reason.

microRNA-328 in exosomes derived from M2 macrophages exerts a promotive effect on the progression of pulmonary fibrosis via FAM13A in a rat model

Meng-Ying Yao,Wei-Hong Zhang,Wen-Tao Ma,Qiu-Hong Liu,Li-Hua Xing,Gao-Feng Zhao 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

Currently, exosome-enclosed microRNAs (miRs) in exhaled breath have potential for biomarker discovery in patients with pulmonary diseases. This study was performed to investigate the roles of M2 macrophage-derived exosomes expressing miR-328 in pulmonary fibrosis (PF). Microarray-based analysis was used to screen differentially expressed genes (DEGs) and regulatory miRs in PF. The miR-target relationship between FAM13A and miR-328 was confirmed. The expression of FAM13A and miR-328 was measured in PF rats, and gain- and loss-of-function assays were conducted to determine the regulatory effects of FAM13A and miR-328 on PF. In addition, exosomes derived from M2 macrophages were isolated and then cocultured with pulmonary interstitial fibroblasts to identify the role of these exosomes in PF. Furthermore, the effects of M2 macrophage-derived exosomes overexpressing miR-328 on pulmonary fibroblast proliferation and the progression of PF were assessed in vivo. miR-328 might perform a vital function in PF by regulating FAM13A. FAM13A expression was downregulated while miR-328 expression was upregulated in rats with PF, and a miR-target relationship between miR-328 and FAM13A was observed. Additionally, miR-328 overexpression and FAM13A silencing each were suggested to promote pulmonary interstitial fibroblast proliferation and the expression of Collagen 1A, Collagen 3A and α-SMA. Then, in vitro experiments demonstrated that M2 macrophage-derived exosomes overexpressing miR-328 contributed to enhanced pulmonary interstitial fibroblast proliferation and promoted PF. Furthermore, in vivo experiments confirmed the promotive effects of M2 macrophagederived exosomes overexpressing miR-328 on the progression of PF. Collectively, the results showed that

3,7-Dihydroxy-2,4,6-trimethoxyphenanthrene, A New Phenanthrene from Bulbophyllum Odoratissimum

Chen, Ye-Gao,Xu, Jun-Ju,Yu, Hong,Qing, Chen,Zhang, Yan-Li,Liu, Ying,Wang, Ji-Hua Korean Chemical Society 2007 대한화학회지 Vol.51 No.4

Efficient stereoselective synthesis of α,β-Unsaturated acids, α-Cyanoacrylonitriles and α-Cyanoacrylates has been carried out in the presence of NaHSO4·SiO2 under solvent?free conditions with an E-geometry. A new phenanthrene derivative 3,7-dihydroxy-2,4,6-trimethoxyphenanthrene was isolated from the all plant of Bulbophyllum odoratissimum, and its structure was elucidated by extensive spectral studies and chemical transformation. The compound displayed cytotoxicity against the growth of human leukemia cell lines K562 and HL-60, human lung adenocarcinoma A549, human hepatoma BEL-7402 and human stomach cancer cell lines SGC-7901 with IC50 values of 14.23, 10.02, 3.42, 15.36 and 1.13 mg/ml respectively.

An international Comparison Measurement of Silicon Wafer Sheet Resistance using the Four-point Probe Method

Kang, Jeon-Hong,Ying, Gao,Cheng, Yuh-Chuan,Kim, Chang-Soo,Lee, Sang-Hwa,Yu, Kwang-Min The Korean Institute of Electrical Engineers 2015 Journal of Electrical Engineering & Technology Vol.10 No.1

With approval from the Asia Pacific Metrology Program Working Group on Materials Metrology (APMP WGMM), an international comparison for sheet resistance standards for silicon wafers was firstly conducted among Korea Research Institute of Standards and Science (KRISS) in Korea, CMS/ITRI in Taiwan, and NIM in China, which are national metrology institutes (NMIs), from August 2011 to January 2012. The sheet resistance values of the standards are $10{\Omega}$, $100{\Omega}$, and $1000{\Omega}$; the measurement was conducted in sequence at KRISS, CMS/ITRI, NIM, and KRISS again using the four-point probe method with single and dual configuration techniques. The reference value for the measurement results of the three NMIs was obtained through averaging the values of the three results for each sheet resistance range. The differences between the reference value and the measured values is within 0.22% for $10{\Omega}$, 0.17% for $100{\Omega}$, and 0.12% for $1000{\Omega}$. Therefore, the international consistency for conducting sheet resistance measurements is confirmed within 0.22% through the APMP WGMM approved comparison.