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.

Removal of Cs+, Sr2+, and Co2+ Ions from the Mixture of Organics and Suspended Solids Aqueous Solutions by Zeolites

Xiang-Hong Fang,Fang Fang,Chun-Hai Lu,Lei Zheng 한국원자력학회 2017 Nuclear Engineering and Technology Vol.49 No.3

Serving as an excellent adsorbent and inorganic ion exchanger in the water purification field, zeolite 4A has in this work presented a strong capability for purifying radioactive waste, such as Sr2+, Csþ, and Co2+ in water. During the processes of decontamination and decommissioning of suspended solids and organics in low-level radioactive wastewater, the purification performance of zeolite 4A has been studied. Under ambient temperature and neutral condition, zeolite 4A absorbed simulated radionuclides such as Sr2+, Csþ, and Co2+ with an absorption rate of almost 90%. Additionally, in alkaline condition, the adsorption percentage even approached 98.7%. After conducting research on suspended solids and organics of zeolite 4A for the treatment of radionuclides, it was found that the suspended clay was conducive to absorption, whereas the absorption of organics in solution was determined by the species of radionuclides and organics. Therefore, zeolite 4A has considerable potential in the treatment of radioactive wastewater.

Steel Bridge Construction of Hong Kong–Zhuhai–Macao Bridge

Wen-bo Gao,Quan-ke Su,Jin-wen Zhang,Hong-bing Xie,Feng Wen,Fang Li,Ji-zhu Liu 한국강구조학회 2020 International Journal of Steel Structures Vol.20 No.5

The 55-km-long Hong Kong–Zhuhai–Macao Bridge (HZMB) is the world’s longest sea-crossing bridge, connecting Hong Kong with Zhuhai and Macao at the mouth of the Pearl River Estuary in China, comprising 22.9-km-long steel bridges. HZMB is the leading steel bridge in China, with top-level manufacturing and installation technology. This paper outlines the steel bridge construction experiences of HZMB to provide comparisons for the construction of other long sea-crossing steel bridges at home or abroad. The main considerations of construction constraints, scheme selection, structural and aesthetic design of HZMB are presented, and the following points related to new strategies in the steel bridge construction of HZMB are elaborated: (1) construction quality assurance, (2) automatic manufacturing technology, (3) large segment off shore installation, (4) eco-friendly paint (content limitation of volatile organic compounds) and new multifunctional inspection gantry, and (5) Guss Mastic Asphalt steel deck pavement system. The successful implementation of those strategies shows that the steel bridge construction of HZMB promotes improvement in the overall construction and management level of the Chinese bridge industry. The advanced experience of HZMB has opened up broad prospects for the design and construction of off shore bridge engineering in China.

Efficacy and Survival-associated Factors with Gefitinib Combined with Cisplatin and Gemcitabine for Advanced Non-small Cell Lung Cancer

Fang, Hong,Lin, Rong-Yan,Sun, Ming-Xia,Wang, Qian,Zhao, Yu-Liang,Yu, Jing-Lin,Tian, Yan,Wang, Xiao-Yun Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.24

Objective: To analyze the efficacy and survival associated factors of gefitinib combined with cisplatin and gemcitabine for advanced non-small cell lung cancer. Materials and Methods: A total of 57 patients with advanced non-small cell lung cancer (NSCLC), who received platinum-based chemotherapy regimens for more than 1 cycle, were treated with gefitinib combined with cisplatin and gemcitabine until disease progression. Efficacy, survival time and adverse reactions were observed. The Kaplan-Meier method was adopted for analysis of survival and Cox regression for associated influencing factors. Results: The patients were followed up until October 31, 2013, and the median follow-up time was 19 months. Of 57 patients, there were 4 (7.0%) with complete remission (CR), 8 (14.0%) with partial remission, 31 (54.4%) with stable disease, and 14 (24.6%) with disease progression. The remission rate was 21.1% and the disease control rate was 75.4%. The median progression-free survival (PFS) time and the median overall survival time were 10 months and 15.2 months. The one-year, two-year and three-year survival rates were 47.4%, 23.3% and 10.0%. Gender and pathological types were the independent risk factors influencing PFS time (P=0.028, P=0.009). Tumor pathological type and early efficacy were independent factors for the prognosis (P=0.018, P=0.000). Adverse reactions were mostly rashes of I~II degree and diarrhea and slightly increasing level of aminopherase. The skin adverse event incidence of III degree or above was 1.8% (1/57) and brain metastasis was foudn in 31.6% (18/57). Conclusions: Gefitinib combined with cisplatin andgemcitabine, is effective for patients with IIIb~IV NSCLC who received multiple cycles of chemotherapy.

Melatonin Synergizes with Sorafenib to Suppress Pancreatic Cancer via Melatonin Receptor and PDGFR-β/STAT3 Pathway

Fang, Zhenghuan,Jung, Kyung Hee,Yan, Hong Hua,Kim, Soo-Jung,Rumman, Marufa,Park, Jung Hee,Han, Boreum,Lee, Ji Eun,Kang, Yeo wool,Lim, Joo Han,Hong, Soon Sun S. Karger AG 2018 CELLULAR PHYSIOLOGY AND BIOCHEMISTRY Vol.47 No.5

<P><B><I>Background/Aims:</I></B> Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignant tumors with poor prognosis. Conventional chemotherapies including gemcitabine have failed owing to weak response and side effects. Hence novel treatment regimens are urgently needed to improve the therapeutic efficacy. In this study, we aimed to assess the anticancer activity of melatonin and sorafenib as a novel therapy against PDAC. <B><I>Methods:</I></B> We used various apoptosis assay and PDAC xenograft model to assess anticancer effect <I>in vitro</I> and <I>in vivo</I>. We applied phospho-receptor tyrosine kinase (RTK) array and phospho-tyrosine kinase array to explore the mechanism of the combined therapy. Western blotting, proximity ligation assay, and immunoprecipitation assay were also performed for validation. <B><I>Results:</I></B> Melatonin synergized with sorafenib to suppress the growth of PDAC both <I>in vitro</I> and <I>in vivo</I>. The effect was due to increased apoptosis rate of PDAC cells that was accompanied by mitochondria dysfunction. The enhanced anticancer efficacy by the co-treatment could be explained by blockade of PDGFR-β/STAT3 signaling pathway and melatonin receptor (MT)-mediated STAT3. <B><I>Conclusions:</I></B> Melatonin reinforces the anticancer activity of sorafenib by downregulation of PDGFR-β/STAT3 signaling pathway and melatonin receptor (MT)-mediated STAT3. The combination of the two agents might be a potential therapeutic strategy for treating PDAC.</P>

Statistical Optimization of Culture Media and Conditions for Production of Mannan by Saccharomyces cerevisiae

Hong-Zhi Liu,Qiang Wang,Yuan-Yuan Liu,Fang Fang 한국생물공학회 2009 Biotechnology and Bioprocess Engineering Vol.14 No.5

In view of the increase in Saccharomyces cerevisiae mannan content, the culture medium and condition for S.cerevisiae were optimized in this study. The influence of culture medium ingredients such as carbon and nitrogen sources, inorganic ion, and enzyme activator on mannan production were evaluated using factional design. The mathematical model was established by the quadratic rotary combination design through response surface analysis. The optimized concentrations of culture medium were determined as follows: 4.98 g/100 mL, sucrose; 4.39 g/100 mL, soybean peptone; 3.10 g/100 mL, yeast extract; and 2.21 g/100 mL, glycerol. The optimized culture medium increased mannan production from 82.7 ± 3.4 mg/100 mL to 162.53 ± 3.47 mg/100 mL. The influence of original pH, inoculum size, temperature, and media volume on mannan production was evaluated and confirmed by orthogonale experimental design, with the order of effect as follows: media volume > temperature > initial pH > inoculation size. The optimized culture condition was pH, 5; inoculum size, 5 ml; temperature, 32oC; and media volume, 40 mL. The maximum mannan production increased to 258.5 ± 9.1 mg/100 mL at the optimum culture condition.=It was evident that the mannan production was affected significantly by culture medium and condition optimization (é < 0.01). In view of the increase in Saccharomyces cerevisiae mannan content, the culture medium and condition for S.cerevisiae were optimized in this study. The influence of culture medium ingredients such as carbon and nitrogen sources, inorganic ion, and enzyme activator on mannan production were evaluated using factional design. The mathematical model was established by the quadratic rotary combination design through response surface analysis. The optimized concentrations of culture medium were determined as follows: 4.98 g/100 mL, sucrose; 4.39 g/100 mL, soybean peptone; 3.10 g/100 mL, yeast extract; and 2.21 g/100 mL, glycerol. The optimized culture medium increased mannan production from 82.7 ± 3.4 mg/100 mL to 162.53 ± 3.47 mg/100 mL. The influence of original pH, inoculum size, temperature, and media volume on mannan production was evaluated and confirmed by orthogonale experimental design, with the order of effect as follows: media volume > temperature > initial pH > inoculation size. The optimized culture condition was pH, 5; inoculum size, 5 ml; temperature, 32oC; and media volume, 40 mL. The maximum mannan production increased to 258.5 ± 9.1 mg/100 mL at the optimum culture condition.=It was evident that the mannan production was affected significantly by culture medium and condition optimization (é < 0.01).

Genome-wide Analysis of Aberrant DNA Methylation for Identification of Potential Biomarkers in Colorectal Cancer Patients

Fang, Wei-Jia,Zheng, Yi,Wu, Li-Ming,Ke, Qing-Hong,Shen, Hong,Yuan, Ying,Zheng, Shu-Sen Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.5

Background: Colorectal cancer is one of the leading causes of mortality worldwide. Genome wide analysis studies have identified sequence mutations causing loss-of-function that are associated with disease occurrence and severity. Epigenetic modifications, such DNA methylation, have also been implicated in many cancers but have yet to be examined in the East Asian population of colorectal cancer patients. Methods: Biopsies of tumors and matched non-cancerous tissue types were obtained and genomic DNA was isolated and subjected to the bisulphite conversion method for comparative DNA methylation analysis on the Illumina Infinium HumanMethylation27 BeadChip. Results: Totals of 258 and 74 genes were found to be hyper- and hypo-methylated as compared to the individual's matched control tissue. Interestingly, three genes that exhibited hypermethylation in their promoter regions, CMTM2, ECRG4, and SH3GL3, were shown to be significantly associated with colorectal cancer in previous studies. Using heatmap cluster analysis, eight hypermethylated and 10 hypomethylated genes were identified as significantly differentially methylated genes in the tumour tissues. Conclusions: Genome-wide methylation profiling facilitates rapid and simultaneous analysis of cancerous cells which may help to identify methylation markers with high sensitivity and specificity for diagnosis and prognosis. Our results show the promise of the microarray technology in identification of potential methylation biomarkers for colorectal cancers.

Complete mitochondrial genome of the meadow moth, Loxostege sticticalis (Lepidoptera: Pyraloidea: Crambidae), compared to other Pyraloidea moths

Hong-Fang Ma,Xi-Xi Zheng,Ming-Hui Peng,Hai-Xu Bian,Miao-Miao Chen,Yan-Qun Liu,Xing-Fu Jiang,Li Qin 한국응용곤충학회 2016 Journal of Asia-Pacific Entomology Vol.19 No.3

The mitochondrial genome (mitogenome) is an important topic for comparative and evolutionary genomics, as well as phylogenetic and population genetics. However, there are limited data regarding the mitochondrial genome available of Pyraloidea, one of the largest superfamilies in Lepidoptera. In this report, we present the complete mitogenome of the meadow moth, Loxostege sticticalis L. (Lepidoptera: Pyraloidea: Crambidae), which is a serious economic pest of both crops and weedsworldwide, thereby enhancing the available genomic information for Pyraloidea. This circular genome is 15,218 bp in length, containing 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), and 22 tRNA genes (tRNAs), with a typical gene orientation and order comparable to other sequenced Pyraloidea insects. The genome composition of the major strand exhibits highly AT bias (80.82%), with a slightly positive AT skew indicating the occurrence of more As than Ts. The L. sticticalis mitogenome has a total of 130 bp of intergenic spacer sequences spread over 15 regions, ranging in size from 1 to 48 bp, of which only two are common among the 23 total Pyraloidea moths that have data collected on the mitogenome (one is located between tRNAGln and ND2 with variation change in length and a limited sequence conservation, and the other is located between tRNASer(UCN) and ND1 with a conserved 6 bp motif ‘ATACTA’). The A + Trich region of 331 bp in the genome is comprised of non-repetitive sequences but contains an ATAGN motif followed by a poly-T stretch of 17 bp, a microsatellite-like (TA)11 element preceded by an ATTTA motif, and a poly-A stretch upstream tRNAMet. These conserved structures identified in the A + T-rich region are presented in all of the sequenced Pyraloidea species. We provide a mitogenome-based phylogeny of Pyraloidea species, in which L. sticticalis shares close ancestry to Ostrinia species with substantial evidence. Our phylogenetic analyses strongly divide Crambidae into two sister lineages, one consisting of Pyraustinae and Spilomelinae, while the other contains Crambinae, Acentropinae, Scopariinae, Schoenobiinae and Glaphyriinae. The mitogenome dataset also supports the basal split between Pyraustinae and Spilomelinae.

The Effectiveness of Two Hospitals Implementing Magnet Hospital Concept to Improve Nursing Staff Retention

Fang Chih Yeh,Li Fang Liu,Nai Hong Wang 한국간호과학회 2009 한국간호과학회 학술대회 Vol.2009 No.10

Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians

( Fang Wang ),( Ting Yu ),( Guo Hong Huang ),( Da Cai ),( Xiaolin Liang ),( Hai Yan Su ),( Zhenjun Zhu ),( Danlei Li ),( Yang Yang ),( Pei Hong Shen ),( Rui Feng Mao ),( Lian Yu ),( Mou Ming Zhao ),( 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.8

Increasing evidence suggests that gut microbiota underpin the development of health and longevity. However, our understanding of what influences the composition of this community of the longevous has not been adequately described. Therefore, illumina sequencing analysis was performed on the gut microbiota of centenarians (aged 100-108 years; RC) and younger elderlies (aged 85-99 years; RE) living in Bama County, Guangxi, China and the elderlies (aged 80-92 years; CE) living in Nanning City, Guangxi, China. In addition, their diet was monitored using a semiquantitative dietary questionary (FFQ 23). The results revealed the abundance of Roseburia and Escherichia was significantly greater, whereas that of Lactobacillus, Faecalibacterium, Parabacteroides, Butyricimonas, Coprococcus, Megamonas, Mitsuokella, Sutterella, and Akkermansia was significantly less in centenarians at the genus level. Both clustering analysis and UniFraq distance analysis showed structural segregation with age and diet among the three populations. Using partial least square discriminate analysis and redundancy analysis, we identified 33 and 34 operational taxonomic units (OTUs) as key OTUs that were significantly associated with age and diet, respectively. Age-related OTUs were characterized as Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and the former two were increased in the centenarians; diet-related OTUs were classified as Bacteroidales, Lachnospiraceae, and Ruminococcaceae. The former two were deceased, whereas the later one was increased, in the high-fiber diet. The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and high-fiber diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of centenarians.