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.

중·한 교육 현황 및 개혁 동향의 비교

황현옥,정홍섭 新羅大學校 2003 論文集 Vol.52 No.-

There are a lot of similarities between China and Korea in their cultural and historical background. Both countries have adopted the 6:3:3:4 pattern for their elementary school, junior high school, senior high school and college education. Their difference lies in the fact that most schools in China are public schools but the schools in Korea are both private and public ones. Korea is superior to China in teachers' quality, teaching facilities and ratio of high school students who can enter colleges and universities. But Korea is not as good as China in the quality of higher education owing to its over-reliance on private school education and students' tuition fees. In recent years both China and Korea have made great efforts in reformation of education. For example, they have given more financial support to education, changed their college entrance examination from purely written examination to comprehensive evaluation, and decentralized their control over education. But China falls behind Korea in financial support, reform of teaching methodology and introduction of market economy into education. At present, China is trying to put the idea of market economy into the development of private schools and the decision on the amount of tuition fees. Korean government, on the other hand, is giving more support to its private schools. This paper holds that China should learn from Korea in private school management, teachers' training and occupational education whereas Korea should learn from China in improving the quality of tertiary education.

Robust Reliability Analysis of Vibration Components

Hong-Zhong Huang,Yong-Hua Li,Ming J. Zuo 한국신뢰성학회 2004 International Journal of Reliability and Applicati Vol.5 No.2

Bayesian case influence analysis for GARCH models based on Kullback–Leibler divergence

Hong-Xia Hao,Jinguan Lin,Hong-Xia Wang,Xing-Fang Huang 한국통계학회 2016 Journal of the Korean Statistical Society Vol.45 No.4

Influence analysis has become an important tool for statistical analysis. This paper is concerned with Bayesian case influence analysis for generalized autoregressive conditional heteroscedasticity (GARCH) model. Case influence analysis is developed for both the joint and marginal posterior distributions based on the Kullback–Leibler divergence (K–L divergence). A simplified expression is presented for computing the K–L divergence between the full data posterior distribution and the case-deleted posterior distributions. The related computations can be done numerically by Markov Chain Monte Carlo samples from posterior distribution with full data. Some simulation studies are carried out to examine the performance of the proposed methods and show the relations between case-deletion model (CDM) and mean-shift outlier model (MSOM) for the GARCH models. Meanwhile, the methods are also illustrated by a real data.

CFD analysis of ventilation efficiency around an elevated highway using visitation frequency and purging flow rate

Hong Huang,Shinsuke Kato,Ryozo Ooka,Taifeng Jiang 한국풍공학회 2006 Wind and Structures, An International Journal (WAS Vol.9 No.4

The concentration of air pollution along roads is higher than the surrounding area because ventilation efficiency has decreased due to the high-density use of space along roads in recent years. In this study, ventilation efficiency around a heavily traffic road covered by an elevated highway and hemmed in along its side by buildings is evaluated using Visitation Frequency (VF, the frequency for pollutant to return to the objective domain) and Purging Flow Rate (PFR, the air flow rate for defining the local domain-averaged concentration). These are analyzed using Computational Fluid Dynamics (CFD) based on the standard k-e model. The VF and PFR characteristics of four objective domains are analyzed in terms of the changes in wind direction and arrangements of the fencing dividing up and down direction in the road center under the elevated highway. The resulting VFs are more than 1.0 for all cases, which means that pollutants return to the objective domain restricted by the elevated highway and side buildings. The influence of the arrangement of the buildings around the objective domain and the structure in the domain on the VF is substantial. In cases where there are no obstacles under the elevated highway, the local air exchange rate in the domain tends to be improved. Using these indices, the urban ventilation efficiencies between different urban areas can be compared easily.

Prolactin Inhibits BCL6 Expression in Breast Cancer Cells through a MicroRNA-339-5p-Dependent Pathway

Hong Yan,Min Zhao,Shan Huang,Ping Chen,Wen-yong Wu,Jin Huang,Zheng-sheng Wu,Qiang Wu 한국유방암학회 2016 Journal of breast cancer Vol.19 No.1

Purpose: Prolactin (PRL) plays a critical role in breast cancer progression by activating its cognate receptor and promotes the growth and differentiation of breast cancer cells. Studies have shown that B-cell lymphoma 6 (BCL6) is the target gene of microRNA- 339-5p (miR-339-5p) and that BCL6 expression contributes to breast cancer progression. Herein, we identified PRL as a potent suppressor of BCL6 expression in human breast cancer cells. Methods: Western blotting and quantitative reverse transcription-polymerase chain reaction were used to investigate molecular mechanisms underlying miR-339-5p expression and BCL6 manipulation in MCF-7, T47D, and SKBR3 breast cancer cells. Phenotypic changes in these breast cancer cell lines were assessed by performing cell viability (MTT), colony formation, migration, and invasion assays. Results: PRL suppressed BCL6 protein and mRNA expression and upregulated miR-339-5p expression in MCF-7 and T47D breast cancer cells. Selective downregulation of miR-339-5p expression significantly reversed PRL-induced suppression of BCL6 mRNA and protein expression. Exogenous PRL stimulation significantly decreased the proliferation, colony formation, migration, and invasion of breast cancer cells, and suppression of miR-339-5p expression reversed these processes in vitro. Conclusion: These results indicated that PRL inhibited BCL6 expression and regulated breast cancer progression through a miR-339-5p-dependent pathway.

Ginsenoside Ro, an oleanolic saponin of Panax ginseng, exerts antiinflammatory effect by direct inhibiting toll like receptor 4 signaling pathway

Hong-Lin Xu,Guang-Hong Chen,Yu-Ting Wu,Ling-Peng Xie,Zhang-Bin Tan,Bin Liu,Hui-Jie Fan,Hong-Mei Chen,Gui-Qiong Huang,Min Liu,Ying-Chun Zhou 고려인삼학회 2022 Journal of Ginseng Research Vol.46 No.1

Background: Panax ginseng Meyer (P. ginseng), a herb distributed in Korea, China and Japan, exerts benefits on diverse inflammatory conditions. However, the underlying mechanism and active ingredients remains largely unclear. Herein, we aimed to explore the active ingredients of P. ginseng against inflammation and elucidate underlying mechanisms. Methods: Inflammation model was constructed by lipopolysaccharide (LPS) in C57BL/6 mice and RAW264.7 macrophages. Molecular docking, molecular dynamics, surface plasmon resonance imaging (SPRi) and immunofluorescence were utilized to predict active component. Results: P. ginseng significantly inhibited LPS-induced lung injury and the expression of proinflammatory factors, including TNF-a, IL-6 and IL-1b. Additionally, P. ginseng blocked fluorescence-labeled LPS (LPS488) binding to the membranes of RAW264.7 macrophages, the phosphorylation of nuclear factor-kB (NF-kB) and mitogen-activated protein kinases (MAPKs). Furthermore, molecular docking demonstrated that ginsenoside Ro (GRo) docked into the LPS binding site of toll like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD2) complex. Molecular dynamic simulations showed that the MD2-GRo binding conformation was stable. SPRi demonstrated an excellent interaction between TLR4/MD2 complex and GRo (KD value of 1.16 × 10<SUP>-9</SUP> M). GRo significantly inhibited LPS488 binding to cell membranes. Further studies showed that GRo markedly suppressed LPS-triggered lung injury, the transcription and secretion levels of TNF-α, IL-6 and IL-1β. Moreover, the phosphorylation of NF-kB and MAPKs as well as the p65 subunit nuclear translocation were inhibited by GRo dose-dependently. Conclusion: Our results suggest that GRo exerts anti-inflammation actions by direct inhibition of TLR4 signaling pathway.

A GENERALIZATION OF OSTROWSKI-TYPE INEQUALITY

Hong, Huang The Kangwon-Kyungki Mathematical Society 2018 한국수학논문집 Vol.26 No.4

A generalization of Ostrowski-type inequality involving functions of two independent variables is given.

Study on the book of Rites - rural special offerings concern with Sacrifice food outlook

Huang Ji-hong 한국식생활문화학회 2017 한국식생활문화학회학술대회논문집 Vol.2017 No.11

Highly Oriented Monolayer Graphene Grown on a Cu/Ni(111) Alloy Foil

Huang, Ming,Biswal, Mandakini,Park, Hyo Ju,Jin, Sunghwan,Qu, Deshun,Hong, Seokmo,Zhu, Zhili,Qiu, Lu,Luo, Da,Liu, Xiaochi,Yang, Zheng,Liu, Zhongliu,Huang, Yuan,Lim, Hyunseob,Yoo, Won Jong,Ding, Feng,Wa American Chemical Society 2018 ACS NANO Vol.12 No.6

<P>Fast-growth of single crystal monolayer graphene by CVD using methane and hydrogen has been achieved on “homemade” single crystal Cu/Ni(111) alloy foils over large area. Full coverage was achieved in 5 min or less for a particular range of composition (1.3 at.% to 8.6 at.% Ni), as compared to 60 min for a pure Cu(111) foil under identical growth conditions. These are the bulk atomic percentages of Ni, as a superstructure at the surface of these foils with stoichiometry Cu<SUB>6</SUB>Ni<SUB>1</SUB> (for 1.3 to 7.8 bulk at.% Ni in the Cu/Ni(111) foil) was discovered by low energy electron diffraction (LEED). Complete large area monolayer graphene films are either single crystal or close to single crystal, and include folded regions that are essentially parallel and that were likely wrinkles that “fell over” to bind to the surface; these folds are separated by large, wrinkle-free regions. The folds occur due to the buildup of interfacial compressive stress (and its release) during cooling of the foils from 1075 °C to room temperature. The fold heights measured by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) prove them to all be 3 layers thick, and scanning electron microscopy (SEM) imaging shows them to be around 10 to 300 nm wide and separated by roughly 20 μm. These folds are always essentially perpendicular to the steps in this Cu/Ni(111) substrate. Joining of well-aligned graphene islands (in growths that were terminated prior to full film coverage) was investigated with high magnification SEM and aberration-corrected high-resolution transmission electron microscopy (TEM) as well as AFM, STM, and optical microscopy. These methods show that many of the “join regions” have folds, and these arise from interfacial adhesion mechanics (they are due to the buildup of compressive stress during cool-down, but these folds are different than for the continuous graphene films-they occur due to “weak links” in terms of the interface mechanics). Such Cu/Ni(111) alloy foils are promising substrates for the large-scale synthesis of single-crystal graphene film.</P> [FIG OMISSION]</BR>