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.

자돈에 있어 게르마늄 용질액의 급여가 성장 및 혈액학적 변화에 미치는 영향

홍종욱,권오석,민병준,조진호,진영걸,손경승,강종옥,김인호 한국국제농업개발학회 2004 韓國國際農業開發學會誌 Vol.16 No.4

본 연구의 목적은 이산화게르마늄을 함유한 게르마늄 용질액을 자돈에 급여하였을 때 성장 및 혈액학적 변화에 미치는 영향을 조사하기 위하여 실시하였다. 3원 교잡종 자돈 60두 (평균체중 11.22±0.10㎏)를 공시하였다. 시험설계는 옥수수-대두박 위주의 대조구(CON)와, 대조구 사료내 게르마늄 용질액을 0.5 ppm 첨가한 구(GC0.5) 및 대조구 사료내 게르마늄 용질액을 1.0 ppm 첨가한 구(GC1.0)로 3개 처리를 하였다. 0-10일간 사양시험기간동안, 일당증체량에 있어서 GC0.5 처리구가 약간 높게 평가되었다(quadratic effect, P<0.02). 그러나 전체 시험기간동안, 일당증체량, 일당사료섭취량 및 사료효율에 있어서 처리구간에 유의적인 차이는 보이지 않았다. 영양소 소화율에 있어서는 GC0.5 처리구가 조회분(linear effect, P<0.01; quadratic effect, P<0.04), 칼슘(linear effect, P<0.01; quadratic effect, P<0.01), 인 (linear effect, P<0.02; quadratic effect, P<0.04) 소화율이 유의적으로 높게 평가되었다. 혈액내 neutrophil 농도에 있어서는 게르마늄 용질액의 첨가 수준이 증가함에 따라 유의적으로 증가하는 경향을 나타내었다(quadratic effect, P<0.02). 결론적으로, 자돈 사료내 게르마늄 용질액의 급여가 성장 및 혈액학적 수치에는 영향을 미치지 못하는 것으로 사료된다. This study was conducted to investigate the effects of dietary germanium colloid on the growth performance and hematological values in nursery pigs. Sixty pigs (11.22(0.10 ㎏ average initial body weight) were used in a 20 d growth assay. Dietary treatments included 1) CON (basal diet), 2) GC0.5 (basal diet+0.5 ppm germanium colloid) and 3) GC1.0 (basal diet+1.0 ppm germanium colloid). For d 0 to 10, pigs fed GC0.5 diet grew faster than pigs fed CON and GC1.0 diets (Quadratic effect, P<0.02). However, through the entire experimental period, no statistical differences were found for aver-age daily gain, average daily feed intake and gain/feed. Apparent digestibilities of crude ash (Linear effect, P<0.01; Quadratic effect, P<0.04), calcium (Linear effect, P<0.01; Quadratic effect, P<0.01) and phosphorus (Linear effect, P<0.02; Quadratic effect, P<0.04) in pigs fed GC0.5 diet were greater than for pigs fed CON and GC1.0. Neutrophil concentration in blood increased as the concentration of germanium colloid in the diets was increased with significant difference (Quadratic effect, P<0.02). In conclusion, growth performance and hematological values were not influenced by dietary germanium colloid.

A new proof of generalized Tychonoff theorem in $(L,M)$-fuzzy topological spaces

Hu Zhao,Hong-ying Zhang 원광대학교 기초자연과학연구소 2018 ANNALS OF FUZZY MATHEMATICS AND INFORMATICS Vol.16 No.2

In this paper, using the structures of $(L,M)$-fuzzy topological product spaces which were introduced by Hu Zhao, Sheng-Gang Li and Gui-Xiu Chen, we directly give another version on the proof of generalized Tychonoff theorem in $(L,M)$-fuzzy topological spaces which was introduced by Hong-Yan Li and Fu-Gui Shi

Inhibitory effects of osteoprotegerin on osteoclast formation and function under serum-free conditions

Ying-Xiao Fu,Jian-Hong Gu,Yi-Ran Zhang,Xi-Shuai Tong,Hong-Yan Zhao,Yan Yuan,Xue-Zhong Liu,Jian-Chun Bian,Zong-Ping Liu 대한수의학회 2013 Journal of Veterinary Science Vol.14 No.4

The purpose of this study was to determine whether osteoprotegerin (OPG) could affect osteoclat differentiation and activation under serum-free conditions. Both duck embryo bone marrow cells and RAW264.7 cells were incubated with macrophage colony stimulatory factor (M-CSF) and receptor activator for nuclear factor κB ligand (RANKL) in serum-free medium to promote osteoclastogenesis. During cultivation, 0,10, 20, 50, and 100 ng/mL OPG were added to various groups of cells. Osteoclast differentiation and activation were monitored via tartrate-resistant acid phosphatase (TRAP) staining,filamentous-actin rings analysis, and a bone resorption assay. Furthermore, the expression osteoclast-related genes, such as TRAP and receptor activator for nuclear factor κB (RANK),that was influenced by OPG in RAW264.7 cells was examined using real-time polymerase chain reaction. In summary,findings from the present study suggested that M-CSF with RANKL can promote osteoclast differentiation and activation,and enhance the expression of TRAP and RANK mRNA in osteoclasts. In contrast, OPG inhibited these activities under serum-free conditions.

Bio-toxicity and bio-stability: the important evaluation indices of chemical oxidation process for water reclamation and reuse

Hong-Ying HU 대한환경공학회 2015 대한환경공학회 학술발표논문집 Vol.2015 No.10

Thermal Immune NiGermanide for High Performance Ge MOSFETs on Ge-on- Si Substrate Utilizing <tex> $ \hbox{Ni}_{0.95}\hbox{Pd}_{0.05}$</tex> Alloy

Ying-Ying Zhang,Jungwoo Oh,In-Shik Han,Zhun Zhong,Shi-Guang Li,Soon-Yen Jung,Kee-Young Park,Hong-Sik Shin,Won-Ho Choi,Hyuk-Min Kwon,Wei-Yip Loh,Majhi, P.,Jammy, R.,Hi-Deok Lee IEEE 2009 IEEE transactions on electron devices Vol.56 No.2

<P>Highly thermally stable Ni germanide technology for high performance germanium metal-oxide-semiconductor field-effect transistors (Ge MOSFETs) is proposed, utilizing Pd incorporation into Ni germanide. The proposed Ni germanide shows not only the improvement of thermal stability but also the reduction of hole barrier height, which can improve the device on-current by reducing the Ni germanide to p+ source/drain contact resistance. The proposed Ni germanide showed a stable sheet resistance of up to 500 degrees C 30-min postgermanidation annealing due to the suppression of agglomeration and oxidation of Ni germanide and the diffusion of Ni and Ge atoms by the incorporated Pd. Therefore, the proposed Ni0.95Pd0.05, alloy could be promising for the high mobility Ge MOSFET applications.</P>

Effectiveness and Safety of Dabrafenib in the Treatment of 20 Chinese Children with BRAFV600E-Mutated Langerhans Cell Histiocytosis

Ying Yang,Dong Wang,Lei Cui,Hong-Hao Ma,Li Zhang,Hong-Yun Lian,Qing Zhang,Xiao-Xi Zhao,Li-Ping Zhang,Yun-Ze Zhao,Na Li,Tian-You Wang,Zhi-Gang Li,Rui Zhang 대한암학회 2021 Cancer Research and Treatment Vol.53 No.1

Purpose We sought to investigate the effectiveness and safety of dabrafenib in children with BRAFV600E-mutated Langerhans cell histiocytosis (LCH). Materials and Methods A retrospective analysis was performed on 20 children with BRAFV600E-mutated LCH who were treated with dabrafenib. Results The median age at which the patients started taking dabrafenib was 2.3 years old (range, 0.6 to 6.5 years). The ratio of boys to girls was 2.3:1. The median follow-up time was 30.8 months (range, 18.9 to 43.6 months). There were 14 patients (70%) in the risk organ (RO)+ group and six patients (30%) in the RO– group. All patients were initially treated with traditional chemotherapy and then shifted to targeted therapy due to poor control of LCH or intolerance to chemotherapy. The overall objective response rate and the overall disease control rate were 65% and 75%, respectively. During treatment, circulating levels of cell-free BRAFV600E (cfBRAFV600E) became negative in 60% of the patients within a median period of 3.0 months (range, 1.0 to 9.0 months). Grade 2 or 3 adverse effects occurred in five patients. Conclusion Some children with BRAFV600E-mutated LCH may benefit from monotherapy with dabrafenib, especially high-risk patients with concomitant hemophagocytic lymphohistiocytosis and intolerance to chemotherapy. The safety of dabrafenib is notable. A prospective study with a larger sample size is required to determine the optimal dosage and treatment duration.

Multicultural Mind versus Multicultural Self : Linking Culture, Cognition, and Identity

Ying-yi Hong 인하대학교 다문화융합연구소 2018 다문화와 교육 Vol.3 No.1

In the face of rapid globalization, many individuals are being exposed to multiple cultural traditions and practices. Although multiple cultural exposures have been shown to have beneficial effects (such as enhancing cultural frame switching and creativity), it could also threaten individuals’ own cultural identity. To understand the interplay between these two opposing consequences, I will delineate the concepts of Multicultural Mind and Multicultural Self. Multicultural mind entails acquiring and applying knowledge of new cultures. This process could benefit creativity and even reduce prejudice and discrimination. By contrast, multicultural self entails using cultural traditions to define the self, a process that could lead to negative reactions toward new cultures if individuals endorse racial essentialism (believing that race has biological essence rather than it is a social construction). In my talk, I will first present empirical findings of multicultural mind and multicultural self, and then discuss the latest extension to cultural mixing and cultural attachment.

Gentiopicroside Ameliorates the Progression from Hepatic Steatosis to Fibrosis Induced by Chronic Alcohol Intake

( Hong-xu Yang ),( Yue Shang ),( Quan Jin ),( Yan-ling Wu ),( Jian Liu ),( Chun-ying Qiao ),( Zi-ying Zhan ),( Huan Ye ),( Ji-xing Nan ),( Li-hua Lian ) 한국응용약물학회 2020 Biomolecules & Therapeutics(구 응용약물학회지) Vol.28 No.4

In current study, we aimed to investigate whether the gentiopicroside (GPS) derived from Gentiana manshurica Kitagawa could block the progression of alcoholic hepatic steatosis to fibrosis induced by chronic ethanol intake. C57BL/6 mice were fed an ethanol- containing Lieber-DeCarli diet for 4 weeks. LX-2 human hepatic stellate cells were treated with GPS 1 h prior to transforming growth factor-β (TGF-β) stimulation, and murine hepatocyte AML12 cells were pretreated by GPS 1 h prior to ethanol treatment. GPS inhibited the expression of type I collagen (collagen I), α-smooth muscle actin (α-SMA) and tissue inhibitor of metal protease 1 in ethanol-fed mouse livers with mild fibrosis. In addition, the imbalanced lipid metabolism induced by chronic ethanol-feeding was ameliorated by GPS pretreatment, characterized by the modulation of lipid accumulation. Consistently, GPS inhibited the expression of collagen I and α-SMA in LX-2 cells stimulated by TGF-β. Inhibition of lipid synthesis and promotion of oxidation by GPS were also confirmed in ethanol-treated AML12 cells. GPS could prevent hepatic steatosis advancing to the inception of a mild fibrosis caused by chronic alcohol exposure, suggesting GPS might be a promising therapy for targeting the early stage of alcoholic liver disease.

On Power Flow Transmission for the Finite Continuous Isolation System of Asymmetry

Ying Hong Mao,Kong Jie Song,Zun Min Gen,Li Lin 대한기계학회 1997 Asia-Pacific Vibration Conference Vol.2 No.1