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.

Identification of candidate odorant‐degrading enzyme genes in the antennal transcriptome of Aphidius gifuensis

Kang Zhi‐Wei,Liu Fang‐Hua,Xu Yong‐Yu,Cheng Jia‐Hui,Lin Xiao‐Li,Jing Xiang‐Feng,Tian Hong‐Gang,Liu Tong‐Xian 한국곤충학회 2021 Entomological Research Vol.51 No.1

Odorant‐degrading enzymes (ODEs) have been found in insect antennae and play a critical role in signal chemical degradation once the message is conveyed. Significant progress has been made in characterizing ODEs in a variety of pests but very little is known in their natural enemies. We have carried out an antennae‐ and sex‐specific transcriptome of Aphidius gifuensis, a natural enemy of aphid, to identify the candidate ODEs. Based on the antennae‐ and sex‐specific transcriptome, a total of 100 putative ODEs were identified including one aldehyde oxidase (AOX), four alcohol dehydrogenases (ADs), eight UDP‐glucuronosyltransferases (UGTs), 45 cytochrome P450 (P450s), nine glutathione S‐transferases (GSTs) and 40 carboxylesterases (CCEs or CXEs). Additionally, we used RT‐qPCR to determine the expression profiles of these genes in tissues of both sexes. Based on the phylogenic analysis and tissue‐expression patterns, AgifEstE4, AgifCXE3, AgifCCE4, AgifCCE7, and AgifCCE18 were suggested as key ODEs in A. gifuensis. In addition, the female or male specifically enriched genes, such as AgifCCE17, AgifEstB1, AgifCYP18a1, AgifUGT2C2, were also considered to involve in the chemosensory processing in A. gifuensis. This study not only identified the candidate ODEs in A. gifuensis but also provided source for further exploration of the molecular mechanisms of chemical signal transductions in A. gifuensis, as well as other hymenopteran species.

The Correlation between NK Cell and Liver Function in Patients with Primary Hepatocellular Carcinoma

( Wei Hong Sha ),( Xiao Hui Zeng ),( Lu Min ) 대한소화기학회 2014 Gut and Liver Vol.8 No.3

Background/Aims: This study aimed to detect the expression of natural killer (NK) cell receptor natural killer group 2D (NKG2D) in the peripheral blood of patients with primary hepatocellular carcinoma and to discuss the correlation between NK cell cytotoxicity and liver function. Methods: The number of NK cells and the expression of NK cell receptor NKG2D in peripheral blood were determined by flow cytometry in patients with primary hepatocellular carcinoma, hepatitis B cirrhosis, chronic hepatitis B, and healthy controls. Results: When compared with patients in the healthy and the chronic hepatitis B groups, the primary hepatocellular carcinoma group showed significant decreases in all parameters, including the cytotoxicity of NK cells on K562 cells, expression rate of NKG2D in NK cells, number of NKG2D+ NK cells, expression level of NKG2D, and number of NK cells (p<0.05). The activity of NK cells showed a positive correlation, whereas the Child-Pugh scores in the primary hepatocellular carcinoma and the hepatitis B cirrhosis groups showed a negative correlation with all parameters detected above. Conclusions: The decrease of NK cell activity in patients with primary hepatocellular carcinoma is closely related to their lower expression of NKG2D. Liver function affects the expression of NKG2D and the activity of NK cells.

Vibration Frequency Adaptive Control of the Flexible Sampling Robot based on ANFIS

Wei Lu,Yun Ling,Ai-guo Song,Wei-min Ding,Xian-lin Zhao,Hong Zeng 보안공학연구지원센터 2014 International Journal of Control and Automation Vol.7 No.3

Appropriate nitrogen application enhances saponin synthesis and growth mediated by optimizing root nutrient uptake ability

Wei, Wei,Ye, Chen,Huang, Hui-Chuan,Yang, Min,Mei, Xin-Yue,Du, Fei,He, Xia-Hong,Zhu, Shu-Sheng,Liu, Yi-Xiang The Korean Society of Ginseng 2020 Journal of Ginseng Research Vol.44 No.4

Background: Cultivation of medicinal crops, which synthesize hundreds of substances for curative functions, was focused on the synthesis of secondary metabolites rather than biomass accumulation. Nutrition is an important restrict factor for plant growth and secondary metabolites, but little attention has been given to the plasticity of nutrient uptake and secondary metabolites synthesis response to soil nitrogen (N) change. Methods: Two year-field experiments of Sanqi (Panax notoginseng), which can synthesize a high level of saponin in cells, were conducted to study the effects of N application on the temporal dynamics of biomass, nutrient absorption, root architecture and the relationships between these parameters and saponin synthesis. Results: Increasing N fertilizer rates could improve the dry matter yields and nutrient absorption ability through increasing the maximum daily growth (or nutrient uptake) rate. Under suitable N level (225 kg/ha N), Sanqi restricted the root length and surface and enhanced the root diameter and N uptake rate per root length (NURI) to promote nutrient absorption, but the opposite status of Sanqi root architecture and NURI was found when soil N was deficient. Furthermore, increasing N rates could promote the accumulation of saponin in roots through improving the NURI, which showed a significant positive relationship with the content of saponin in the taproots. Conclusion: Appropriate N fertilizer rates could optimize both root architecture and nutrient uptake efficiency, then promote both the accumulation of dry matter and the synthesis of saponins.

Cytotoxic Constituents of the Marine Invertebrates Collected from Korean Waters

( Wei Hong Wang ),( Yong Hong Liu ),( Jee H. Jung ) 한국응용약물학회 2004 학술대회 Vol.2004 No.1

A Discovery of Low Hydraulic Resistance Channel Along Meridians

Wei-Bo Zhang,Yu-Ying Tian,Hong Li,Jia-He Tian,Ming-Fu Luo,Fa-Liang Xu,Guang-Jun Wang,Tao Huang,Yi-Hui Xu,Rui-Hong Wang 사단법인약침학회 2008 Journal of Acupuncture & Meridian Studies Vol.1 No.1

A hydro-mechanic model was put forward to study the fundamental nature of acupuncture meridians. The basic state of low hydraulic resistance was tested on humans and mini pigs using three methods. The first, a modified Guyton’s method, proved that there was lower hydraulic resistance on meridians compared with nonmeridians. The second scanning method involved a single pressure transducer that can find the lowest resistance point in tissue, and the third method used two transducers and provided a more stable measurement. Using the latter method, low hydraulic resistance points were found very close to low impedance points along meridians. The transmission of artificial interstitial fluid pressure waves was measured to examine their connection to the low resistance points, with the result that a good connection between the points was confirmed. This means the points form channels along the meridians that we refer to as low hydraulic resistance channels. The channel was imaged through isotopic tracing and a migration of isotope 99mTe could be found along the channel. The layer of the channel was detected by injecting Alcian blue and the track was found beneath the skin. All of the above experiments suggest the existence of a new type of channel in living tissues that has not yet been described in modern science, but coincides quite well with the Qi channel theory of traditional Chinese medicine. A hydro-mechanic model was put forward to study the fundamental nature of acupuncture meridians. The basic state of low hydraulic resistance was tested on humans and mini pigs using three methods. The first, a modified Guyton’s method, proved that there was lower hydraulic resistance on meridians compared with nonmeridians. The second scanning method involved a single pressure transducer that can find the lowest resistance point in tissue, and the third method used two transducers and provided a more stable measurement. Using the latter method, low hydraulic resistance points were found very close to low impedance points along meridians. The transmission of artificial interstitial fluid pressure waves was measured to examine their connection to the low resistance points, with the result that a good connection between the points was confirmed. This means the points form channels along the meridians that we refer to as low hydraulic resistance channels. The channel was imaged through isotopic tracing and a migration of isotope 99mTe could be found along the channel. The layer of the channel was detected by injecting Alcian blue and the track was found beneath the skin. All of the above experiments suggest the existence of a new type of channel in living tissues that has not yet been described in modern science, but coincides quite well with the Qi channel theory of traditional Chinese medicine.

Medicinal Chemistry : Artice ; Monanchosterols A and B, Bioactive Bicyclo[4.3.1]steroids from a korean Sponge Monanchora sp

( Wei Hong Wang ),( Tae Gu Lee ),( Ra Hul S. Patil ),( Bara Mun ),( In Ho Yang ),( Hi Young Kim ),( Dong Yup Hahn ),( Dong Hwan Won ),( Ji Hye Lee ),( Ye Hee Lee ),( Hyuk Jae Choi ),( Sang Jip Nam ),( 영남대학교 약품개발연구소 2015 영남대학교 약품개발연구소 연구업적집 Vol.25 No.-

Chemical investigation of a Korean marine sponge, Minanchora sp. led to the isplation of three new steriodes (1-3). Compounds 1 and 2, designated as monan chosterols A abd B, resoectubely, represent the first example of steriods possessing the bicyclo[4.3.1] A/Brubg ststem from a natural source, Compounds 1-3 were investigated for their anti-inflammatory activity by evaluating their inhibitory effects on the mRna expression of 1L-6, TNF-a and COX-2 in the LPS-stimulated murine RAW264.7 macrophage cells, Compounds 2 and 3 exhibited significant inhibitpry effects on the mRNA expression of 1L-6 without notable cytotoxocotu tp tje cells in a dose-dependent manner.

Overexpression of afsR and Optimization of Metal Chloride to Improve Lomofungin Production in Streptomyces lomondensis S015(s)

( Wei Wang ),( Hua Sheng Wang ),( Hong Bo Hu ),( Hua Song Peng ),( Xue Hong Zhang ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.5

As a global regulatory gene in Streptomyces, afsR can activate the biosynthesis of many secondary metabolites. The effect of afsR on the biosynthesis of a phenazine metabolite, lomofungin, was studied in Streptomyces lomondensis S015. There was a 2.5-fold increase of lomofungin production in the afsR-overexpressing strain of S. lomondensis S015 N1 compared with the wild-type strain. Meanwhile, the transcription levels of afsR and two important genes involved in the biosynthesis of lomofungin (i.e., phzC and phzE) were significantly upregulated in S. lomondensis S015 N1. The optimization of metal chlorides was investigated to further increase the production of lomofungin in the afsR-overexpressing strain. The addition of different metal chlorides to S. lomondensis S015 N1 cultivations showed that CaCl2, FeCl2, and MnCl2 led to an increase in lomofungin biosynthesis. The optimum concentrations of these metal chlorides were obtained using response surface methodology. CaCl2 (0.04 mM), FeCl2 (0.33 mM), and MnCl2 (0.38 mM) gave a maximum lomofungin production titer of 318.0 ± 10.7 mg/l, which was a 4.1-fold increase compared with that of S. lomondensis S015 N1 without the addition of a metal chloride. This work demonstrates that the biosynthesis of phenazine metabolites can be induced by afsR. The results also indicate that metal chlorides addition might be a simple and useful strategy for improving the production of other phenazine metabolites in Streptomyces.

Cadmium induces apoptosis in primary rat osteoblasts through caspase and mitogen-activated protein kinase pathways

Hong-Yan Zhao,Wei Liu,Yi Wang,Nannan Dai,Jian-Hong Gu,Yan Yuan,Xue-Zhong Liu,Jian-Chun Bian,Zong-Ping Liu 대한수의학회 2015 Journal of Veterinary Science Vol.16 No.3

Exposure to cadmium (Cd) induces apoptosis in osteoblasts (OBs); however, little information is available regarding the specific mechanismsof Cd-induced primary rat OB apoptosis. In this study, Cd reduced cell viability, damaged cell membranes and induced apoptosis in OBs. We observed decreased mitochondrial transmembrane potentials, ultrastructure collapse, enhanced caspase-3 activity, and increasedconcentrations of cleaved PARP, cleaved caspase-9 and cleaved caspase-3 following Cd treatment. Cd also increased the phosphorylationof p38-mitogen-activated protein kinase (MAPK), extracellular signal-regulated kinases (ERK)1/2 and c-jun N-terminal kinase (JNK) in OBs. Pretreatment with the caspase inhibitor, N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone, ERK1/2 inhibitor (U0126), p38 inhibitor(SB203580) and JNK inhibitor (SP600125) abrogated Cd-induced cell apoptosis. Furthermore, Cd-treated OBs exhibited signs of oxidativestress protection, including increased antioxidant enzymes superoxide dismutase and glutathione reductase levels and decreased formationof reactive oxygen species. Taken together, the results of our study clarified that Cd has direct cytotoxic effects on OBs, which are mediatedby caspase- and MAPK pathways in Cd-induced apoptosis of OBs.