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.

Dynamic simulation and control of a triple column process for dimethyl carbonate- methanol separation

Hong-Mei Wei,Qiang Gao,Wei-zhou Jiao,Wei Wei 한국화학공학회 2022 Korean Journal of Chemical Engineering Vol.39 No.12

Separation of dimethyl carbonate/methanol azeotropic mixture by using pressure-swing distillation processhas been a hot-point in the study of the synthesis process of dimethyl carbonate by urea methanolysis method. Thisstudy updates the work of the writers (Ind.Eng.Chem.Res,2013,52,11463-11478), which explores the dynamic controlstructure of the three-column separation dimethyl carbonate (DMC)/methanol (MeOH) process from an actual pilotplant. At first, the conventional DMC/MeOH separation process in the pilot test of the DMC synthesis process throughalcoholysis of urea was described in detail. Then an optimized control structure for the entire DMC/MeOH separationunit was obtained by implementing a general heuristic design procedure. An economic analysis was performed to evaluatethe optimized process. Finally, three dynamic control schemes were proposed and evaluated with several large disturbances,an improved control scheme CS3, using the multiplier blocks “QR1/F1” and “RR1” in T1, “QR1/F1” and “R/F”in both T2 and T3, outperformed CS1 and CS2 by maintaining the product specification in each column.

Concurrent Weekly Docetaxel Chemotherapy in Combination with Radiotherapy for Stage III and IVA-B Nasopharyngeal Carcinoma

Wei, Wei-Hong,Cai, Xiu-Yu,Xu, Tao,Zhang, Guo-Yi,Wu, Yong-Feng,Feng, Wei-Neng,Lin, Li,Deng, Yan-Ming,Lu, Qiu-Xia,Huang, Zhe-Li Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.3

Background and Purpose: Cisplatin is the most common chemotherapeutic agent for loco-regionally advanced nasopharyngeal carcinoma (NPC); however, toxicity is a limiting factor for some patients. We retrospectively compared the efficacy and toxicity of weekly docetaxel-based and cisplatin-based concurrent chemoradiotherapy in loco-regionally advanced NPC. Methods and Materials: Eighty-four patients with Stage III and IVA-B NPCs, treated between 2007 and 2008, were retrospectively analyzed. Thirty received weekly docetaxel-based concurrent chemotherapy, and 43 were given weekly cisplatin-based concurrent chemotherapy. Radiotherapy was administered using a conventional technique (seven weeks, 2.0 Gy per fraction, total dose 70-74 Gy) with 6-8 Gy boosts for some patients with locally advanced disease. Results: Median follow-up time was 42.3 months (range, 8.6-50.8 months). There were no significant differences in the 3-year loco-regional failure-free survival (85.6% vs. 92.3%; p=0.264), distant failure-free survival (87.0% vs. 92.5%; p=0.171), progression-free survival (85.7% vs. 88.4%; p=0.411) or overall survival (86.5% vs. 92.5%, p=0.298) of patients treated concurrently with docetaxel or cisplatin. Severe toxicity was not common in either group. Conclusions: Weekly docetaxel-based concurrent chemoradiotherapy is potentially effective and has a tolerable toxicity; however, further investigations are required to determine if docetaxel is superior to cisplatin for advanced stage NPC.

Analysis of Indoleamine 2-3 Dioxygenase (IDO) and EGFR Co-expression in Breast Cancer Tissue by Immunohistochemistry

Bi, Wei-Wei,Zhang, Wei-Hua,Yin, Gui-Hua,Luo, Hong,Wang, Shou-Qin,Wang, Hongran,Li, Chao,Yan, Wei-Qun,Nie, De-Zhi Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Background: To determine the amount of co-expression of IDO and EGFR in breast cancer patients. Materials and Methods:In order to obtain the distribution of co-expression of IDO and EGFR in breast cancer, we tested 110 breast cancer paraffin tissue blocks with immunohistochemical methods. Then we investigated the relationship between the diagnostic and pathologic characteristics (tumor size, lymph node status, histologic grade, the gene expression of ER, PR, HER2, p53, Ki67 and PCNA) with the situation of co-expression of IDO and EGFR by reviewing the medical records of 32 breast cancer patients. Results: Among 110 breast cancers, 32 cases demonstrated IDO and EGFR co-expression (29.1%), IDO and EGFR synchronous co-expression being found in 19.1% and asynchronous in 10.0%. Conclusions: IDO and EGFR were co-expressed in breast cancer, including synchronous and asynchronous co-expression. The results suggest that considering IDO and EGFR as two indicators for breast cancer treatment or prognosis analysis provides a potential option of individual treatment for the portion of breast cancer patients with co-expression of IDO and EGFR.

RING Finger Proteins Are Involved in the Progression of Barrett Esophagus to Esophageal Adenocarcinoma: A Preliminary Study

( Xing Wei Wang ),( Wei Wei ),( Wei Qiang Wang ),( Xiao Yan Zhao ),( Hong Guo ),( Dian Chun Fang ) 대한소화기학회 2014 Gut and Liver Vol.8 No.5

Background/Aims: To investigate the differential expression of RING finger (RNF) proteins in Barrett esophagus (BE) and esophageal adenocarcinoma (EAC). Methods: The differential expression of RNFs in normal esophagus (NE), BE, and EAC was screened using microarray assay. Real-time quantitative polymerase chain reaction (PCR), tissue microarray assay, and Western blot analysis were independently performed to detect the mRNA and protein expression of screened RNFs. Results: The expression of nine RNFs in the BE or EAC was 2-fold higher than those in NE. Among these proteins, the RNF32 and RNF121 expression in BE was 20.3-fold and 16.4-fold higher, respectively, than that in NE, and the expression of RNF24, RNF130, RNF141, RNF139, RNF11, RNF14, and RNF159 was upregulated more than 2-fold compared with NE. The expression of nine RNFs was not only upregulated in the EAC but was also positively related to the RNF expression in BE. The PCR results also indicated increased expression of these RNFs in BE and EAC compared to NE. Furthermore, the mRNA expression of all RNFs, except for RNF141 in EAC, was dramatically higher than those in the BE. Similar results were also obtained from the Western blot analysis. Conclusions: A total of nine RNFs play critical roles in the progression of BE to EAC. (Gut Liver 2014;8:487-494)

러시아의 미국 대통령 선거 개입 사건과 중국 對 대만 정보전

위홍위(Wei, hong-wei) 한국외국어대학교 대만연구센터 2019 대만연구 Vol.- No.14

Unlike conventional warfare, the center of gravity in a hybrid warfare is a person, a resident of a chosen country. The adversary combines kinetic operations with subversive actions to influence key decision-makers and decision makers. Sometimes invaders rely on covert behavior to avoid accountability and retaliation. Hybridization is therefore essentially subversive. This is particularly dangerous for countries with high levels of multi-ethnic, political, social and ideological conflict. Hybrid warfare is not found in the frontiers of the frontiers, but in the gray areas of security. Gray is a new color that emerged from hybrid warfare. Song Seung - jong, above, p. 87. Therefore, in order to cope with hybrid threats, it is necessary to collect and analyze information quickly and accurately, and to be flexible and responsive to the situation quickly and effectively. If you fight on the battlefield where the enemy is composed, you will be seriously wounded. I think we should be able to counter the gray attack of the enemy forces by educating the people about the state of war now.

FBW7 Upregulation Enhances Cisplatin Cytotoxicity in Non-small Cell Lung Cancer Cells

Yu, Hao-Gang,Wei, Wei,Xia, Li-Hong,Han, Wei-Li,Zhao, Peng,Wu, Sheng-Jun,Li, Wei-Dong,Chen, Wei Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Introduction: Lung cancer is extremely harmful to human health and has one of the highest worldwide incidences of all malignant tumors. Approximately 80% of lung cancers are classified as non-small cell lung cancers (NSCLCs). Cisplatin-based multidrug chemotherapy regimen is standard for such lesions, but drug resistance is an increasing problem. F-box/WD repeat-containing protein 7 (FBW7) is a member of the F-box protein family that regulates cell cycle progression, and cell growth and differentiation. FBW7 also functions as a tumor suppressor. Methods: We used cell viability assays, Western blotting, and immunofluorescence combined with siRNA interference or plasmid transfection to investigate the underlying mechanism of cisplatin resistance in NSCLC cells. Results: We found that FBW7 upregulation significantly increased cisplatin chemosensitivity and that cells expressing low levels of FBW7, such as NCI-H1299 cells, have a mesenchymal phenotype. Furthermore, siRNA-mediated silencing or plasmid-mediated upregulation of FBW7 resulted in altered epithelial-mesenchymal transition (EMT) patterns in NSCLC cells. These data support a role for FBW7 in regulating the EMT in NSCLC cells. Conclusion: FBW7 is a potential drug target for combating drug resistance and regulating the EMT in NSCLC cells.

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

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.