A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies

Wei Tong,Qiang He,Xiao-Qiang Wang,Min-Young Yoon,Won-Hee Ra,Feng Peng Li,Jie Yu,Win Htet Oo,Sun-Kyung Min,Buung Choi,Eun-Beom Heo,Byoung-Kook Yun,Kyu-Won Kim,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

Association study of vitamin E content in rice using whole genome re-sequencing

Xiao-Qiang Wang,Qiang He,Wei Tong,Byung-Kook Yun,Young-Sang Lee,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Rice is the major food for half of the world population. The nutrition component in rice is critical for improvement of people’s health. Vitamin E serves as important antioxidant by quenching the free radical intermediates and thus protects the cell membrane. Because of the high nutritional value and the benefits of vitamin E in human health, increasing the tocochromanol content of major agricultural crops has long been in the focus of breeding programs and genetic engineering approaches. The key genes involved in tocopherol biosynthesis have been elucidated in Arabidopsis and other model organisms. Quantitative trait locus (QTL) study performed in Arabidopsis suggested that some of these key genes and a few additional loci contribute to natural tocopherol variations. Identifying such genetic variations in rice, enrich our understanding of the genetic mechanisms controlling tocopherol variation, which can be directly applied to rice breeding programs. In this study, we used genome-wide association mapping with high-resolution density SNPs of rice core set to identify natural allelic variations, which contribute to tocopherol increase in rice

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)

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.

Synergistic Anticancer Activity of 5-Aminolevulinic Acid Photodynamic Therapy in Combination with Low-dose Cisplatin on Hela Cells

Wei, Xiao-Qiang,Ma, Hui-Qing,Liu, Ai-Hong,Zhang, You-Zhong Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.5

Objective: Photodynamic therapy (PDT ) is a promising modality for the treatment of various tumors. In order to assist in optimizing treatment, we applied 5-ALA/PDT in combination with low-dose cisplatin to evaluate cytotoxicity in Hela cells. Methods: Antiproliferative effects of 5-ALA/PDT and cisplatin, alone and in combination, were assessed using MTT assay. To examine levels of apoptosis, Hela cells treated with 5-ALA/PDT, and combination treatment were assessed with Annexin-V/PI by flow cytometry. To investigate the molecular mechanisms underlying alterations in cell proliferation and apoptosis, Western blot analysis was conducted to determine the expression of p53, p21, Bax and Bcl-2 proteins. Results: MTT assays indicated that combination treatment obviously decreased the viability of Hela cells compared to individual drug treatment. In addition, it was confirmed that exposure of Hela cells to 5-ALA/PDT in combination with low-dose cisplatin resulted in more apoptosis in vitro. Synergistic anticancer activity was related to upregulation p53 expression and alteration in expression of p21, Bcl-2 and Bax. Conclusion: Our findings suggest that administration of 5-ALA/PDT in combination with the low-dose cisplatin may be an effective and feasible therapy for cervical cancer.

Non-alcoholic fatty liver disease: the pathologist’s perspective

Wei-Qiang Leow,Anthony Wing-Hung Chan,Paulo Giovanni L. Mendoza,Regina Lo,Kihan Yap,Haeryoung Kim 대한간학회 2023 Clinical and Molecular Hepatology(대한간학회지) Vol.29 No.-

Non-alcoholic fatty liver disease (NAFLD) is a spectrum of diseases characterized by fatty accumulation in hepatocytes, ranging from steatosis, non-alcoholic steatohepatitis, to cirrhosis. While histopathological evaluation of liver biopsies plays a central role in the diagnosis of NAFLD, limitations such as the problem of interobserver variability still exist and active research is underway to improve the diagnostic utility of liver biopsies. In this article, we provide a comprehensive overview of the histopathological features of NAFLD, the current grading and staging systems, and discuss the present and future roles of liver biopsies in the diagnosis and prognostication of NAFLD.

Efficacy and Safety of a Steroid-Free Immunosuppressive Regimen after Liver Transplantation for Hepatocellular Carcinoma

Qiang Wei,Xiao Xu,Chao Wang,Runzhou Zhuang,Li Zhuang,Lin Zhou,Haiyang Xie,Jian Wu,Min Zhang,Yan Shen,Weilin Wang,Shusen Zheng 거트앤리버 소화기연관학회협의회 2016 Gut and Liver Vol.10 No.4

Background/Aims: We aimed to evaluate the efficacy and safety of an immunosuppressive regimen without steroids after liver transplantation (LT) for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Methods: Sixty-six HCC patients who underwent an immunosuppressive regimen without steroids after LT were enrolled in the steroid-free group. The preoperative characteristics and postoperative outcomes of these patients were compared with those of 132 HCC recipients who were placed on an immunosuppressive regimen using steroids (steroid group). The incidence of acute rejection, HBV recurrence, infection, and new-onset diabetes mellitus and the overall and tumor-free survival rates were compared between the two groups. Results: Differences were not observed in the 1-year (83.3% vs 97.0%, p=0.067), 3-year (65.4% vs 75.8%, p=0.067) or 5-year (56.3% vs 70.7%, p=0.067) patient survival rates or in the 1-year (62.1% vs 72.7%, p=0.067), 3-year (49.8% vs 63.6%, p=0.067) or 5-year (48.6% vs 63.6%, p=0.067) tumor-free survival rates between the two groups, respectively. In the steroid-free group, the patients who fulfilled the Milan criteria had higher overall and tumor-free survival rates than those in the steroid group (p<0.001). The prevalence of HBV recurrence (3.0% vs 13.6%, p=0.02) was significantly lower in the steroid-free group compared with the steroid group. Conclusions: After LT, an immunosuppressive regimen without steroids could be a safe and feasible treatment for HBVrelated HCC patients, thus resulting in the reduction of HBV recurrence. Based on the observed survival rates, patients who fulfill the Milan criteria may derive benefits from steroidfree immunosuppression.

Characterization of 1,4-Dihydropyridine Derivatives by Electrospray Ionization Ion-Trap Time-of-Flight Tandem Mass Spectrometry

Qiang Wei,Guoquan Yan,Qianrong Li 대한화학회 2015 Bulletin of the Korean Chemical Society Vol.36 No.10

1,4-Dihydropyridines provide the principal structural components for calcium channel blockers, which are usually studied by expeditious qualitative and quantitative analyses in pharmaceutical research and development. In this work, through the use of high-resolution electrospray ionization ion-trap time-of-flight multistage tandem mass spectrometry (ESI-IT-TOF/MSn), the accurate masses and fragmentation pathways of protonated derivatives (1–12) of 1,4-dihydropyridine derivatives are determined and rationalized. All protonated molecules are further fragmented by loss of the neutral groups 4-R1H, 3-C2H4 , 5-C2H4 , R2OH, or CO, yielding three fragmentation pathways with two different fragment nuclei of pyridine or 1,4-dihydropyridine. During the formation process of the pyridine nucleus, one pathway is that product ions at m/z 224 or 252 are the common diagnostic masses in most compounds; the other pathway is that the product ions are obtained by the loss of R2OH. The 1,4-dihydropyridine nucleus in three compounds arises from double C2H4 elimination. Simultaneously, this study supplies abundant special fragment information, which potentially provides a new method for structural studies of 1,4-dihydropyridine derivatives.

Chemical Constituents from the Aerial Parts of Isodon coetsa and their Cytotoxicity

Wei Zhao,Jian Xin Pu,Xue Du,Yong Zhao,Fei He,Hai Bo Zhang,Yong Bo Xue,Wei Lie Xiao,Han Dong Sun,Ying Li Wu,Guo Qiang Chen 대한약학회 2011 Archives of Pharmacal Research Vol.34 No.12

Three new compounds (1-3), including a neolignan, a triterpenoid, and a diterpenoid, together with twenty known compounds (4-23), were isolated from the aerial parts of Isodon coetsa. Their structures and relative configurations were elucidated on the basis of spectroscopic data. Compounds 1, 3, 5-9, 11-13, 16-17, and 19-23 were evaluated for their cytotoxicity against HT-29, BEL-7402, and SK-OV-3 human tumor cell lines. Compound 7 showed significant inhibitory effects on all three types of cells, with IC50 values of 2.52, 3.06, 2.14 μM, respectively.

An OpenFlow User-Switch Remapping Approach for DDoS Defense

( Qiang Wei ),( Zehui Wu ),( Kalei Ren ),( Qingxian Wang ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.9

DDoS attacks have had a devastating effect on the Internet, which can cause millions of dollars of damage within hours or even minutes. In this paper we propose a practical dynamic defense approach that overcomes the shortage of static defense mechanisms. Our approach employs a group of SDN-based proxy switches to relay data flow between users and servers. By substituting backup proxy switches for attacked ones and reassigning suspect users onto the new proxy switches, innocent users are isolated and saved from malicious attackers through a sequence of remapping process. In order to improve the speed of attacker segregation, we have designed and implemented an efficient greedy algorithm which has been demonstrated to have little influence on legitimate traffic. Simulations, which were then performed with the open source controller Ryu, show that our approach is effective in alleviating DDoS attacks and quarantining the attackers by numerable remapping process. The simulations also demonstrate that our dynamic defense imposes little effect on legitimate users, and the overhead introduced by remapping procedure is acceptable.