Resequencing 295 accessions of heuristic and Korean breeding rice deciphers the milestones for breeding and domestication history of Korean rice

Qiang He,Byung-Kook Yun,Min-Young Yoon,Xiao-Qiang Wang,Feng-Peng Li,Aye-Aye Khaing,Won-Hee Ra,Win Htet Oo,Cheol-Soon Park,Sun-Kyung Min,Wei Tong,Jie Yu,Bu-Woong Choi,Eun-Beom Heo,Khandakar Md.Rayhanul 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.

Association analysis of vitamin E and phytosterols content in dehulled rice

Xiao-Qiang Wang,Sun-Kyung Min,Soon-Wook Kwon,Young-Sang Lee,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Vitamin E and phytosterols are both valuable nutrients that act as antioxidants in human bodies. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. In this study, 119 rice accessions of diverse origin were genotyped using 232 SSR markers to identify marker–trait associations with Vitamin E and phytosterols in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.3361. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 81 marker–trait associations were identified using 232 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping. The results from this association mapping study will be the basis for improving rice nutritional quality.

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.

Role of Blood Pressure Management in Stroke Prevention: A Systematic Review and Network Meta-Analysis of 93 Randomized Controlled Trials

Xiao-Ling Zhong,Yi Dong,Wei Xu,Yu-Yuan Huang,Hui-Fu Wang,Tian-Song Zhang,Li Sun,Lan Tan,Qiang Dong,Jin-Tai Yu 대한뇌졸중학회 2021 Journal of stroke Vol.23 No.1

Background and Purpose: The present study aimed to compare the efficacy and tolerability of different blood pressure (BP)-lowering strategies. Methods: Randomized controlled trials that compared various antihypertensive treatments and stroke outcomes were included. Eligible trials were categorized into three scenarios: single or combination antihypertensive agents against placebos; single or combination agents against other agents; and different BP-lowering targets. The primary efficacy outcome was the risk reduction pertaining to strokes. The tolerability outcome was the withdrawal of drugs, owing to drug-related side effects (PROSPERO registration number CRD42018118454 [20/12/2018]). Results: The present study included 93 trials (average follow-up duration, 3.3 years). In the pairwise analysis, angiotensin-converting enzyme inhibitors (ACEis) and beta-blockers (BBs) were inferior to calcium channel blockers (CCBs) (odds ratio [OR], 1.123; 95% confidence interval [CI], 1.008 to 1.252) (OR, 1.261; 95% CI, 1.116 to 1.425) for stroke prevention, BB was inferior to angiotensin II receptor blockers (ARB) (OR, 1.361; 95% CI, 1.142 to 1.622), and diuretics were superior to ACEi (OR, 0.871; 95% CI, 0.771 to 0.984). The combination of ACEi+CCB was superior to ACEi+diuretic (OR, 0.892; 95% CI, 0.823 to 0.966). The network meta-analysis confirmed that diuretics were superior to BB (OR, 1.34; 95% CI, 1.11 to 1.58), ACEi+diuretic (OR, 1.47; 95% CI, 1.02 to 2.08), BB+CCB (OR, 2.05; 95% CI, 1.05 to 3.79), and renin inhibitors (OR, 1.87; 95% CI, 1.25 to 2.75) for stroke prevention. Regarding the tolerability profile, the pairwise analysis revealed that ACEi was inferior to CCB and less tolerable, compared to the other treatments. Conclusions: Monotherapy using diuretics, CCB, or ARB, and their combinations could be employed as first-line treatments for stroke prevention in terms of efficacy and tolerability.

Clinical Application of Recombinant Human Endostatin in Postoperative Early Complementary Therapy on Patients with Non-small Cell Lung Cancer in Chinese Mainland

Zhu, Qiang,Zang, Qi,Jiang, Zhong-Min,Wang, Wei,Cao, Ming,Su, Gong-Zhang,Zhen, Tian-Chang,Zhang, Xiao-Tian,Sun, Ning-Bo,Zhao, Cheng Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.9

Objective: To explore the clinical application of recombinant human endostatin (Endostar) in the treatment of patients with non-small cell lung cancer (NSCLC) in Chinese mainland. Materials and Methods: A total of 75 patients diagnosed as NSCLC were randomly divided into control group (37 cases) and treatment group (38 cases). Control group was treated with postoperative complementary chemotherapy containing two-agent platinum protocol on postoperative d21, 3 weeks as a cycle, for totally 4~6 cycles. On this basis, treatment group was added with Endostar $7.5mg/m^2$ on postoperative d8~9, 3~4 h/time, qd, 14 weeks as a cycle, for totally 4 cycles. The interval between every two cycles was 7 d. The 5-year progression-free survival (PFS), 5-year survival time and complications in both groups were observed. Results: Compared with control group, the average PFS increased evidently in treatment group by 9.8 months (41.6 months vs. 31.8 months), and there was significant difference (P<0.05). And the median PFS was 42.5 months in treatment group, obviously longer than that in control group (33.7 months) by 8.8 months (P<0.05). Additionally, the 5-year overall survival rate (OS), average survival time and median survival time (MST) were 47.4%, 50.1 months and 59.3 months in treatment group, significantly higher than the 29.7%, 42.1 months and 43.5 months in control group (P<0.05). Only 1 patient showed poor healing of surgical wound in treatment group, but no surgery-associated complication was found in control group. Moreover, the postoperative complementary therapy-connected complication rates were 63.2% (24/38) and 59.5% (22/37) in treatment group and control group respectively, but there was no significant difference (P>0.05). Conclusions: The application of Endostar combined with sensitive platinum-contained chemotherapeutic agents in the postoperative complementary chemotherapy can be widely used in clinic because it can significantly prolong the long-term survival time of patients with NSCLC.

Molecular characterization and expression analysis of putative odorant carrier proteins in Adelphocoris lineolatus

Yong Xiao,Liang Sun,Qi Wang,Qiang Zhang,Shao-Hua Gu,Adel Khashaveh,Ze-Wen Liu,Yong-Jun Zhang 한국응용곤충학회 2018 Journal of Asia-Pacific Entomology Vol.21 No.3

The alfalfa plant bug Adelphocoris lineolatus (Goeze) (Hemiptera: Miridae), a serious pest of several agricultural crops, is extremely attracted by flowering plants to perform season host switching. Generally, chemoreception of A. lineolatus plays a crucial role in detecting food sources, locating mates and oviposition sites. In addition, odorant carrier proteins are believed to participate in the initial chemical communication and perception in insects. In this work, we identified 31 putative odorant carrier protein genes from the antennal transcriptomes of A. lineolatus, including 17 new odorant binding proteins (OBPs), 10 new chemosensory proteins (CSPs) and four Niemann-Pick type C2 proteins (NPC2s). Phylogenetic analysis demonstrated that the OBP and CSP genes from four mirid bug species (A. lineolatus, Adelphocoris suturalis, Apolygus lucorum and Lygus lineolaris) had a relatively close evolutionary relationship. Regular patterns and key conserved motifs of OBPs and CSPs in Hemiptera insects are also identified by using Multiple EM for Motif Elicitation (MEME) tool. Tissue expression profiles analysis showed that nine of the 17 OBPs, 10 CSPs and two of the four NPC2s were primarily or uniquely expressed in the adult antennae suggesting their putative roles in chemoreception. Our study provides the first insight into the roles of odorant carrier proteins in chemoreception of A. lineolatus, which will help to facilitate biological functions of odorant carrier proteins and develop novel insect behavioral regulation strategy

Electroacupuncture Promotes Motor Function Recovery in MCAO/R Rats by Activating Astrocyte-Related PI3K/AKT Pathway

Zhang Xiao-Qing,Wang Yi-He,Sun Li,Dong Bao-Qiang,Sui Yue-Jiao,Dong Jia-Zi,Han Yang 사단법인약침학회 2022 Journal of Acupuncture & Meridian Studies Vol.15 No.5

Background: Electroacupuncture (EA) is a widely used traditional Chinese medicine method to manage various diseases, including cerebral ischemia-reperfusion injury (CIRI). Objectives: We assessed the neuroprotective effects of EA and examined its mechanism in a rat model of the middle cerebral artery occlusion-reperfusion (MCAO/R). The gait analysis was performed to evaluate the neuroprotective effects. Western blot and immunohistochemistry assays were carried out to determine the molecular mechanisms of EA. Methods: Male SD rats were randomly divided into the sham operation group, right MCAO/R group, and EA group. EA was administered every day (4/20 Hz, 10 min/1 d) at the following acupoints: Baihui (DU20), Yintang (EX-HN3), and Zusanli (ST36). Gait and motor function were analyzed from day 8 onward. Results: The plantar support and balance coordination of MCAO/R rats decreased, and the cellular structure of the ischemic penumbra was unclear. EA improved the gait dynamics of the rats, adjusted the cell structure, further activated astrocytes, and increased the expression and phosphorylation of phosphoinositide 3-kinase/protein kinase B (PI3K/PKB or AKT). Conclusion: EA promoted astrocyte-related effects in the rat model. Our findings suggest that the neuroprotective mechanism of EA may be related to the activation of the PI3K/ AKT signaling pathway. The intervention enhanced brain protection and improved motor functions.

Subdivision of Nasopharyngeal Carcinoma Patients with Bone-Only Metastasis at Diagnosis for Prediction of Survival and Treatment Guidance

Xue-Song Sun,Yu-Jing Liang,Sai-Lan Liu,Qiu-Yan Chen,Shan-Shan Guo,Yue-Feng Wen,Li-Ting Liu,Hao-Jun Xie,Qing-Nan Tang,Xiao-Yun Li,Jin-Jie Yan,Lin-Quan Tang,Hai-Qiang Mai 대한암학회 2019 Cancer Research and Treatment Vol.51 No.4

Purpose The purpose of this study was to subdivide M1 stage nasopharyngeal carcinoma (NPC) patients with bone-only metastases for prognosis prediction while identifying the treatment effect of locoregional radiotherapy (LRRT) and metastasis radiotherapy (MRT) among patients with different risk. Materials and Methods From November 2006 to October 2016, a total of 226 patients with bone-only metastasic NPC were retrospectively enrolled. All patients developed distant lesions before receiving treatment. All potential prognostic factors were considered and the correlation of the M1 subdivisions with overall survival (OS) was determined by Cox regression hazards model. Kaplan-Meier curves were used to appraise survival condition and log-rank testing was used to compare the differences. Results The median follow-up time was 33.9 months (range, 3 to 126 months). According to multivariate Cox proportional hazard analysis, the number of metastatic lesions and Epstein-Barr virus (EBV) DNA status after palliative chemotherapy (PCT) were independent prognostic factors for OS. Thus, we subdivided patients into three risk groups according to these two factors. Systemic chemotherapy combined with LRRT may benefit patients in low- and intermediate-risk groups but not in the high-risk group. Further aggressive MRT based on systemic chemotherapy showed no survival benefit in any risk group. Conclusion The stratification of NPC patients with bone-only metastasis based on EBV DNA after PCT and the number of metastatic lesions provided promising prognostic value and could aid clinicians in person-specific treatment.

Patterns of Failure and Survival Trends in 3,808 Patients with Stage II Nasopharyngeal Carcinoma Diagnosed from 1990 to 2012: A Large-Scale Retrospective Cohort Study

Xue-Song Sun,Di-Han Liu,Sai-Lan Liu,Qiu-Yan Chen,Shan-Shan Guo,Yue-Feng Wen,Li-Ting Liu,Hao-Jun Xie,Qing-Nan Tang,Yu-Jing Liang,Xiao-Yun Li,Jin-Jie Yan,Ming-Huang Hong,Jun Ma,Lin-Quan Tang,Hai-Qiang M 대한암학회 2019 Cancer Research and Treatment Vol.51 No.4

Purpose The purpose of this study was to investigate the survival trends and patterns of failure in patients with stage II nasopharyngeal carcinoma (NPC) treated with radiotherapy (RT) and chemotherapy over the last 20 years. Materials and Methods Thirty-eight hundred and eight patients diagnosed with stage II NPC between January 1990 and December 2012 were involved in this retrospective cohort study. All patients were treated with RT. According to the main imaging techniques and RT technology, we categorized these patients into four calendar periods: 1990-1996, 1997-2002, 2003-2007, and 2008-2012. Overall survival (OS), progression-free survival (PFS), locoregional relapse-free survival (LRFS), and distant metastasis–free survival (DMFS) were served as the clinical outcome. Results After a median follow-up period of 84.7 months, we observed increasing trends in survival and disease control. The 3- and 5-year OS rates increased from 87.1% and 78.7% in the first calendar period to 97.4% and 94.5% in the last calendar period, respectively (p < 0.001). Additionally, significant increasing trends could be seen in the PFS and LRFS during the four calendar periods. In the subgroup analysis, the LRFS in patients older than 50 years at diagnosis showed greater improvement than younger patients. However, the rate of distant metastasis was stable and relatively low, as the 5-year DMFS ranged from 90.5% to 94.7% among the four calendar periods. Conclusion The survival rates in patients with stage II NPC showed increasing trends from 1990 to 2012. The advance of RT provided excellent locoregional control and enhanced OS.

Efficacy of Multiple Low-dose Photodynamic TMPYP4 Therapy on Cervical Cancer Tumour Growth in Nude Mice

Liu, Ai-Hong,Sun, Xuan,Wei, Xiao-Qiang,Zhang, You-Zhong Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.9

Objective: Photodynamic therapy (PDT) is an emerging therapeutic procedure suitable for the treatment of cervical cancer. However, the side effects of PDT are severe, including skin ulceration, so we designed an experiment to examine the effects of multiple low-dose photodynamic therapy of 5, 10, 15, 20-tetrakis(1-methylpyridinium-4-yl) porphyrin (Tmpyp4) on tumour growth by utilizing a model in nude mice implanted with Hela cervical cancer cells. Materials and Methods: Female BALB/c nude mice (aged 5-6 weeks, weighing 18-20 g) were used. Hela cervical cancer cells were injected subcutaneously ($1{\times}10^7cells/200{\mu}L$). Ten days after injection, the mice were divided into three groups (n=6), the A group of controls without any treatment, the B group receiving a single-treatment with Tmpyp4 (10 mg/kg, intratumor injection) and irradiation (blue laser, $108J/cm^2$), and the C group given three-treatments with Tmpyp4 (10 mg/kg, intratumor injection) and irradiation at intervals of two days. After starting treatment, tumours were measured every two days, to assess growth. At 2 weeks after the last treatment of C group, tumour tissue and organs were collected from each mouse to evaluate tumor histology and organ damage. Results: Tumour growth in C group was significantly inhibited compared with A and B groups (P<0.05), without any injury to the skin and internal organs. Conclusion: Our novel findings demonstrated that multiple low-dose photodynamic therapy of Tmpyp4 could inhibit cervical cancer growth significantly with no apparent side effects.