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Resequencing reveals different domestication rate for BADH1 and BADH2 in rice (Oryza sativa)
Qiang He,Jie Yu,Tae-Sung Kim,Yoo-Hyun Cho,Young-Sang Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcription region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP P11483(T/A)ishighlycorrelatedwithsalttoleranceindex(STI)(P<10-4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (P23036, P25390) explain 97% of aroma variation in our germplasm. It indicated that there are no overlapping functions between the two homology genes. In addition, a large LD block was detected in BADH2 region, however, no large LD blocks in a 4-Mb region of BADH1. Only BADH2 region shown significant bias Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (P23036) of BADH2, while both of the BADH1 alleles (SNP P11483(T/A)) did not show large extended LDblock. All these results suggested that BADH2 was identified as a domesticated gene during rice evolution, while BADH1 was not selected by human beings.
Zeng, Yu-Jie,Liu, Lu,Wu, Heng,Lai, Wei,Cao, Jie-Zhi,Xu, He-Yang,Wang, Jie,Chu, Zhong-Hua Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.10
Background: The gastroenteropancreatic neuroendocrine neoplasm (GEP-NEN) is the most common type of neuroendocrine neoplasm. We summarized data in our centre to investigate the clinicopathological features, diagnostic methods, therapeutic approaches and prognosis for this neoplasm to increase knowledge of this disease in Asian populations. Method: A total of 122 patients treated at Sun Yet-san Memorial Hospital of Sun Yat-sen University between January 2000 and December 2011 were analyzed retrospectively. Results: Pancreas was the most common site of involvement (65/122, 53.3%); this disease has no special symptoms; positive rates of chromogranin A (CgA) and synaptophysin (Syn) were 81.1% and 87.7%, respectively. The positive rate of Syn had statistical difference among the three grades, but not CgA. Some 68 patients had G1 tumors, 32 G2 tumors and 22 G3 tumors, and Chi-square test showed that higher grading was correlated with worse prognosis (${\chi}^2=32.825$, P=0.0001). A total of 32 patients presented with distant metastasis, and 8 cases emerged during following up. Cox proportional hazards regression modeling showed that the tumor grade (P=0.01), lymphatic metastasis (P=0.025) and distant metastasis (P=0.031) were predictors of unfavorable prognosis. The overall 5-year survival rate was 39.6%, the 5-year survival rate of G1 was 55.7%, and the G2 and G3 were 34.2% and 0%, respectively. Conclusions: The incidence of gastroenteropancreatic neuroendocrine tumors has risen over the last 12 years. All grades of these diseases metastasize readily, and further research regarding the treatment of patients after radical surgery is needed to prolong disease-free survival.
Yu, Ligang,Gao, Chang,Zeng, Maomao,He, Zhiyong,Wang, Linxiang,Zhang, Shuang,Chen, Jie 한국식품과학회 2016 Food Science and Biotechnology Vol.25 No.4
This work aimed to investigate the effects of stored raw meat and process procedures on $N^{\varepsilon}$-carboxymethyl-lysine (CML) and $N^{\varepsilon}$-carboxyethyl-lysine (CEL) generation in meat products. Meat products of raw pork were sterilized and pasteurized at different storage times (0-4 months) and the CML/CEL contents were determined. The results showed that the extent of lipid and protein oxidation of raw pork increased with increasing storage time. A linear correlation was found between thiobarbituric acid-reactive substances value/carbonyl content and CML/CEL in sterilized meat products, indicating that stored raw pork could promote CML/CEL formation under high temperature processing. Furthermore, mild heating temperatures seemed to favor CML formation, while high temperature could accelerate CEL generation. Therefore, formation kinetics of CML and CEL might be different for different process procedures. These results suggested that stored raw meat and processing temperature could significantly affect CML and CEL generation in meat products.
He, Wentao,Yao, Yong,He, Min,Kai, Zhang,Long, Lijuan,Zhang, Minmin,Qin, Shuhao,Yu, Jie Korean Chemical Society 2013 Bulletin of the Korean Chemical Society Vol.34 No.1
Surface modification of montmorillonite (MMT) with 3-glycidoxypropyl trimethoxysilane (3GTO) in mild methanol/water mixture has been investigated in detail. The influence of reaction conditions (including silane concentration in feed, reaction time and reaction temperature) on the grafting amount and yield of silane, and further on the grafting pattern of silanes was studied by thermogravimetric analysis, elemental analysis, X-ray diffraction (XRD) and BET. Higher silane concentration, longer reaction time and higher reaction temperature are all benefit to higher grafting amount. When the grafting reaction was performed with 3 mmol/g silane concentration, at $90^{\circ}C$ for 24 h, the grafted amount and yield of silane reached 1.4443 mmol/g and 30%, respectively. Based on the XRD and BET data analysis, a speculation that the grafting pattern of silanes was concentration dependence was proposed.
He, Feng,Wen, Hai-Shen,Li, Ji-Fang,Yu, Da-Hui,Ma, Rui-Qin,Shi, Dan,Mu, Wei-Jie,Zhang, Yuan-Qing,Hu, Jian,Liu, Miao,Han, Wei-Guo,Zhang, Jia-Nan,Wang, Qing-Qing,Yuan, Yu-Ren,Liu, Qun Asian Australasian Association of Animal Productio 2011 Animal Bioscience Vol.24 No.4
Gonadotropin-releasing hormone receptor (GnRHR) gene is expressed at the anterior pituitary gland and plays a key role in gonad development. This study aimed to investigate molecular genetic characteristics of the GnRHR gene and elucidate the effects of single nucleotide polymorphisms (SNPs) of GnRHR gene on sex steroid level in Japanese flounder (Paralichthys olivaceus). We used polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) and sequencing of the GnRHR gene in 75 individuals. We identified three SNPs in the GnRHR gene: P1 locus (C759A and C830T) in the coding region of exon2 which were both linked together and P2 locus (G984T) in the coding region of exon3, which added a new transcript factor (ADR1) and a new methylation site (CG). Only C830T of P1 leads to amino acid changes Thr266Ile. Statistical analysis showed that P1 was significantly associated with $17{\beta}$-estradiol ($E_2$) level (p<0.01) and gonadosomatic index (GSI) (p<0.05). Individuals with genotype BB of P1 had significantly higher serum $E_2$ levels (p<0.01) and GSI (p<0.05) than those of genotype AA or AB. Another SNP, P2, synonymous mutation, was significantly associated with GSI (p<0.05). Individuals with genotype AB of P2 had significantly higher GSI (p<0.05) than that of genotype AA. In addition, there was a significant association between one diplotype based on three SNPs and reproductive traits. The genetic effects for both serum $E_2$ level and GSI of diplotype D4 were super diplotypes (p<0.05). These results suggest that the SNPs in Japanese Flounder GnRHR are associated with $E_2$ level and GSI.
Surface Modification of Colloidal Silica Nanoparticles: Controlling the size and Grafting Process
He, Wentao,Wu, Danhua,Li, Juan,Zhang, Kai,Xiang, Yushu,Long, Lijuan,Qin, Shuhao,Yu, Jie,Zhang, Qin Korean Chemical Society 2013 Bulletin of the Korean Chemical Society Vol.34 No.9
Surface modification of colloidal silica nanoparticles without disrupting the electric double layer of nanoparticles is a major challenge. In the work, silane was employed to modify colloidal silica nanoparticles without inducing bridge flocculation obviously. The effect of pH value of the silica sol, the amount of silane in feed, and reaction temperature on the graft amount and the final size of modified particles was investigated. The increased weight loss by TG and the appearance of $T_2$ and $T_3$ except for $Q_2$ and $Q_3$ signals by CP/MAS $^{29}Si$ NMR of the modified samples verified the successful grafting of silane. The graft amount reached 0.57 mmol/g, which was slightly lower than theory value, and the particle size remained nearly the same as unmodified particles for acidic silica sol at the optimum condition. For alkaline silica sol after modification, aggregates composed of several nanoparticles connected together with silane moleculars as the bridge appeared.
Yu Quan,Wei-Jie Guo,Lin He,Zhe-Zhi Jin 영남수학회 2022 East Asian mathematical journal Vol.38 No.1
This paper is based on Yanbian University's physical test data, and uses statistical analysis methods to study the relationship between college students' physical test scores to promote college physical education. Firstly, using gender as categorical variables, we conduct a general analysis of students in different majors and different grades, and obtain the advantages and disadvantages of male and female college students; then we use Decision Trees and Random Forest algorithms to conduct modeling analysis to provide valuable suggestions for relevant departments of the university. the aiming of this research analyzing about the undergraduates physical test is that giving universities the targeted suggestions to improve the college graduate rate and promote the overall development of higher education, lay the foundation for achieving universal health.
Yu, Jie,Zhao, Weiguo,Tong, Wei,He, Qiang,Yoon, Min-Young,Li, Feng-Peng,Choi, Buung,Heo, Eun-Beom,Kim, Kyu-Won,Park, Yong-Jin MDPI 2018 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.19 No.10
<P>Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, <I>OsMADS31</I>, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.</P>
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.
Lack of Association Between CYP1A1 Polymorphisms and Risk of Bladder Cancer: a Meta-analysis
Lu, Yu,Zhang, Xiao-Lian,Xie, Li,Li, Tai-Jie,He, Yu,Peng, Qi-Liu,Deng, Yan,Wang, Jian,Qin, Xue,Li, Shan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.9
Background: The effects of CYP1A1 gene polymorphisms on the risk of bladder cancer (BC) remain controversial. We carried out a meta-analysis to clarify the role of CYP1A1 gene polymorphisms in BC. Material and Methods: A comprehensive literature search was conducted up to November 20, 2013. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to estimate the strength of the association. Meta-regression, subgroup analysis, sensitivity analysis and publication bias were also performed. Results: Eight studies involving 1,059 BC cases and 1,061 controls were included. The meta-analysis showed that there was no significant association between the two common mutations of CYP1A1 and BC risk. For the I1e462Val A/G polymorphism with GG vs. AA the OR was 1.47 (95 % CI= 0.70-3.07, P =0.308). For the MspI T/C polymorphism, though a slight trend was found this was not statistically nonsignificant (CC vs.TT, OR = 1.24, 95 % CI= 0.98-1.58, P =0.078). Subgroup analyses by ethnicity also found no obvious association between CYP1A1 and BC risk. Conclusion: The present meta-analysis suggests that CYP1A1 polymorphism is not associated with bladder cancer risk.