A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice ( <i>Oryza sativa</i> ) at the Germination Stage

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>

Somatic Embryogenesis and Plant Regeneration from Embryogenic cell Suspension Cultures of Schisandra chinensis Baill

Li, Cheng Hao,Niu, YudA,Zhao, Bo,Ghimire, Bimal Kumar,Kil, Hyun-Young,Heo, Kwon,Kim, Myong-Jo,Eom, Seok-Hyun,Cho, Dong-Ha,Yu, Chang-Yeon The Korean Society of Medicinal Crop Science 2007 韓國藥用作物學會誌 Vol.15 No.5

An efficient somatic embryogenesis and plant regeneration protocol was developed for Schisandra chinensis Baill, using embryogenic cell suspensions and optimized media conditions. Friable embryogenic callus was induced from cotyledonary leaf and hypocotyl explants of 7 days old seedlings on MS agar medium supplemented with 1.0 to $4.0\;mg\;l^{-1}$ of 2,4-dichlorophenoxyacetic acid (2,4-D). Fast growing and well dispersed embryogenic cell suspensions were developed within two months when embryogenic calli were transferred to MS liquid medium containing $1.0\;mg\;l^{-1}\;2,4-D$. One third strength of MS medium was the best for both overall growth and development of somatic embryos in liquid culture. Over 3400 viable somatic embryos were produced from each 150 ml flask with an initial cell density of 30 mg in 30 ml medium. Germinated somatic embryos developed in liquid medium converted into plantlets after transferred to half-strength MS semi-solid medium. Approximately 90% of the converted plantlets were successfully transplanted to soil and grew into fertile plants.

인슐린 비의존형 당뇨병 환자의 체지방 분포와 인슐린 저항성과의 상관성

허갑범 ( Heo Gab Beom ),김유리 ( Kim Yu Li ),안광진 ( An Gwang Jin ),정윤석 ( Jeong Yun Seog ),이은직 ( Lee Eun Jig ),임승길 ( Im Seung Gil ),김경래 ( Kim Gyeong Lae ),이현철 ( Lee Hyeon Cheol ),백인경 ( Baeg In Gyeong ),최미숙 ( 대한내과학회 1993 대한내과학회지 Vol.44 No.1

연구배경 : 인슐린 비의존형 당뇨병은 고혈압, 관상동맥질환, 그리고 고지혈증과 흔히 동반되는데, 이들 질환의 특징은 말초조직에서 인슐린 자극에 의한 포도당의 이용율이 저하되는 인슐린 저항성이 공통분모로서 이들 질환의 발병에 중용한 역할을 한다고 알려져 있다. 본 연구에서는 서구인과 비교할 때 비만증의 정도가 경하고 식사 습관상 지방의 섭취량이 적은 한국인 인슐린 비의존형 당뇨병 환자들에서 인슐린 저항성의 특징과 체지방 분포 양상과의 상관성을 살펴보았다. 방법 : 인슐린 비의존형 당뇨병의 병력이 5년 미만이며 공복혈당이 150mg/dl 이하인 경중의 고혈당을 보이고 당뇨병의 합병증이 없는 환자로서 정상 체중군 6예와 과다 체중근 12예중 중심성 비만군 6예와 말초성 비만군 6예를 대상으로 식사 조사, 신체 계측, Futrex-5000에 의한 체지방량 측정, 복부와 대퇴 컴퓨터 단층 촬영, 경구 당부하 검사, 혈청 지질 측정, euglycemic hyperin-sulinemic glucose clamp study로 포도당 이용율을 측정하였다. 결과 : 1) 중심성 비만군과 말초성 비만군의 평균 체중은 차이가 없었고 waist/hip ratio와 체지방량은 중심성 비만군이 말초성 비만군에 비해 유의하게 높았다. 2) 컴퓨터 단층 촬영으로 측정한 내장 지방 면적은 비만군이 말초성 비만군에 비해 유의하게 넓었고 피하 지방 면적은 양군간에는 유의한 차이가 없었다. 3) 경구 당부하 검사상 혈당 반응에는 세 군간에 차이가 없었고 경구 당부하후 120분의 혈장 C-peptide와 인슐린 농도는 중심성 비만군에서 말초성 비만군에 비해 유의하게 높았다. 4) 포도당 이용율은 중심성 비만군과 말초성 비만군이 정상 체중군에 비해 유의헥 낮았으며 중심성 비만군이 말초성 비만군보다 유의하게 낮았다. 5) 포도당 이용율과 신체 계측치와의 상관성을 보면 전체 환자에서는 waist/hip ratio가 가장 높은 음의 상관 관계를 보였고, 과다 체중군에서는 waist/thigh ratio가 가장 높은 음의 상관 관계를 보였다. 6) 중심성 비만증이 심할수록 고인슐린혈중과 높은 혈중 유리지방산 농도를 보이고 이들에서 포도당 이용율이 낮아 인슐린 저항성은 증가하였다. 결론 : 이상의 결과로 한국인 인슐린 비의존형 당뇨병환자의 인슐린 저항성을 결정하는데는 신장에 대한 체중이나 체지방량 자체보다는 체지방의 분포 양상이 중요한 역할을 하며, 특히 과다 체중환자에서는 적절한 식사와 운동에 의하여 신체의 체형을 변화시키는 것이 당질 및 지질 대사 장애를 개선함에 매우 중요할 것으로 생각한다. Background : The role of insulin resistance is known to be very important in the pathogenesis and clinical courses of human diseases such as diabetes mellitus, hypertension, atherosclerotic coronary vascular disease, and dyslipoproteinemia. Methods : To investigate the correlation between insulin resistance and the pattern of body fat distribution in Korean patients with non-insulin dependent diabetes mellitus (NIDDM), dietary survey, anthropometry, CT scan, measurement of body fat by body composition analyzer, oral glucose tolerance test and measurement of glucose uptake rate by euglycemic hyperinsulinemic glucose clamp technique were performed in 6 normal weight patients and 12 overweight-obese NIDDM patients. Six of 12 overweight-obese patients are centrally obese with waist to hip circumference ratio : WHR?1 and 6 cases are peripherally obese with WHR<1. Results : 1) There was no difference between the mean body weigh of centrally obese patients and peripherally obese patients but WHR and body fat content of centrally obese patients were significantly higher than those of peripherally obese patients. 2) In the centrally obese patients visceral fat area measured by CT scan was significantly wider than in the peripherally obese patients but subcutaneous fat area was not different between the two groups. 3) Plasma glucose levels on oral glucose tolerance tests were not different among the three groups but plasma C-peptide and insulin levels at 2 hour after glucose load were significantly higher in centrally obese patients than in peripherally obese patients. 4) Glucose uptake rate (M/I ratio) of centrally obese patients was significantly lower than that of peripherally obese patients. 5) The WHR showed the highest negative correlation with M/I ratio in the all patients and waist thigh circumference ratio (WTR) showed the highest negative correlation with M/I ratio in overweight-obese patients. 6) Insulin area and fasting level of free fatty acid showed significant positive correlation with WHR and significant negative correlation with M/I ratio. Conclusion : It could be concluded that the pattern of body fat distribution rather than the relative body weight for height or body fat content has a greater role in determining the degree of insulin resistance in Korean patients with NIDDM. And further a change of the body configuration through adequate diet and exercise is highly recommended for overweight-obese NIDDM patients.

Somatic Embryogenesis and Plant Regeneration from Embryogenic cell Suspension Cultures of Schisandra chinensis Baill

Cheng Hao Li,YudA Niu,Bo Zhao,Bimal Kumar Ghimire,Hyun-Young Kil,Kwon Heo,Myong-Jo Kim,Seok-Hyun Eom,Dong-Ha Cho,Chang-Yeon Yu 한국약용작물학회 2007 한국약용작물학회지 Vol.15 No.5

An efficient somatic embryogenesis and plant regeneration protocol was developed for Schisandra chinensis Baill, using embryogenic cell suspensions and optimized media conditions. Friable embryogenic callus was induced from cotyledonary leaf and hypocotyl explants of 7 days old seedlings on MS agar medium supplemented with 1.0 to 4.0 mg l-1 of 2,4-dichlorophenoxyacetic acid (2,4-D). Fast growing and well dispersed embryogenic cell suspensions were developed within two months when embryogenic calli were transferred to MS liquid medium containing 1.0 mg l-1 2,4-D. One third strength of MS medium was the best for both overall growth and development of somatic embryos in liquid culture. Over 3400 viable somatic embryos were produced from each 150 ml flask with an initial cell density of 30 mg in 30 ml medium. Germinated somatic embryos developed in liquid medium converted into plantlets after transferred to half-strength MS semi-solid medium. Approximately 90% of the converted plantlets were successfully transplanted to soil and grew into fertile plants.

Molecular Cloning, Purification, and Characterization of a Cold-Adapted Esterase from Photobacterium sp. MA1-3

Kim, Young-Ok,Heo, Yu Li,Nam, Bo-Hye,Kim, Dong-Gyun,Jee, Young-Ju,Lee, Sang-Jun,An, Cheul-Min The Korean Society of Fisheries and Aquatic Scienc 2013 Fisheries and Aquatic Sciences Vol.16 No.4

The gene encoding an esterase from Photobacterium sp. MA1-3 was cloned in Escherichia coli using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (948 bp) corresponded to a protein of 315 amino acid residues with a molecular weight of 35 kDa and a pI of 6.06. The deduced protein showed 74% and 68% amino acid sequence identities with the putative esterases from Photobacterium profundum SS9 and Photobacterium damselae, respectively. Absence of a signal peptide indicated that it was a cell-bound protein. Sequence analysis showed that the protein contained the signature G-X-S-X-G included in most serine-esterases and lipases. The MA1-3 esterase was produced in both soluble and insoluble forms when E. coli cells harboring the gene were cultured at $18^{\circ}C$. The enzyme was a serine-esterase and was active against $C_2$, $C_4$, $C_8$ and $C_{10}$ p-nitrophenyl esters. The optimum pH and temperature for enzyme activity were pH 8.0 and $30^{\circ}C$, respectively. Relative activity remained up to 45% even at $5^{\circ}C$ with an activation energy of 7.69 kcal/mol, which indicated that it was a cold-adapted enzyme. Enzyme activity was inhibited by $Cd^{2+}$, $Cu^{2+}$, $Zn^{2+}$, and $Hg^{2+}$ ions.

Original Articles : Molecular Cloning, Purification, and Characterization of a Cold-Adapted Esterase from Photobacterium sp. MA1-3

( Young Ok Kim ),( Yu Li Heo ),( Bo Hye Nam ),( Dong Gyun Kim ),( Young Ju Jee ),( Sang Jun Lee ),( Cheul Min An ) 한국수산과학회(구 한국수산학회) 2013 Fisheries and Aquatic Sciences Vol.16 No.4

The gene encoding an esterase from Photobacterium sp. MA1-3 was cloned in Escherichia coli using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (948 bp) corresponded to a protein of 315 amino acid residues with a molecular weight of 35 kDa and a pI of 6.06. The deduced protein showed 74% and 68% amino acid sequence identities with the putative esterases from Photobacterium profundum SS9 and Photobacterium damselae, respectively. Absence of a signal peptide indicated that it was a cell-bound protein. Sequence analysis showed that the protein contained the signature G-X-S-X-G included in most serine-esterases and lipases. The MA1-3 esterase was produced in both soluble and insoluble forms when E. coli cells harboring the gene were cultured at 18°C. The enzyme was a serine-esterase and was active against C2, C4, C8 and C10 p-nitrophenyl esters. The optimum pH and temperature for enzyme activity were pH 8.0 and 30°C, respectively. Relative activity remained up to 45% even at 5°C with an activation energy of 7.69 kcal/mol, which indicated that it was a cold-adapted enzyme. Enzyme activity was inhibited by Cd2+, Cu2+, Zn2+, and Hg2+ ions.

Gene Cloning and Characterization of a Cold-Adapted Esterase from Acinetobacter venetianus V28

( Kim Young Ok ),( Yu Li Heo ),( Hyung Kwoun Kim ),( Bo Hye Nam ),( Hee Jeong Kong ),( Dong Gyun Kim ),( Woo Jin Kim ),( Bong Seok Kim ),( Young Ju Jee ),( Sang Jun Lee ) 한국미생물 · 생명공학회 2012 Journal of microbiology and biotechnology Vol.22 No.9

Acinetobacter venetians V28 was isolated from the intestine of righteye flounder, Poecilopsetta plinthus caught in Vietnam seawater, and the esterase gene was cloned using a shotgun method, The amino acid sequence deduced from the nucleotide sequence (1,017bp) corresponded to a protein of 338 amino acid residues with a molecular weight of 37,186. The esterase had 87% and 72% identities with the lipases of A. junii SH205 and A. calcoaceticus RUH2202, respectively. The esterase contained a putative leader sequence, as well as the conserved catalytic triad (Ser, His, Asp), consensus pentapeptide GXSXG, and oxyanion hole sequence (HG). The protein from the strain V28 was produced in both a soluble and an insoluble form when the Escherichia coli cells harboring the gene were cultured at 18oC. The maximal activity of the purified enzyme was observed at a temperature of 40oC and pH 9.0 using p-NP-caprylate as substrate; however, relative activity still reached to 70% even at 5oC with an activation energy of 3.36 kcal/mol, which indicated that it was a cold-adapted enzyme. The enzyme was a nonmetalloprotein and was active against p-nitrophenyl esters of C4, C8, and C14. Remarkably, this enzyme retained much of its activity in the presence of commercial detergents and organic solvents. This cold-adapted esterase will be applicable as catalysts for reaction in the presence of organic solvents and detergents.

Magnetic Properties and Magnetocaloric Effects on Ni-Fe-Sb Semi-Heusler Alloy

Ying De Zhang,Chul-Min Heo,Seong-Gi Min,Ying Li,Xueling Hou,Seong-Cho Yu,Kyu-Won Lee 한국자기학회 2008 한국자기학회 학술연구발표회 논문개요집 Vol.- No.-

Giant Magnetocaloric Effects on MnFeSb<SUB>1-x</SUB>Sn<SUB>x</SUB> (x=0.8, 0.9, 1.0) Compounds

Ying De Zhang,Chul-Min Heo,Seong-Gi Min,Xueling Hou,Ying Li,Seong-Cho Yu,Kyu- Won Lee 한국자기학회 2008 한국자기학회 학술연구발표회 논문개요집 Vol.- No.-

Magnetic Properties and Giant Magnetocaloric Effects on Gd-Ge-Si Alloy by Substitution of Sn

Seong-Gi Min,Ying De Zhang,Chul-Min Heo,Xueling Hou,Ying Li,Seong-Cho Yu,Kyu- Won Lee 한국자기학회 2008 한국자기학회 학술연구발표회 논문개요집 Vol.- No.-