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Identification of functional SNPs in genes and their effects on plant phenotypes
Md. Amdadul Huq,AKTER SHAHINA,노일섭,김회택,정유진,강권규 한국식물생명공학회 2016 JOURNAL OF PLANT BIOTECHNOLOGY Vol.43 No.1
Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.
Identification of functional SNPs in genes and their effects on plant phenotypes
Huq, Md. Amdadul,Akter, Shahina,Nou, Ill Sup,Kim, Hoy Taek,Jung, Yu Jin,Kang, Kwon Kyoo The Korean Society of Plant Biotechnology 2016 식물생명공학회지 Vol.43 No.1
Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.
Fayeza Md Siraj,Sathishkumar Natarajan,Md Amdadul Huq,Yeon Ju Kim,Deok Chun Yang 고려인삼학회 2015 Journal of Ginseng Research Vol.39 No.2
Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor PPARγ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with PPARγ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between PPARγ and Rf, at the same active site. To determine the druglike and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and PPARγ, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of PPARγ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.
Fayeza Md Siraj,Sathishkumar Natarajan,Md Amdadul Huq,Yeon Ju Kim,양덕춘 고려인삼학회 2015 Journal of Ginseng Research Vol.39 No.2
Background: Adipocytes, which are the main cellular component of adipose tissue, are the buildingblocks of obesity. The nuclear hormone receptor PPARg is a major regulator of adipocyte differentiationand development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fastbecoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that isonly present in Panax ginseng Meyer, interacts with PPARg by molecular docking simulations. After weperformed the docking simulation the result has been analyzed with several different software programs,including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified thesame mechanism of interaction between PPARg and Rf, at the same active site. To determine the druglikeand biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, andtoxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the resultsobtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf andPPARg, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levelsof PPARg and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesitytreatments
Siraj, Fayeza Md,Natarajan, Sathishkumar,Huq, Md Amdadul,Kim, Yeon Ju,Yang, Deok Chun The Korean Society of Ginseng 2015 Journal of Ginseng Research Vol.39 No.2
Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor $PPAR{\gamma}$ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with $PPAR{\gamma}$ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between $PPAR{\gamma}$ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and $PPAR{\gamma}$, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of $PPAR{\gamma}$ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.