• Title/Summary/Keyword: PLS-DA

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Discrimination model of cultivation area of Corni Fructus using a GC-MS-Based metabolomics approach (GC-MS 기반 대사체학 기법을 이용한 산수유의 산지판별모델)

  • Leem, Jae-Yoon
    • Analytical Science and Technology
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    • v.29 no.1
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    • pp.1-9
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    • 2016
  • It is believed that traditional Korean medicines can be managed more scientifically through the development of logical criteria to verify their region of cultivation, and that this could contribute to the advancement of the traditional herbal medicine industry. This study attempted to determine such criteria for Sansuyu. The volatile compounds were obtained from 20 samples of domestic Corni fructus (Sansuyu) and 45 samples of Chinese Sansuyu by steam distillation. The metabolites were identified in the NIST Mass Spectral Library via the obtained gas chromatography/mass spectrometer (GC/MS) data of 53 training samples. Data binning at 0.2 min intervals was performed to normalize the number of variables used in the statistical analysis. Multivariate statistical analyses, such as principle component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) were performed using the SIMCA-P software package. Significant variables with a variable importance in the projection (VIP) score higher than 1.0 were obtained from OPLS-DA, and variables that resulted in a p-value of less than 0.05 through one-way ANOVA were selected to verify the marker compounds. Finally, among the 11 variables extracted, 1-ethylbutyl-hydroperoxide (9.089 min), nonadecane (20.170 min), butylated hydroxytoluene (25.319 min), 5β,7βH,10α-eudesm-11-en-1α-ol (25.921 min), 7,9-bis(2-methyl-2-propanyl)-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione (34.257 min), and 2-decyldodecyl-benzene (54.717 min) were selected as markers to indicate the origin of Sansuyu. The statistical model developed was suitable for the determination of the geographical origin of Sansuyu. The cultivation areas of four Korean and eight Chinese Sansuyu samples were predicted via the established OPLS-DA model, and it was confirmed that 11 of the 12 samples were accurately classified.

Rapid comparison of metabolic equivalence of standard medicinal parts from medicinal plants and their in vitro-generated adventitious roots using FT-IR spectroscopy (한약자원 품목별 표준시료와 기내 생산 부정근의 FT-IR 스펙트럼 기반 대사체 동등성 신속 비교)

  • Ahn, Myung Suk;Min, Sung Ran;Jie, Eun Yee;So, Eun Jin;Choi, So Yeon;Moon, Byeong Cheol;Kang, Young Min;Park, So-Young;Kim, Suk Weon
    • Journal of Plant Biotechnology
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    • v.42 no.3
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    • pp.257-264
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    • 2015
  • To determine whether metabolite fingerprinting for whole cell extracts based on Fourier transform infrared (FT-IR) spectroscopy can be used to discriminate and compare metabolic equivalence, standard medicinal parts from four medicinal plants (Cynanchum wilfordii Hemsley, Atractylodes japonica Koidz, Polygonum multiflorum Thunberg and Astragalus membranaceus Bunge) and their in vitro-produced adventitious roots were analyzed by FT-IR spectroscopy. The principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) from the FT-IR spectral data showed that the whole metabolic pattern from Cynanchum wilfordii was highly similar to Astragalus membranaceus. However, Atractylodes japonica and Polygonum multiflorum showed significantly different metabolic patterns. Furthermore, adventitious roots from Cynanchum wilfordii and Astragalus membranaceus also showed similar metabolic patterns compared to their standard medicinal parts. These results clearly show that mass proliferation of adventitious roots may be applied to aquire novel supply of standard medicinal parts from medicinal plants. However, the whole metabolic pattern from adventitious roots of Atractylodes japonica and Polygonum multiflorum were not similar to their standard medicinal parts. Furthermore, FT-IR spectroscopy combined with multivariate analyses established in this study may be applied as an alternative tool to discriminate the whole metabolic equivalence from several standard medicinal parts. Thus, we suggest that these metabolic discrimination systems may be applied for metabolic standardization of herbal medicinal resources.

Metabolic comparison between standard medicinal parts and their adventitious roots of Cynanchum wilfordii (Maxim.) Hemsl. using FT-IR spectroscopy after IBA and elicitor treatment (IBA 및 elicitor 처리에 따른 백수오 기내 생산 부정근 및 표준품의 FT-IR 스펙트럼 기반 대사체 비교 분석)

  • Ahn, Myung Suk;So, Eun Jin;Jie, Eun Yee;Choi, So Yeon;Park, Sang Un;Moon, Byeong Cheol;Kang, Young Min;Min, Sung Ran;Kim, Suk Weon
    • Journal of Plant Biotechnology
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    • v.45 no.3
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    • pp.250-256
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    • 2018
  • To determine whether metabolite fingerprinting for whole cell extracts based on Fourier transform infrared spectroscopy (FT-IR) can be used to discriminate and compare metabolic equivalence, standard medicinal parts of Cynanchum wilfordii (Maxim.) Hemsl. and their adventitious roots were subjected to FT-IR. The principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) from FT-IR spectral data showed that whole metabolic pattern from the adventitious root of Cynanchum wilfordii was highly similar to its standard medicinal parts. These results clearly showed that mass proliferation of adventitious roots could be applied for the novel supply of standard medicinal parts of medicinal plants. Furthermore, FT-IR spectroscopy combined with multivariate analysis established in this study could be applied as an alternative tool for discriminating of whole metabolic equivalence from standard medicinal parts. Thus, it is proposed that these metabolic discrimination systems from the adventitious root of Cynanchum wilfordii could be applied for metabolic standardization of in vitro grown Cynanchum wilfordii.

Discrimination of African Yams Containing High Functional Compounds Using FT-IR Fingerprinting Combined by Multivariate Analysis and Quantitative Prediction of Functional Compounds by PLS Regression Modeling (FT-IR 스펙트럼 데이터의 다변량 통계분석을 이용한 고기능성 아프리칸 얌 식별 및 기능성 성분 함량 예측 모델링)

  • Song, Seung Yeob;Jie, Eun Yee;Ahn, Myung Suk;Kim, Dong Jin;Kim, In Jung;Kim, Suk Weon
    • Horticultural Science & Technology
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    • v.32 no.1
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    • pp.105-114
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    • 2014
  • We established a high throughput screening system of African yam tuber lines which contain high contents of total carotenoids, flavonoids, and phenolic compounds using ultraviolet-visible (UV-VIS) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy in combination with multivariate analysis. The total carotenoids contents from 62 African yam tubers varied from 0.01 to $0.91{\mu}g{\cdot}g^{-1}$ dry weight (wt). The total flavonoids and phenolic compounds also varied from 12.9 to $229{\mu}g{\cdot}g^{-1}$ and from 0.29 to $5.2mg{\cdot}g^{-1}$dry wt. FT-IR spectra confirmed typical spectral differences between the frequency regions of 1,700-1,500, 1,500-1,300 and $1,100-950cm^{-1}$, respectively. These spectral regions were reflecting the quantitative and qualitative variations of amide I, II from amino acids and proteins ($1,700-1,500cm^{-1}$), phosphodiester groups from nucleic acid and phospholipid ($1,500-1,300cm^{-1}$) and carbohydrate compounds ($1,100-950cm^{-1}$). Principal component analysis (PCA) and subsequent partial least square-discriminant analysis (PLS-DA) were able to discriminate the 62 African yam tuber lines into three separate clusters corresponding to their taxonomic relationship. The quantitative prediction modeling of total carotenoids, flavonoids, and phenolic compounds from African yam tuber lines were established using partial least square regression algorithm from FT-IR spectra. The regression coefficients ($R^2$) between predicted values and estimated values of total carotenoids, flavonoids and phenolic compounds were 0.83, 0.86, and 0.72, respectively. These results showed that quantitative predictions of total carotenoids, flavonoids, and phenolic compounds were possible from FT-IR spectra of African yam tuber lines with higher accuracy. Therefore we suggested that quantitative prediction system established in this study could be applied as a rapid selection tool for high yielding African yam lines.

Changes in Carotenoid Contents of Colored Pumpkin (Cucurbita spp.) Germplasms (유색 호박 (Cucurbita spp.) 유전자원별 카로테노이드 대사체 분석)

  • Lee, Min-Ki;Cho, Soo-Yeon;Cho, Soo-Jung;Shin, Jae-Hyeong;Kim, Heon-Woong;Kim, Sang-Gyu;Ko, Ho-Cheol;Ro, Na-Young;Kim, Jung-Bong;Baek, Hyung-Jin
    • Korean Journal of Environmental Agriculture
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    • v.34 no.3
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    • pp.186-191
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    • 2015
  • BACKGROUND: Carotenoids which are a major source of vitamin A are contributed to have great potential role in anti-carcinogenic effects and eyesight. Carotenoids which can not synthesize in human body are required for food supply. The objectives of this study are to investigate compositions and contents of pumpkin (Cucurbita spp.) germplasms based on their pulp color. METHODS AND RESULTS: Carotenoids were extracted with 0.2% ascorbic acid in ethanol and saponified with 80% potassium hydroxide. Insoluble compounds were extracted into hexane. A total of nine carotenoids (three xanthophylls and six carotenes) were identified from pumpkin germplasms using HPLC equipped with photodiode array detector (450 nm). Especially, lutein and ${\beta}$-carotenes were major compound in germplasms. Among isomers of ${\beta}$-carotene, all-trans-${\beta}$-carotene (16-27% of total carotenoids) was predominant compositions. The mean of total carotenoid contents was showed as brown (286.1 mg/100 g dw) > dark green (217.0) > orange (153.4) > primrose (85.8) > dark yellow (80.3). On the basis of carotenoid information, PLS-DA score plots showed different patterns by cluster in pumpkin germplasms. It was considered that these differences of phenotype were relative closely to genotype. CONCLUSION: This study indicated that dark color of pumpkin pulp was presented in high-level of biological pigments. It may contribute to develop potentially beneficial functional food ingredients.

$^1H$ NMR-Based Metabolomic Approach for Understanding the Fermentation Behaviors of Wine Yeast Strains

  • Son, Hong-Seok;Hwang, Geum-Sook;Kim, Ki-Myong;Kim, Eun-Young;Berg, Frans van den;Park, Won-Mok;Lee, Cherl-Ho;Hong, Young-Shick
    • Proceedings of the Microbiological Society of Korea Conference
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    • 2009.05a
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    • pp.78-78
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    • 2009
  • $^1H$ NMR spectroscopy coupled with multivariate statistical analysis was used for the first time to investigate metabolic changes in musts during alcoholic fermentation and wines during ageing. Three Saccharomyces cerevisiae yeast strains (RC-212, KIV-1116 and KUBY-501) were also evaluated for their impacts on the metabolic changes in must and wine. Pattern recognition (PR) methods, including PCA, PLS-DA and OPLS-DA scores plots, showed clear differences for metabolites among musts or wines for each fermentation stage up to 6 months. Metabolites responsible for the differentiation were identified to valine, 2,3-butanediol (2,3-BD), pyruvate, succinate, proline, citrate, glycerol, malate, tartarate, glucose, N-methylnicotinic acid (NMNA), and polyphenol compounds. PCA scores plots showed continuous movements away from days 1 to 8 in all musts for all yeast strains, indicating continuous and active fermentation. During alcoholic fermentation, highest levels of 2,3-BD, succinate and glycerol were found in musts with the KIV-1116 strain, which showed the fastest fermentation or highest fermentative activity of the 3 strains, whereas the KUBY-501 strain showed the slowest fermentative activity. This study highlights the applicability of NMR-based metabolomics for monitoring wine fermentation and evaluating the fermentative characteristics of yeast strains.

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Identity of the 155 ATPase with the Eukarvotic Mg"'-Arpase and Its Immunoreactivitv to the 26S protease Complex from Chick Skeletal Muscle (15S ATPase와 진핵세포에 존재하는 Mg2+-ATPase의 동질성 및 계 골격근에서 분리된 26S 단백질 분해효소와의 면역반응에 관한 연구)

  • 심규석;채광수
    • The Korean Journal of Zoology
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    • v.37 no.4
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    • pp.531-537
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    • 1994
  • Partial internal amino acid sequences of the 15S ATPase from chick skeletal muscle were determined and found to be identical to the corresponding regions of the Mg2+_ATPase from Xenopus laevis oocytes, that is a close homolog of N-ethvlmaleimide-sensitive factor (called NSF) in hamster and Sec18p in yeast, both of which are believed to plaN an essential role in vesicle fusion in secretory process. Thus, the 15S Arpase in chick skeletal muscle maw also belong to a protein family of the "vesicle fusion proteins". Unlike the Mg2'-Afpase with an isoelectric point (pl) of 5.5, however, the 15S Arpase was separated into four spots with pls of 4.9,6.4 and 6.9 upon analysis by twoiimensional gel electrophoresis. In addition, the anti-15S ATPase IgG was found to be capable of interacting with the 265 protease complex upon analysis by immunoprecipitation. Moreover, immunoblot analysis revealed that the anti-155 Arpase IgG recognizes three subunits, ko of which show the same mobilities as the 510-kDa subunit 4 and 48-kDa subunit 7 of the 26S protease complex that are known to contain a highly consented ATP-binding motif. These results surest that a common antigenic site, likely the consensus nucleotide-binding site, exists in the 15S ATPase and the 26S pretense complex and hence both the enzymes maw also be related ATPases.d ATPases.

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Classficiation of Bupleuri Radix according to Geographical Origins using Near Infrared Spectroscopy (NIRS) Combined with Supervised Pattern Recognition

  • Lee, Dong Young;Kang, Kyo Bin;Kim, Jina;Kim, Hyo Jin;Sung, Sang Hyun
    • Natural Product Sciences
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    • v.24 no.3
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    • pp.164-170
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    • 2018
  • Rapid geographical classification of Bupleuri Radix is important in quality control. In this study, near infrared spectroscopy (NIRS) combined with supervised pattern recognition was attempted to classify Bupleuri Radix according to geographical origins. Three supervised pattern recognitions methods, partial least square discriminant analysis (PLS-DA), quadratic discriminant analysis (QDA) and radial basis function support vector machine (RBF-SVM), were performed to establish the classification models. The QDA and RBF-SVM models were performed based on principal component analysis (PCA). The number of principal components (PCs) was optimized by cross-validation in the model. The results showed that the performance of the QDA model is the optimum among the three models. The optimized QDA model was obtained when 7 PCs were used; the classification rates of the QDA model in the training and test sets are 97.8% and 95.2% respectively. The overall results showed that NIRS combined with supervised pattern recognition could be applied to classify Bupleuri Radix according to geographical origin.

The Interactive Effect of Level of Education and Environmental Concern toward Organic Food in Vietnam

  • HOANG, Hung Cuong;CHOVANCOVA, Miloslava;HOANG, Thi Que Huong
    • Journal of Distribution Science
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    • v.18 no.9
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    • pp.19-30
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    • 2020
  • Purpose: As an environmental concern increases, customers pay more attention to purchase organic food. While customers' purchase intention of organic food has been widely studied, there are lacks of researches regarding the moderation effect of environmental concern and the interactive effect of level of education based on the Theory of Planned Behavior (TPB). This study examines the influence of level of education and environmental concern on purchase intention based on the Theory of Planned Behavior and organic food in Vietnam. Research design, data and methodology: The methodology of mixed methods of qualitative and quantitative is applied with a survey of 420 customers being conducted to collect data from three biggest cities in Vietnam: Ho Chi Minh, DaNang and Hanoi. SPSS 23 and SMART-PLS 3.2 are used for data analysis. Results: The result shows that the customers have more environmental concern which increases their attitude to the intention of purchasing organic food. Moreover, there has not the three-way interactive effect of level of education, environmental concern and attitude on purchase intention toward organic food. Conclusions: This enriches the existing literature with the moderation of environmental concern to the relationship between attitude and purchase intention toward organic food in Vietnam based on the Theory of Planned Behavior.

A Study on the Privacy Concern of e-commerce Users: Focused on Information Boundary Theory (전자상거래 이용자의 프라이버시 염려에 관한 연구 : 정보경계이론을 중심으로)

  • Kim, Jong-Ki;Oh, Da-Woon
    • The Journal of Information Systems
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    • v.26 no.2
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    • pp.43-62
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    • 2017
  • Purpose This study provided empirical support for the model that explain the formation of privacy concerns in the perspective of Information Boundary Theory. This study investigated an integrated model suggesting that privacy concerns are formed by the individual's disposition to value privacy, privacy awareness, awareness of privacy policy, and government legislation. The Information Boundary Theory suggests that the boundaries of information space dependends on the individual's personal characteristics and environmental factors of e-commerce. When receiving a request for personal information from e-commerce websites, an individual assesses the risk depending on the risk-control assessment, the perception of intrusion give rise to privacy concerns. Design/methodology/approach This study empirically tested the hypotheses with the data collected in a survey that included the items measuring the constructs in the model. The survey was aimed at university students. and a causal modeling statistical technique(PLS) is used for data analysis in this research. Findings The results of the survey indicated significant relationships among environmental factors of e-commerce websites, individual's personal privacy characteristics and privacy concerns. Both individual's awareness of institutional privacy assurance on e-commerce and the privacy characteristics affect the risk-control assessment towards information disclosure, which becomes an essential components of privacy concerns.