Chemometric Feature Selection and Classification of <i>Ganoderma lucidum</i> Spores and Fruiting Body Using ATR-FTIR Spectroscopy — Oak Academic Publishing
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Chemometric Feature Selection and Classification of <i>Ganoderma lucidum</i> Spores and Fruiting Body Using ATR-FTIR Spectroscopy
Mathematics and Mathematics Education, National Institute of Education, Nanyang Technological University, Singapore
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Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore
1 Mathematics and Mathematics Education, National Institute of Education, Nanyang Technological University, Singapore
2 Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore
Ganoderma lucidum ( G. lucidum ) spores as a valuable Chinese herbal medicine have vast marketable prospect for its bioactivities and medicinal efficacy. This study aims at the development of an effective and simple analytical method to distinguish G. lucidum spores from its fruiting body, which is of essential importance for the quality control and fast discrimination of raw materials of Chinese herbal medicine. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy combined with the appropriate chemometric methods including penalized discriminant analysis, principal component discriminant analysis and partial least squares discriminant analysis has been proven to be a rapid and powerful tool for discrimination of G. lucidum spores and its fruiting body with classification accuracy of 99%. The model leads to a well-performed selection of informative spectral absorption bands which improve the classification accuracy, reduce the model complexity and enhance the quantitative interpretations of the chemical constituents of G. lucidum spores regarding its anticancer effects.
KeywordsFeature SelectionAttenuated Total Reflection Fourier Transform Infrared SpectroscopyPenalized Linear Discriminant AnalysisPrincipal Component Discriminant AnalysisPartial Least Squares Discriminant Analysis
Liu, X., Yuan, J.P. and Chen, X.J. (2002) Antitumor Activity of the Sporederm-Broken Germinating Spores of Ganodermalucidum. Cancer Letters, 182, 155-161. http://dx.doi.org/10.1016/S0304-3835(02)00080-0
Lin, Z.B. and Wang, P.Y. (2006) The Pharmacological Study of Ganoderma Spores. Journal of Peking University Health Science, 38, 541-547.
Chew, O.S., Hamdan, M.R., Ismail, Z. and Ahmad, M.N. (2004) Assessment of Herbal Medicines by Chemometrics-Assisted Interpretation of FTIR Spectra. Analytica Chimica Acta, 570, 116-123.
Lai, Y.H., Ni, Y.N. and Kokot, S. (2010) Classification of Raw and Roasted Semen Cassiae Samples with the Use of Fourier Transform Infrared Fingerprints and Least Squares Support Vector Machines. Applied Spectroscopy, 64, 649-656. http://dx.doi.org/10.1366/000370210791414362
Stuart, B. (1997) Biological Applications of Infrared Spectroscopy. Analytical Chemistry of Open Learning (115). John Wiley & Sons, Chichester.
Dritsa, V. (2012) FT-IR Spectroscopy in Medicine. Infrared Spectroscopy-Life and Biomedical Science, 272-288. http://dx.doi.org/10.5772/37049
Yap, K.Y.L., Chan, S.Y. and Lim, C.S. (2007) Authentication of Traditional Chinese Medicine Using Infrared Spectroscopy: Distinguishing between Ginseng and Its Morphological Fakes. Journal of Biomedical Science, 14, 265-273. http://dx.doi.org/10.1007/s11373-006-9133-3
Woo, Y.A., Kim, H.J. and Cho, J. (1999) Identification of Herbal Medicines Using Pattern Recognition Techniques with Near-Infrared Reflectance Spectra. Microchemical Journal, 63, 61-70. http://dx.doi.org/10.1006/mchj.1999.1768
Savitzky, A. and Golay, M.J.E. (1964) Smoothing and Differentiation of Data by Simplified Least-Squares Procedures. Analytical Chemistry, 36, 1627-1639. http://dx.doi.org/10.1021/ac60214a047
Barnes, R.J., Dhanoa, M.S. and Lister, S.J. (1989) Standard Normal Variate Transformation and De-Trending of Near-Infrared Diffuse Reflectance Spectra. Applied Spectroscopy, 43, 772-777. http://dx.doi.org/10.1366/0003702894202201
Davies, A.M.C. and Fearn, T. (2005) Back to Basics: The Principles of Principal Component Analysis. Spectroscopy Europe, Tony Davies Column, 16, 20-23.
Næs, T., Isaksson, T., Fearn, T. and Davies, T. (2002) A User-Friendly Guide to Multivariate Calibration and Classification. NIR Publications, Chichester.
Barker, M. and Rayens, W. (2003) Partial Least Squares for Discrimination. Journal of Chemometrics, 17, 166-173. http://dx.doi.org/10.1002/cem.785
Zhu, Y., Fearn, T., Samuel, D., Dhar, A., Hameed, O., Bown, S.G. and Lovat, L.B. (2008) Error Removal by Orthogonal Subtraction (EROS): A Customised Pre-Treatment for Spectroscopic Data. Journal of Chemometrics, 22, 130-134. http://dx.doi.org/10.1002/cem.1117
Roger, J.M., Palagos, B., Guillaume, S. and Bellon-Maurel, V. (2005) Discriminating from Highly Multivariate Data by Focal Eigen Function Discriminant Analysis; Application to NIR Spectra. Chemometrics and Intelligent Laboratory Systems, 79, 31-41. http://dx.doi.org/10.1016/j.chemolab.2005.03.006
Zhu, Y. and Tan, T.L. (2015) Discrimination of Wild-Grown and Cultivated Ganoderma lucidum by Fourier Transform Infrared Spectroscopy and Chemometric Methods. American Journal of Analytical Chemistry, 6, 480-491. http://dx.doi.org/10.4236/ajac.2015.65047
Lelong, C.C.D., Roger, J.M., Brégand, S., Dubertret, F., Lanore, M., Sitorus, N.A., Raharjo, D.A. and Caliman, J.P. (2010) Evaluation of Oil-Palm Fungal Disease Infestation with Canopy Hyperspectral Reflectance Data. Sensors, 10, 734-747. http://dx.doi.org/10.3390/s100100734
Hastie, T., Buja, A. and Tibshirani, R. (1995) Penalized Discriminant Analysis. The Annals of Statistics, 23, 73-102. http://dx.doi.org/10.1214/aos/1176324456
Hastie, T., Tibshirani, R. and Friedman, J. (2009) The Elements of Statistical Learning: Data Mining, Inference and Prediction. Springer, New York. http://dx.doi.org/10.1007/978-0-387-84858-7
Witten, D.M. and Tibshirani, R. (2011) Penalized Classification Using Fisher’s Linear Discriminant. Journal of the Royal Statistical Society: Series B, 73, 753-772. http://dx.doi.org/10.1111/j.1467-9868.2011.00783.x
Dudoit, S., Fridlyand, J. and Speed, T. (2001) Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. The Journal of the American Statistical Association, 96, 1115-1160.
R Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
Wang, Y.L. (2012) Application of Fourier Transform Infrared Microspectroscopy (FTIR) and Thermogravimetric Analysis (TGA) for Quick Identification of Chinese Herb Solanum lyratum. Plant Omics Journal, 5, 508-513.
Jin, W.Y., Wan, C.Y. and Cheng, C.G. (2015) Study on the Identification of Radix Bupleuri from Its Unofficial Varieties Based on Discrete Wavelet Transformation Feature Extraction of ATR-FTIR Spectroscopy Combined with Probability Neural Network. International Journal of Analytical Chemistry, 2015, Article ID: 950209.
Chen, X.L., Liu, X.C., Sheng, D.P., Huang, D.K., Li, W.Z. and Wang, X. (2012) Distinction of Broken Cellular Wall Ganoderma lucidum Spores and G. lucidum Spores Using FTIR Microspectroscopy. Spectrochimica Acta Part A, 97, 667-672. http://dx.doi.org/10.1016/j.saa.2012.07.046
Gorgulu, S.T., Dogan, M. and Severcan, F. (2007) The Characterization and Differentiation of Higher Plants by Fourier Transform Infrared Spectroscopy. Applied Spectroscopy, 61, 300-308. http://dx.doi.org/10.1366/000370207780220903
Wang, X., Chen, X.L., Qi, Z.M., Liu, X.C., Li, W.Z. and Wang, S.Y. (2012) A Study of Ganoderma lucidum Spores by FTIR Microspectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 91, 285-289. http://dx.doi.org/10.1016/j.saa.2012.02.004
Russell, R. and Paterson, M. (2006) Ganoderma—A Therapeutic Fungal Biofactory. Phytochemistry, 67, 1985-2001. http://dx.doi.org/10.1016/j.phytochem.2006.07.004
Yue, G.L., Fung, K.P., Leung, P.C. and Lau, B.S. (2008) Comparative Studies on the Immunomodulatory and Antitumor Activities of the Different Parts of Fruiting Body of Ganoderma lucidum and Ganoderma spores. Phytotherapy Research, 2, 1282-1291. http://dx.doi.org/10.1002/ptr.2478