PeerJ
| Autor: | Ryan S. Senger, Imen Tanniche, Eva Collakova, Cynthia J. Denbow |
|---|---|
| Přispěvatelé: | Biological Systems Engineering, Chemical Engineering, School of Plant and Environmental Sciences |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Analytical chemistry
Principal component analysis lcsh:Medicine Plant Science Cyanobacteria Rametrix™ Microbiology General Biochemistry Genetics and Molecular Biology Chemometrics 03 medical and health sciences symbols.namesake 030304 developmental biology Microbial phenotyping chemistry.chemical_classification 0303 health sciences biology 030306 microbiology General Neuroscience Biomolecule Synechocystis Data Science lcsh:R Fatty acid Computational Biology General Medicine biology.organism_classification Phenotype Discriminant analysis Amino acid chemistry Raman spectroscopy symbols Rametrix (TM) General Agricultural and Biological Sciences Biotechnology |
| Zdroj: | PeerJ, Vol 8, p e8535 (2020) PeerJ |
| ISSN: | 2167-8359 |
| Popis: | BackgroundDuring their long evolution,Synechocystissp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (RametrixTM) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods.MethodsSynechocystiscells were grown in the presence of (i) acetate (7.5–30 mM), (ii) NaCl (50–150 mM) and (iii) limiting levels of MgSO4(0–62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the RametrixTMLITE Toolbox for MATLABⓇ. Next, validation of these models was realized via RametrixTMPRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules.ResultsDistinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, RametrixTMPRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands. |
| Databáze: | OpenAIRE |
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