Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy

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dc.contributor.authorTanniche, Imenen
dc.contributor.authorCollakova, Evaen
dc.contributor.authorDenbow, Cynthia J.en
dc.contributor.authorSenger, Ryan S.en
dc.contributor.departmentBiological Systems Engineeringen
dc.contributor.departmentChemical Engineeringen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2020-05-06T12:35:01Zen
dc.date.available2020-05-06T12:35:01Zen
dc.date.issued2020-03-30en
dc.description.abstractBackground. During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (Rametrix (TM)) 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. Methods. Synechocystis cells 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 Rametrix (TM) LITE Toolbox for MATLABR (R). Next, validation of these models was realized via Rametrix (TM) PRO 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. Results. Distinguishable 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, Rametrix (TM) PRO 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.en
dc.description.notesThis research was funded by the National Science Foundation award NSF1243988. Eva Collakova and Ryan Senger are also supported by HATCH funds. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.description.sponsorshipNational Science FoundationNational Science Foundation (NSF) [NSF1243988]; HATCH fundsen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.7717/peerj.8535en
dc.identifier.issn2167-8359en
dc.identifier.othere8535en
dc.identifier.pmid32266110en
dc.identifier.urihttp://hdl.handle.net/10919/97984en
dc.identifier.volume8en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectRaman spectroscopyen
dc.subjectCyanobacteriaen
dc.subjectSynechocystisen
dc.subjectMicrobial phenotypingen
dc.subjectRametrix (TM)en
dc.subjectPrincipal component analysisen
dc.subjectDiscriminant analysisen
dc.titleCharacterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopyen
dc.title.serialPeerJen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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