Mustafa Kansiz - Academia.edu (original) (raw)
Papers by Mustafa Kansiz
Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS... more Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells.
Phytochemistry, 1999
Fourier Transform Infrared (FTIR) microspectroscopy, in combination with chemometrics, was invest... more Fourier Transform Infrared (FTIR) microspectroscopy, in combination with chemometrics, was investigated as a novel method to discriminate between cyanobacterial strains. In total, 810 absorbance spectra were recorded from one eukaryotic and ®ve cyanobacterial taxa spanning three genera and including two strains of one species, Microcystis aeruginosa. Principal Component Analysis (PCA) based classi®cation techniques such as Soft Independent Modelling of Class Analogy (SIMCA) and K-Nearest Neighbours (KNN) were investigated. Dierent spectral regions using derivative spectra were investigated to ®nd the best combinations for classi®cation. The highest rate of correct classi®cations (99±100%) was achieved using ®rst derivative spectra with a spectral region of 1800±950 cm À1 for both the SIMCA and KNN. A dendrogram constructed using averaged spectra of the six taxa studied showed that the two strains of Microcystis aeruginosa exhibited the highest degree of similarity, while the eukaryotic taxon was the most dissimilar from the prokaryotic taxa. #
Analytica Chimica Acta, 2001
Fourier transform infrared (FTIR) spectroscopy, coupled to sequential injection analysis (SIA) wa... more Fourier transform infrared (FTIR) spectroscopy, coupled to sequential injection analysis (SIA) was employed for the on-line monitoring of an acetone-butanol fermentation by simultaneously determining acetone, acetate, n-butanol, butyrate and glucose from the mid-IR spectra of the samples. The analysis system (SIA-FTIR) developed was completely computer controlled, requiring only minute amounts of NaOH and Na 2 CO 3 as reagents and was capable of performing 30 analyte determinations per hour. From a batch fermentation run of 55 h duration, samples were automatically drawn and analysed at 14 different points of time. The analysis by SIA-FTIR comprised of triplicate injections, from each of which two spectra one with 4 cm −1 the other with 8 cm −1 spectral resolution were obtained. In addition, triplicate reference analysis by gas chromatography and enzymatic test kits were also done at corresponding points of time. Based on the data of the reference analysis a partial least squares (PLS) model was established and validated by a leave-one-out cross validation. Best results were obtained using the second derivatised spectra collected at 8 cm −1 resolution. The regression coefficients and standard errors of prediction (S.E.P.) were as follows: acetone, r = 0.999, S.E.P. = 0.077 g/l; acetate, r = 0.998, S.E.P. = 0.063 g/l; butyrate, r = 0.955 and S.E.P. = 0.058 g/l; n-butanol, r = 0.999, S.E.P. = 0.301 g/l and glucose, r = 0.999, S.E.P. = 0.493 g/l. The high quality of the results obtained, and the observation that the precision of the SIA-FTIR analysis was as good and often better than those of the reference methods, showed that SIA-FTIR is a powerful tool for rapid on-line bioprocess monitoring.
Biopolymers, 2008
The secondary structures of proteins (α-helical, β-sheet, β-turn, and random coil) in the solid s... more The secondary structures of proteins (α-helical, β-sheet, β-turn, and random coil) in the solid state and when bound to polymer beads, containing immobilized phenyl and butyl ligands such as those as commonly employed in hydrophobic interaction chromatography, have been investigated using FTIR-ATR spectroscopy and partial least squares (PLS) methods. Proteins with known structural features were used as models, including 12 proteins in the solid state and 7 proteins adsorbed onto the hydrophobic surfaces. A strong PLS correlation was achieved between predictions derived from the experimental data for 4 proteins adsorbed onto the phenyl-modified beads and reference data obtained from the X-ray crystallographic structures with r2 values of 0.9974, 0.9864, 0.9924, and 0.9743 for α-helical, β-sheet, β-turn, and random coiled structures, respectively. On the other hand, proteins adsorbed onto the butyl sorbent underwent greater secondary structural changes compared to the phenyl sorbent as evidenced from the poorer PLS r2 values (r2 are 0.9658, 0.9106, 0.9571, and 0.9340). The results thus indicate that the secondary structures for these proteins were more affected by the butyl sorbent, whereas the secondary structure remains relatively unchanged for the proteins adsorbed onto the phenyl sorbent. This study has important ramifications for understanding the nature of protein secondary structural changes following adsorption onto hydrophobic sorbent surfaces. This knowledge could also enable the development of useful protocols for enhancing the chromatographic purification of proteins in their native bioactive states. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 895–905, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Analytical and Bioanalytical Chemistry, 2007
FTIR spectroscopy has been used to monitor and determine the degree of crystallisation in a sampl... more FTIR spectroscopy has been used to monitor and determine the degree of crystallisation in a sample of polyhydroxybutyrate-co-14%valerate (PHB–co-14%HV). Time series spectra of solution-cast films of the polymer revealed spectral changes attributed to the onset of crystallisation. Curve fitting was used to obtain an absolute measure of crystallinity. Mean centred principal-component analysis (PCA) revealed that 99.9% of the spectral variance could be attributed to factor 1. The loadings plot for factor 1 contained features attributable to crystalline and amorphous phases. These features were opposite in sign, indicating that changes in the spectra with the onset of crystallisation are simultaneous and opposite in direction, i.e. as the crystalline band increases the amorphous band decreases. Cross-peaks in asynchronous 2D correlation maps indicate there are likely to be very minor components that are changing out of phase. The presence of these minor components is supported by examination of the loadings of higher factors in the PCA model. PCA has been shown to be suitable for determining the number of dynamic spectral features and has enabled relative and objective monitoring of crystallisation kinetics.
Applied and Environmental Microbiology, 2000
Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS... more Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells.
Journal of Phycology, 2001
Fourier Transform Infrared (FT-IR) spectroscopy was used to study carbon allocation patterns in r... more Fourier Transform Infrared (FT-IR) spectroscopy was used to study carbon allocation patterns in response to changes in nitrogen availability in the diatom Chaetoceros muellerii Lemmerman. The results of the FT-IR measurements were compared with those obtained with traditional chemical methods. The data obtained with both FT-IR and chemical methods showed that nitrogen starvation led to the disappearance of the differences in cell constituents and growth rates existing between cells cultured at either high [NO3−] or high [NH4+]. Irrespective of the nitrogen source supplied before nitrogen starvation, a diversion of carbon away from protein, chlorophyll, and carbohydrates into lipids was observed. Under these conditions, cells that had previously received nitrogen as nitrate appeared to allocate a larger amount of mobilized carbon into lipids than cells that had been cultured in the presence of ammonia. All these changes were reversed by resupplying the cultures with nitrogen. The rate of protein accumulation in the N-replete cells was slower than the rate of decrease under nitrogen starvation. This study demonstrates that the relative proportions of the major macromolecules contained in microalgal cells and their changes in response to external stimuli can be determined rapidly, simultaneously, and inexpensively using FT-IR. The technique proved to be equally reliable to and less labor intensive than more traditional chemical methods.
Spectroscopy Letters, 2005
Mid-infrared spectroscopy together with sequential injection analysis (SIA) and partial least squ... more Mid-infrared spectroscopy together with sequential injection analysis (SIA) and partial least squares (PLS) regression analysis was used to monitor acetonebutanol-ethanol (ABE) fermentations under different fermentation conditions. Five analytes were simultaneously predicted (acetone, acetate, butyrate, n-butanol, and glucose). In order to compare the overall model prediction ability, a relative average 677 of the root mean square error of prediction (RMSEP) across all five analytes was employed. To form a PLS model devoid of any cross-correlations between analytes, a synthetic calibration data set was created by the SIA system. As a test of their robustness, PLS models from synthetic samples and those from real fermentation samples were compared and used to predict samples from the opposite data set and from independent "acid-crash" fermentations. The PLS model developed from the synthetic samples proved to be far more robust and accurate and used fewer factors than PLS models from the real fermentations, which were found to contain analyte crosscorrelations. The use of synthetic data enabled more accurate selection of factors and showed the importance of investigating spectral regression coefficients plots to aid and confirm appropriate factor selection. In addition, an alternative method of factor selection was proposed, using a "similarity measure" between the regression coefficient plots of factors for certain analytes and their standard spectra. Predictions using this method of factor selection over the common "minimum from an error vs. factor" plot proved to be more accurate and used far fewer factors.
Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS... more Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells.
Phytochemistry, 1999
Fourier Transform Infrared (FTIR) microspectroscopy, in combination with chemometrics, was invest... more Fourier Transform Infrared (FTIR) microspectroscopy, in combination with chemometrics, was investigated as a novel method to discriminate between cyanobacterial strains. In total, 810 absorbance spectra were recorded from one eukaryotic and ®ve cyanobacterial taxa spanning three genera and including two strains of one species, Microcystis aeruginosa. Principal Component Analysis (PCA) based classi®cation techniques such as Soft Independent Modelling of Class Analogy (SIMCA) and K-Nearest Neighbours (KNN) were investigated. Dierent spectral regions using derivative spectra were investigated to ®nd the best combinations for classi®cation. The highest rate of correct classi®cations (99±100%) was achieved using ®rst derivative spectra with a spectral region of 1800±950 cm À1 for both the SIMCA and KNN. A dendrogram constructed using averaged spectra of the six taxa studied showed that the two strains of Microcystis aeruginosa exhibited the highest degree of similarity, while the eukaryotic taxon was the most dissimilar from the prokaryotic taxa. #
Analytica Chimica Acta, 2001
Fourier transform infrared (FTIR) spectroscopy, coupled to sequential injection analysis (SIA) wa... more Fourier transform infrared (FTIR) spectroscopy, coupled to sequential injection analysis (SIA) was employed for the on-line monitoring of an acetone-butanol fermentation by simultaneously determining acetone, acetate, n-butanol, butyrate and glucose from the mid-IR spectra of the samples. The analysis system (SIA-FTIR) developed was completely computer controlled, requiring only minute amounts of NaOH and Na 2 CO 3 as reagents and was capable of performing 30 analyte determinations per hour. From a batch fermentation run of 55 h duration, samples were automatically drawn and analysed at 14 different points of time. The analysis by SIA-FTIR comprised of triplicate injections, from each of which two spectra one with 4 cm −1 the other with 8 cm −1 spectral resolution were obtained. In addition, triplicate reference analysis by gas chromatography and enzymatic test kits were also done at corresponding points of time. Based on the data of the reference analysis a partial least squares (PLS) model was established and validated by a leave-one-out cross validation. Best results were obtained using the second derivatised spectra collected at 8 cm −1 resolution. The regression coefficients and standard errors of prediction (S.E.P.) were as follows: acetone, r = 0.999, S.E.P. = 0.077 g/l; acetate, r = 0.998, S.E.P. = 0.063 g/l; butyrate, r = 0.955 and S.E.P. = 0.058 g/l; n-butanol, r = 0.999, S.E.P. = 0.301 g/l and glucose, r = 0.999, S.E.P. = 0.493 g/l. The high quality of the results obtained, and the observation that the precision of the SIA-FTIR analysis was as good and often better than those of the reference methods, showed that SIA-FTIR is a powerful tool for rapid on-line bioprocess monitoring.
Biopolymers, 2008
The secondary structures of proteins (α-helical, β-sheet, β-turn, and random coil) in the solid s... more The secondary structures of proteins (α-helical, β-sheet, β-turn, and random coil) in the solid state and when bound to polymer beads, containing immobilized phenyl and butyl ligands such as those as commonly employed in hydrophobic interaction chromatography, have been investigated using FTIR-ATR spectroscopy and partial least squares (PLS) methods. Proteins with known structural features were used as models, including 12 proteins in the solid state and 7 proteins adsorbed onto the hydrophobic surfaces. A strong PLS correlation was achieved between predictions derived from the experimental data for 4 proteins adsorbed onto the phenyl-modified beads and reference data obtained from the X-ray crystallographic structures with r2 values of 0.9974, 0.9864, 0.9924, and 0.9743 for α-helical, β-sheet, β-turn, and random coiled structures, respectively. On the other hand, proteins adsorbed onto the butyl sorbent underwent greater secondary structural changes compared to the phenyl sorbent as evidenced from the poorer PLS r2 values (r2 are 0.9658, 0.9106, 0.9571, and 0.9340). The results thus indicate that the secondary structures for these proteins were more affected by the butyl sorbent, whereas the secondary structure remains relatively unchanged for the proteins adsorbed onto the phenyl sorbent. This study has important ramifications for understanding the nature of protein secondary structural changes following adsorption onto hydrophobic sorbent surfaces. This knowledge could also enable the development of useful protocols for enhancing the chromatographic purification of proteins in their native bioactive states. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 895–905, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Analytical and Bioanalytical Chemistry, 2007
FTIR spectroscopy has been used to monitor and determine the degree of crystallisation in a sampl... more FTIR spectroscopy has been used to monitor and determine the degree of crystallisation in a sample of polyhydroxybutyrate-co-14%valerate (PHB–co-14%HV). Time series spectra of solution-cast films of the polymer revealed spectral changes attributed to the onset of crystallisation. Curve fitting was used to obtain an absolute measure of crystallinity. Mean centred principal-component analysis (PCA) revealed that 99.9% of the spectral variance could be attributed to factor 1. The loadings plot for factor 1 contained features attributable to crystalline and amorphous phases. These features were opposite in sign, indicating that changes in the spectra with the onset of crystallisation are simultaneous and opposite in direction, i.e. as the crystalline band increases the amorphous band decreases. Cross-peaks in asynchronous 2D correlation maps indicate there are likely to be very minor components that are changing out of phase. The presence of these minor components is supported by examination of the loadings of higher factors in the PCA model. PCA has been shown to be suitable for determining the number of dynamic spectral features and has enabled relative and objective monitoring of crystallisation kinetics.
Applied and Environmental Microbiology, 2000
Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS... more Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells.
Journal of Phycology, 2001
Fourier Transform Infrared (FT-IR) spectroscopy was used to study carbon allocation patterns in r... more Fourier Transform Infrared (FT-IR) spectroscopy was used to study carbon allocation patterns in response to changes in nitrogen availability in the diatom Chaetoceros muellerii Lemmerman. The results of the FT-IR measurements were compared with those obtained with traditional chemical methods. The data obtained with both FT-IR and chemical methods showed that nitrogen starvation led to the disappearance of the differences in cell constituents and growth rates existing between cells cultured at either high [NO3−] or high [NH4+]. Irrespective of the nitrogen source supplied before nitrogen starvation, a diversion of carbon away from protein, chlorophyll, and carbohydrates into lipids was observed. Under these conditions, cells that had previously received nitrogen as nitrate appeared to allocate a larger amount of mobilized carbon into lipids than cells that had been cultured in the presence of ammonia. All these changes were reversed by resupplying the cultures with nitrogen. The rate of protein accumulation in the N-replete cells was slower than the rate of decrease under nitrogen starvation. This study demonstrates that the relative proportions of the major macromolecules contained in microalgal cells and their changes in response to external stimuli can be determined rapidly, simultaneously, and inexpensively using FT-IR. The technique proved to be equally reliable to and less labor intensive than more traditional chemical methods.
Spectroscopy Letters, 2005
Mid-infrared spectroscopy together with sequential injection analysis (SIA) and partial least squ... more Mid-infrared spectroscopy together with sequential injection analysis (SIA) and partial least squares (PLS) regression analysis was used to monitor acetonebutanol-ethanol (ABE) fermentations under different fermentation conditions. Five analytes were simultaneously predicted (acetone, acetate, butyrate, n-butanol, and glucose). In order to compare the overall model prediction ability, a relative average 677 of the root mean square error of prediction (RMSEP) across all five analytes was employed. To form a PLS model devoid of any cross-correlations between analytes, a synthetic calibration data set was created by the SIA system. As a test of their robustness, PLS models from synthetic samples and those from real fermentation samples were compared and used to predict samples from the opposite data set and from independent "acid-crash" fermentations. The PLS model developed from the synthetic samples proved to be far more robust and accurate and used fewer factors than PLS models from the real fermentations, which were found to contain analyte crosscorrelations. The use of synthetic data enabled more accurate selection of factors and showed the importance of investigating spectral regression coefficients plots to aid and confirm appropriate factor selection. In addition, an alternative method of factor selection was proposed, using a "similarity measure" between the regression coefficient plots of factors for certain analytes and their standard spectra. Predictions using this method of factor selection over the common "minimum from an error vs. factor" plot proved to be more accurate and used far fewer factors.