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PubMed2004

[Identification of gastrodia elata blume by Fourier transform infrared spectroscopy].

In this paper, a method of rapid and undamaged identification of wild and cultivated Gastrodia elata Blume, and one of its fakes by Fourier transform infrared spectroscopy (FTIR) is reported. The results show that Gastrodia elata Blume and its fake have different characteristic infrared spectra, by which Gastrodia elata Blume can be identified from its fake. Wild winter, wild spring, and cultivated Gastrodia elata Blume can be discriminated by FTIR, according to the differences of their spectral peaks and absorbance ratios. By the differences of absorbance ratios of several peaks, different grade of Gastrodia elata Blume may be classified. FTIR has proved to be a rapid, simple and nondestructive method for the identification of Gastrodia elata Blume.

DNA, Plant↗
PubMed2004

Determination of urea, glucose, and phosphate in dialysate with Fourier transform infrared spectroscopy.

Individual control and quantification of phosphate removal is desirable in dialysis treatment. Currently, no on-line method exists to quantify phosphate removal. We demonstrate that a multivariate calibration model based on infrared transmission spectra is capable of predicting phosphate, urea, and glucose concentrations at clinically relevant levels. The on-line monitoring of these components by infrared spectroscopy is therefore feasible.

Aged↗
PubMed2006

Artificial neural network based identification of Campylobacter species by Fourier transform infrared spectroscopy.

Two prototypes of artificial neural network (ANN), multilayer perceptron (MLP), and probabilistic neural network (PNN), were used to analyze infrared (IR) spectral data obtained from intact cells belonging to the species Campylobacter coli and Campylobacter jejuni. In order to establish a consistent identification and typing procedure, mid infrared spectra of these species were obtained by means of a Fourier transform infrared (FT-IR) spectroscope. FT-IR patterns belonging to 26 isolates subclassified into 4 genotypes were pre-processed (normalized, smoothed and derivatized) and grouped into training, verification and test sets. The two architectures tested (PNN, MLP) were developed and trained to identify or leave unassigned a number of IR patterns. Two window ranges (w(4), 1200 to 900 cm(-1); and w(5), 900 to 700 cm(-1)) in the mid IR spectrum were presented as input to the ANN models functioning as pattern recognition systems. No matter the ANN used all the training sets were correctly identified at subspecies level. For the test set, the four-layer MLP network was found to be specially suitable to recognize FT-IR data since it correctly identified 99.16% of unknowns using the w(4) range, and was fully successful in detecting atypical patterns from closely related Campylobacter strains and other bacterial species. The PNN network obtained lower percentages in assignation and rejection. Overall, ANNs constitute an excellent mathematical tool in microbial identification, since they are able to recognize with a high degree of confidence typical as well as atypical FT-IR fingerprints from Campylobacter spp.

Campylobacter↗
PubMed2007

Continuous nondestructive monitoring of Bordetella pertussis biofilms by Fourier transform infrared spectroscopy and other corroborative techniques.

This work describes the application of several analytical techniques to characterize the development of Bordetella pertussis biofilms and to examine, in particular, the contribution of virulence factors in this development. Growth of surface-attached virulent and avirulent B. pertussis strains was monitored in continuous-flow chambers by techniques such as the crystal violet method, and nondestructive methodologies like fluorescence microscopy and Fourier transform (FT) IR spectroscopy. Additionally, B. pertussis virulent and avirulent strains expressing green fluorescent protein were grown adhered to the base of a glass chamber of 1-microm thickness. Three-dimensional images of mature biofilms, acquired by confocal laser scanning microscopy, were quantitatively analysed by means of the computer program COMSTAT. Our results indicate that only the virulent (Bvg(+)) phase of B. pertussis is able to attach to surfaces and develop a mature biofilm. In the virulent phase these bacteria are capable of producing a biofilm consisting of microcolonies of approximately 200 microm in diameter and 24 microm in depth. FTIR spectroscopy allowed us not only to follow the dynamics of biofilm growth through specific biomass and biofilm marker absorption bands, but also to monitor the maturation of the biofilm by means of the increase of the carbohydrate-to-protein ratio.

Biofilms↗
PubMed1994

Beta-sheet secondary structure of the trimeric globular domain of C1q of complement and collagen types VIII and X by Fourier-transform infrared spectroscopy and averaged structure predictions.

C1q plays a key role in the recognition of immune complexes, thereby initiating the classical pathway of complement activation. Although the triple-helix conformation of its N-terminal segment is well established, the secondary structure of the trimeric globular C-terminal domain is as yet unknown. The secondary structures of human C1q and C1q stalks and pepsin-extracted human collagen types I, III and IV (with no significant non-collagen-like structure) were studied by Fourier-transform i.r. spectroscopy in 2H2O buffers. After second-derivative calculation to resolve the fine structure of the broad amide I band, the Fourier-transform i.r. spectrum of C1q showed two major bands, one at 1637 cm-1, which is a characteristic frequency for beta-sheets, and one at 1661 cm-1. Both major bands were also detected for Clq in H2O buffers. Only the second major band was observed at 1655 cm-1 in pepsin-digested C1q which contains primarily the N-terminal triple-helix region. The Fourier-transform i.r. spectra of collagen in 2H2O also showed a major band at 1659 cm-1 (and minor bands at 1632 cm-1 and 1682 cm-1). It is concluded that the C1q globular heads contain primarily beta-sheet structure. The C-terminal domains of C1q show approximately 25% sequence identity with the non-collagen-like C-terminal regions of the short-chain collagen types VIII and X. To complement the Fourier-transform-i.r. spectroscopic data, averaged Robson and Chou-Fasman structure predictions on 15 similar sequences for the globular domains of C1q and collagen types VIII and X were performed. These showed a clear pattern of ten beta-strands interspersed by beta-turns and /or loops. Residues thought to be important for C1q-immune complex interactions with IgG and IgM were predicted to be at a surface-exposed loop. Sequence insertions and deletions, glycosylation sites, the free cysteine residue and RGD recognition sequences were also predicted to be at surface-exposed positions.

Amino Acid Sequence↗
PubMed2004

Conformational changes in gastric H+/K+-ATPase monitored by difference Fourier-transform infrared spectroscopy and hydrogen/deuterium exchange.

Gastric H+/K+-ATPase is a P-type ATPase responsible for acid secretion in the stomach. This protein adopts mainly two conformations called E1 and E2. Even though two high-resolution structures for a P-ATPase in these conformations are available, little structural information is available about the transition between these two conformations. In the present study, we used two experimental approaches to investigate the structural differences that occur when gastric ATPase is placed in the presence of various ligands and ligand combinations. We used attenuated total reflection-Fourier-transform IR experiments under a flowing buffer to modify the environment of the protein inside the measurement cell. The high accuracy of the results allowed us to demonstrate that the E1-E2 transition induces a net change in the secondary structure that concerns 10-15 amino acid residues of a total of 1324 in the proteins. The E2.K+ structure is characterized by a decreased beta-sheet content and an increase in the disordered structure content with respect to the E1 form of the enzyme. Modifications in the absorption of the side chain of amino acids are also suggested. By using hydrogen/deuterium-exchange kinetics, we show that tertiary-structure modifications occurred in the presence of the same ligands, but these changes involved several hundreds of residues. The present study suggests that conformational changes in the catalytic cycle imply secondary-structure rearrangements of small hinge regions that have an impact on large domain re-organizations.

Animals↗
PubMed2004

[Application of the SIMCA method to cancer diagnosis with Fourier-transform infrared spectroscopy].

Early detection of cancer with mid-IR spectroscopy is a focal topic in the biomedical engineering field. A method was investigated for the detection of malignant tissues with Fourier Transform Infrared spectroscopy (FTIR) and chemometrics method of pattern recognition. Spectral pretreatment and wavelength range selection were studied to improve the classification effect of soft independent modeling of class analogy (SIMCA). To distinguish the malignant tissues from normal ones, sixty-three stomach tissue samples were investigated in this paper. Forty samples were chosen randomly as calibration set and the rest twenty-three samples as predicting set. The correctness of classification was 91%, which was satisfactory. This approach was proved to be a reliable and practicable method for cancer diagnosis. Benign and malignant tissues can be identified by the combination of FTIR spectroscopy and chemometrics, which is able to be developed as a rapid diagnosis method of cancer.

Animals↗
PubMed2003

Studies of poly(styrene-co-allyl alcohol)/polyester blends using Fourier transform infrared spectroscopy and imaging.

The interaction of poly(styrene-co-allyl alcohol) and aliphatic polyester was studied using FT-IR spectroscopy. The hydrogen bonding between two polymers was investigated by monitoring C=O and OH stretching modes with the variation of concentration and temperature. The phase-separated morphology was also observed using FT-IR imaging, where the spectroscopic analysis of each phase is available.

Materials Testing↗
PubMed2004

Biophysic evaluation of bone quality-application of Fourier transform infrared spectroscopy and phosphorus-31 solid-state nuclear magnetic resonance spectroscopy.

In this review, we focus on findings obtained with biophysic techniques, Fourier transformed infrared (FTIR) spectroscopy and phosphorus-31 solid-state nuclear magnetic resonance (31P solid-state NMR) spectroscopy, which may allow us to evaluate bone quality and to predict bone strength. FTIR measures the absorption energy that produces an increase in the vibrational or rotational energy of atoms or groups of atoms within the molecule. FTIR spectroscopy allows us to examine the relative amount of minerals and matrix content and the arrangement of apatite and organic matrix. FTIR spectroscopy should become an important tool, because the relative amount of minerals and the arrangement of apatite and organic matrix could be a measure for evaluating bone quality. 31P solid-state NMR spectroscopy is useful for evaluating the quality of bone and predicting bone strength by calculating the spine-lattice relaxation time (T1) of bone. 31P solid-state NMR imaging can be used to measure quantitatively the mass of hydroxyapatite. The T1 relaxation time of both bone and deficient hydroxyapatite was much longer than that of pure hydroxyapatite. T1 relaxation time is one of the promising indices of bone quality.

Animals↗
PubMed1995

Discrimination of species in the genus Listeria by Fourier transform infrared spectroscopy and canonical variate analysis.

Infrared spectra of type cultures of the six recognized species of the genus Listeria and of Listeria grayi subsp. murrayi were recorded. By use of a library of 59 spectra, comprising at least six replicates of each type, discrimination by canonical variate analysis of the spectral amplitudes allowed all of the spectra to be correctly classified.

Analysis of Variance↗
PubMed1995

Fourier transform infrared spectroscopy indicates a major conformational rearrangement in the activation of rhodopsin.

The study of the structural differences between rhodopsin and its active form (metarhodopsin II) has been carried out by means of deconvolution analysis of infrared spectra. Deconvolution techniques allow the direct identification of the spectral changes that have occurred, which results in a significantly different view of the conformational changes occurring after activation of the receptor as compared with previous difference spectroscopy analysis. Thus, a number of changes in the bands assigned to solvent-exposed domains of the receptor are detected, indicating significant decreases in extended (beta) sequences and in reverse turns, and increases in irregular/aperiodic sequences and in helices with a non-alpha geometry, whereas there is no decrease in alpha-helices. In addition to secondary structure conversions, qualitative alterations within a given secondary structure type are detected. These are seen to occur in both reverse turns and helices. The nature of this spectral change is of great importance, since a clear alteration in the helices bundle core is detected. All these changes indicate that the rhodopsin --> metarhodopsin II transition involves not a minor but a major conformational rearrangement, reconciling the infrared data with the energetics of the activation process.

Analysis of Variance↗
PubMed2005

Classification of modified starches by fourier transform infrared spectroscopy using support vector machines.

The aim of this study was to compare the performance of different supervised discrimination methods based on IR data for the classification of starches according to the type of chemical modification undergone. The goal of the supervised classification methods is to develop classification rules. Representative samples of each group (known beforehand) were available, from which the relevant characteristics (chemical modification) were known. On the basis of a training data set, classification rules are determined, which can then be applied to classify new (unknown) samples.

Spectroscopy, Fourier Transform Infrared↗
PubMed2000

[Fourier transform infrared spectroscopy, molecular biologic methods and antimyocotic susceptibility patterns for identification and differentiation of cryptococcus species].

Molecular biological methods as well as the FTIR method allows the rapid, reliable and reproducible determination and identification of Cryptococcus species from human, veterinary and environmental origin and their serovars. The results obtained by FTIR could be verified by the molecular methods. In addition, with the PCR and FTIR fingerprinting methods it is possible to distinctly group the serovars and differentiate the different Cryptococcus strains.

Animals↗
PubMed1995

Fourier transform infrared spectroscopy investigations of protein structure.

Infrared spectroscopy can provide insight into protein structure. This technique is sensitive to the backbone amide arrangement of peptide and protein molecules. In many cases, complementary as well as more expansive information is obtained as opposed to information obtained by other methods that examine the molecule's environmental surroundings, require molecular probes, or perhaps cannot investigate the molecule in its native environment. The foundation for spectroscopic differences between the various secondary structures arises not only from geometrical differences and hydrogen bond variations but also transition dipole coupling between neighboring oscillators. Theoretical predictions of protein spectra have been made using normal mode analysis and combined with experimental data. At present the amide I band has provided the most insight into secondary structure. Even more convincing results are obtained when both H2O and D2O are used as solvents. Recent advances in computerized technology and mathematical techniques have expanded the potential contributions of infrared spectroscopy in the area of protein structural determination. However, the limitations of resolution enhancement and curve-fitting techniques must be taken into consideration. The parameters must be carefully and optimally chosen and evaluated on a case-by-case basis. The subjectivity of these techniques makes a thorough understanding of the algorithms necessary, especially those commercially available. Infrared spectroscopy continues to provide insight into protein and peptide structures under biologically relevant conditions that enable the structure-function relationships for such molecules to be better understood.

Amides↗