Use of Fourier transform infrared (FT-IR) spectroscopy as a tool for pollen identification

Airborne pollen are largely studied to obtain information about the atmospheric content of natural allergens. Aerobiological monitoring networks have been established to provide reliable data that facilitate the timely initiation of preventive actions aimed at minimizing allergic symptoms. Airborne pollen are usually identified and counted using an optical microscope, but as such procedures are extremely time-consuming, more expedient options are being explored. We have assessed the potential of Fourier transform infrared (FT-IR) spectroscopy as an alternative method for the rapid and reliable identification of allergenic pollen using six well-known allergenic pollen taxa and obtaining the respective FT-IR spectra. In doing this, a first IR spectral library has been created. The spectra of unknown pollen were compared to those of the reference library, and two pollen taxa of a mixed sample were identified.     

Characterization of cotton fabric scouring by FT-IR ATR spectroscopy

FT-IR attenuated total reflectance (ATR) spectroscopy has been used for the fast characterization of cotton fabric scouring process. The greige and the scoured cotton fabrics showed very similar FT-IR spectrum in transmission mode because the bulk composition of the fabrics are similar. However, FT-IR ATR spectroscopy can provide information about the surface of a fabric. By examination of C–H stretching region at 2800–3000 cm⁻¹, the amount of waxes left on the fabric can be estimated. The presence of pectins and/or waxes can also be probed by observation of carbonyl peak induced by the HCl vapor treatment on the fabric. Based on these changes of FT-IR ATR spectra, the scouring process has been characterized.     

Evaluation of FT-IR spectroscopy as a tool to quantify bacteria in binary mixed cultures

Fourier-transform infrared (FT-IR) spectroscopy is known as a high-resolution method for the rapid identification of pure cultures of microorganisms. Here, we evaluated FT-IR as a method for the quantification of bacterial populations in binary mixed cultures consisting of Pseudomonas putida and Rhodococcus ruber. A calibration procedure based on Principal Component Regression was developed for estimating the ratio of the bacterial species. Data for method calibration were gained from pure cultures and artificially assembled communities of known ratios of the two member populations. Moreover, to account for physiological variability, FT-IR measurements were performed with organisms sampled at different growth phases. Measurements and data analyses were subsequently applied to growing mixed cultures revealing that growth of R. ruber was almost completely suppressed in co-culture with P. putida. Population ratios obtained by fatty acid analysis as an independent reference method were in high agreement with the FT-IR derived ratios.     

Characterisation of Ca- and Al-pectate gels by thermal analysis and FT-IR spectroscopy

Thermal analysis (TG-DTA) and FT-IR spectroscopy have been performed on calcium-pectate membranes to investigate their structure and the consequent variation caused by aluminium sorption. Calcium-polygalacturonate (Ca-PG) membranes, model systems of the soil-root interface, were exposed to aluminium solutions at different concentrations (25-800 microM). Three different pHs (3.50, 4.00 and 4.50) were chosen to study the influence of different aluminium species, such as [Al(H2O)6]3+, [Al(OH)(H2O)5]2+ and [Al(OH)2(H2O)(4)]+, on the structure of the Ca-PG membrane. The DTA profiles and FT-IR spectra showed how aluminium sorption induces structural modifications leading to a reorganisation of the chain aggregates and a weakening of the structure. Higher pH, that is, 4.00 and 4.50, and thus hydrolytic aluminium species and related higher calcium content maintain a more regular structure than at pH 3.50. At pH 3.50, both the effect of [Al(H2O)6]3+ and a major calcium release had a greater impact and thus induced a greater weakening of the structure.     

Developments in mid-infrared FT-IR spectroscopy of selected carbohydrates

FT-IR spectroscopy has become a powerful research tool for elucidating the structure, physical properties and interactions of carbohydrates. It provides a new interpretive and experimental framework for the study of complicated systems of natural polymers. This paper gives an overview over new infrared applications in the study of carbohydrates, both small compounds and macromolecules. These include a wide range of studies of carbohydrates in different physical states, from the crystalline solid state to aqueous solution, and special techniques, which expand the experimental framework to the in-muro studies of plant materials, and quantitative determination.     

Application of FT-IR spectroscopy for control of the medium composition during the biodegradation of nitro aromatic compounds

Previous studies showed that cabbage leaf extract (CLE) added to the growth medium can noticeably promote the degradation of nitro aromatic compounds by specific consortium of bacteria upon their growth. For further development of the approach for contaminated soil remediation it was necessary to evaluate the qualitative and/or quantitative composition of different origin CLE and their relevance on the growth of explosives-degrading bacteria. Six CLE (different by species, cultivars and harvesting time) were tested and used as additives to the growth medium. It was shown that nitro aromatic compounds can be identified in the FT-IR absorption spectra by the characteristic band at 1,527 cm⁻¹, and in CLE by the characteristic band at 1,602 cm⁻¹. The intensity of the CLE band at 1,602 cm⁻¹ correlated with the concentration of total nitrogen (R ² = 0.87) and decreased upon the growth of bacteria. The content of nitrogen in CLE differed (0.22–1.00 vol.%) and significantly influenced the content of total carbohydrates (9.50–16.00% DW) and lipids [3.90–9.90% dry weight (DW)] accumulated in bacterial cells while the content of proteins was similar in all samples. Though this study showed quantitative differences in the composition of the studied CLE and the response of bacterial cells to the composition of the growth media, and proved the potential of this additive for remediation of contaminated soil. It was shown that analysis of CLE and monitoring of the conversion of nitro aromatic compounds can be investigated by FT-IR spectroscopy as well as by conventional chemical methods.     

Monitoring of solid phase peptide synthesis by FT-IR spectroscopy

Aggregation phenomena of growing peptides on the resin have seldom been investigated. We report here how conformations are determined by FT-IR spectroscopy. Therefore the sequence 80–99 of HIV 1-protease was synthesized. After every coupling a resin sample was taken out of the reaction column and a FT-IR spectrum recorded. The results were compared with the UV monitoring obtained from another synthesis of the same peptide. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Crystallization and micro FT-IR spectroscopy investigation of cytochrome bc_1 complex

A simple method to obtain large red crystals of cytochrome bc1 complex from beef heart mitochondria has been developed. These crystals are very stable. Their shapes are retained for a long time in tip-sealed Pasteur pipets placed in a refrigerator. The structure of crystalline cytochrome bc1 complex by micro FT-IR spectroscopy has been investigated. Based on the IR spectra of cytochrome c, the empirical assignments of the major infrared frequencies of cytochrome bc1 complex are given. Infrared frequencies and relative intensities of variable orientation and section of crystal are significantly different. These imply that infrared spectral characterization of the membrane protein crystallization is associated with the variable symmetries and orientations of the structure. Experimental results show that phospholipid exists in the crystal of cytochrome bc1 complex. The membrane protein is probably spanned on the mitochondrial membrane and buried in phospholipid bilayer in an asymmetric manner.     

A methodology for screening haemolymph of intertidal mussels, Mytilus edulis, using FT-IR spectroscopy as a tool for environmental assesment

Developing effective, rapid and inexpensive methods for monitoring and conserving aquatic resources is an important issue for environmental managers. This study focuses on Mytilus edulis, a keystone species of many coastal marine communities, which is frequently used as a biomonitor for a range of pollutants. Recent advances in post-genomic technologies have provided new methods of biochemical screening, and Fourier transform-infrared spectroscopy (FT-IR) is one such method that could enable bioindicator species to be used for environmental assessment. This paper develops a methodology to apply the FT-IR approach to marine intertidal M. edulis and addresses three methodological issues: First, the optimum physical location for biofluid sampling is examined (i.e. laboratory versus field). Secondly, the effects of transportation of frozen biofluid sampling from either the field-site or laboratory to the analytical facility are considered. Finally, the effect of repeated FT-IR measurements on collected M. edulis haemolymph samples is examined. From these results we suggest sampling haemolymph from M. edulis at the top of the shore prior to immediate snap-freezing in liquid nitrogen. Sample transportation can occur on ice for up to eight hours before storage at −80 °C. FT-IR measurements should occur within three months of collection and samples should not be used or thawed more than twice. We show how this method can be used to differentiate successfully between four different estuarine environments. Ultimately, through addressing these methodological questions, we provide a protocol to allow efficient sampling and FT-IR measurement of M. edulis as collected from the intertidal areas of rocky and muddy shores. We conclude that due to current monitoring needs presented by the European Water Framework Directive such an approach could prove to be an invaluable future tool for assessing coastal water quality.     

Characterization of the crystalline structure of cellulose using static and dynamic FT-IR spectroscopy

The cellulose structure is a factor of major importance for the strength properties of wood pulp fibers. The ability to characterize small differences in the crystalline structures of cellulose from fibers of different origins is thus highly important. In this work, dynamic FT-IR spectroscopy has been further explored as a method sensitive to cellulose structure variations. Using a model system of two different celluloses, the relation between spectral information and the relative cellulose Ialpha content was investigated. This relation was then used to determine the relative cellulose Ialpha content in different pulps. The estimated cellulose I allomorph compositions were found to be reasonable for both unbleached and bleached chemical pulps. In addition, it was found that the dynamic FT-IR spectroscopy technique had the potential to indicate possible correlation field splitting peaks of cellulose Ibeta.     

Crystallization and micro FT-IR spectroscopy investigation of cytochrome bc1 complex

A simple method to obtain large red crystals of cytochrome bc1 complex from beef heart mitochondria has been developed. These crystals are very stable. Their shapes are retained for a long time in tip-sealed Pasteur pipets placed in a refrigerator. The structure of crystalline cytochrome bc1 complex by micro FT-IR spectroscopy has been investigated. Based on the IR spectra of cytochrome c, the empirical assignments of the major infrared frequencies of cytochrome bc1 complex are given. Infrared frequencies and relative intensities of variable orientation and section of crystal are significantly different. These imply that infrared spectral characterization of the membrane protein crystallization is associated with the variable symmetries and orientations of the structure. Experimental results show that phospholipid exists in the crystal of cytochrome bc1 complex. The membrane protein is probably spanned on the mitochondrial membrane and buried in phospholipid bilayer in an asymmetric manner.     

Characterization of soil organic matter from a sandy soil in relation to management practice using FT-IR spectroscopy

Previous results from differently fertilized long-term field experiments on a sandy soil suggested that the chemical composition of soil organic matter (SOM) is affected by fertilization. The objective of this paper is to confirm this finding for a site with higher soil-clay contents. Four combinations of different fertilizer treatments at long-term field experiment located at a sandy loam were selected: liquid manure (LM), liquid manure+N (LM+N), straw+N (S+N) and mineral nitrogen only (N). Soil organic matter was extracted using sodium pyrophosphate solution at pH of 10 and hot water. The extracts were analyzed using Fourier-Transform infrared spectroscopy. The results indicate that the composition of SOM from the hot water extracts did not show significant differences while the sodium pyrophosphate extracted SOM is affected by the type of fertilization. Soil samples fertilized with LM+N and S+N show the highest intensity of the carboxyl band. This can be explained by the fact that the combination of S+N fertilization with green manure leads to an enrichment of carboxyl groups in SOM. Differences between the band intensities of the treatments for the SOM samples are, however, not as distinct as for the sandy soil samples. This is possibly a result of the higher clay content and lower age of the long-term experiment at the sandy loam site. The intensity of the carboxyl band of the SOM is correlated with the cation exchange capacity of the soil samples. The composition of SOM may, in addition to the SOM content, be used for studying quantitative effects of different management practices or even land use changes on soil properties. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date. This revised version was published online in June 2006 with corrections to the Cover Date.     

Characterization of bioscoured cotton fabrics using FT-IR ATR spectroscopy and microscopy techniques

The effects of bioscouring were investigated by characterizing the chemical and physical surface changes of cotton fabrics using a purified pectinase enzyme from Bacillus subtilis strain WSHB04-02. Fourier-transform infrared (FT-IR) attenuated total-reflectance (ATR) spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques were employed. FT-IR ATR spectroscopy provided a fast and semi-quantitative assessment of the removal of pectins and/or waxes on the cotton surface by comparing the changes in intensity of the carbonyl peak induced by HCl vapor treatment at around 1736 cm(-1). The bioscoured surface could be clearly distinguished from those of untreated and alkali-treated cotton fibers using a combination of SEM and AFM. The images produced using these techniques revealed that the surface morphography and topography of the cotton fibers were shaped by the etching action mode of pectinases during bioscouring. These findings demonstrated that AFM is a useful supplement to SEM in characterizing cotton surfaces.     

FT-IR spectroscopy as a tool for rapid identification and intra-species characterization of airborne filamentous fungi

Identification of microfungi is time-consuming due to cultivation and microscopic examination and can be influenced by the interpretation of the macro- and micro-morphological characters observed. Fungal conidia contain mycotoxins that may be present in bioaerosols and thus the capacity for production of mycotoxins (and allergens) needs to be investigated to create a basis for reliable risk assessment in environmental and occupational hygiene. The present investigation aimed to create a simple but sophisticated method for the preparation of samples and the identification of airborne fungi by FT-IR spectroscopy. The method was suited to reproducibly differentiate Aspergillus and Penicillium species on the generic, the species, and the strain level. There are strong indications that strains of one taxon differing in metabolite production can be reliably distinguished by FT-IR spectroscopy (e.g. Aspergillus parasiticus). On the other hand, species from different taxa being similar in secondary metabolite production showed comparably higher similarities. The results obtained here can serve as a basis for the development of a database for species identification and strain characterization of microfungi. The method presented here will improve and facilitate the risk assessment in case of bioaerosol exposure, as strains with different physiological properties (e.g. toxic, non-toxic) could be differentiated. Moreover, it has the potential to significantly improve the identification of microfungi in various fields of applied microbiological research, e.g. high throughput screening in view of specific physiological properties, biodiversity studies, inventories in environmental microbiology, and quality control measures.     

Structure analysis and degree of substitution of chitin, chitosan and dibutyrylchitin by FT-IR spectroscopy and solid state C NMR

Chitin, an important constituent of the exoskeleton of many organisms such as crustacea and insects, and its derivates promote the ordered healing of tissues and are therefore very suitable for use in wound dressings. The degree of substitution (DS) is an important parameter when assessing the conversion of chitin into one of its derivates. The degree of acetylation of chitin and chitosan and the degree of butyrylation of dibutyrylchitin was evaluated. It is found that FT-IR spectroscopy is a relatively easy but indirect way of determining the DS. FT-IR spectroscopy proved to be very useful for comparing the degrees of conversion and -substitution, as well as for differentiating between different chitin types. Absolute DS determinations by FT-IR however are only reliable when a calibration, using a direct technique such as ¹³C-NMR, is made.     

Determining the degree of methylesterification of pectin by ATR/FT-IR: Methodology optimisation and comparison with theoretical calculations

The application of FT-IR to the study of the structure and interactions of the major plant-cell wall polysaccharide pectin has been reported for many decades. Nevertheless, here we show that the generally reported methodology for one of its most commonly utilised applications, the measurement of the degree of methylesterification (DM), requires careful interpretation and sample handling; including consideration of the moisture content and ionisation state. We propose instead a different methodology based on the assessment of the magnitude of C–H stretches in the methyl groups relative to those in the backbone and demonstrate experimentally the advantage of this method. In addition, we add a theoretical dimension to our work, performing full quantum chemical (DFT) calculations of monomeric-, dimeric-, and trimeric-pectic compounds, in various states of partial methylesterification. These extensive calculations not only confirm the identity of the proposed methyl-band and illustrate its scaling with DM; but also demonstrate the success of the theoretical approach. Thus, DFT calculations are expected to be a valuable tool in the interpretation of IR spectra obtained from more complex systems such as polysaccharide conjugates.     

Evaluation of restriction fragment length polymorphism analysis of 16S rDNA as a tool for genomovar characterisation within the Burkholderia cepacia complex

The polysaccharides formed on hot alkaline extraction of the ascomycetous lichen Teloschistes flavicans were fractionated to give two glucans, which were characterised by methylation analysis and 1D and 2D NMR spectroscopy. One was a branched beta-glucan containing (1-->3) and (1-->6) linkages, a structure which is more typical of basidiomycetes rather than ascomycetes, which have linear glucans. The other was an alpha-glucan with alternating (1-->4) and (1-->6) linkages, found for the first time in Nature. This structure can be classified as a pullulan, which has been isolated from the fungi Aureobasidium pullulans, Tremella mesenterica, and Cyttaria harioti, but has different ratios of the component glycosidic linkages. The significance of the presence of the isolated alpha- and beta-glucans is discussed.     

Quantification of polymeric mannose in wine extracts by FT-IR spectroscopy and OSC-PLS1 regression

FT-IR spectroscopy has being a widespread technique in the agro-industry for the quick assess of food components, including the wine. Using the region of wavenumbers 1200–800 cm⁻¹ of the FT-IR spectra wine polysaccharides, Partial Least Squares Regression (PLS1) independent calibration models were built for mannose quantification in complex matrices from white and in red wine extracts. With PLS1 it was not possible to build a calibration model that included both white and red wine extracts. However, a predictive ability of the model for quantification of mannose from mannoproteins based on this FT-IR spectral region was achieved by the application of orthogonal signal correction (OSC)-PLS1.     

NMR spectroscopy as a tool for the rapid assessment of the conformation of GST-fusion proteins

Glutathione-S-transferase (GST)-fusion proteins are used extensively for structural, biochemical, and functional analyses. Although the conformation of the target protein is of critical importance, confirmation of the folded state of the target is often not undertaken or is cumbersome because of the requirement to first remove the GST tag. Here, we demonstrate that it is possible to record conventional (15)N-HSQC NMR spectra of small GST-fusion proteins and that the observed signals arise almost exclusively from the target protein. This approach constitutes a rapid and straightforward means of assessing the conformation of a GST-fusion protein without having to cleave the GST and should prove valuable, both to biochemists seeking to check the conformation of their proteins prior to functional studies and to structural biologists screening protein constructs for suitability as targets for structural studies.     

Gastrointestinal ischemia monitoring through impedance spectroscopy as a tool for the management of the critically ill

Impedance spectroscopy (IS) has been proposed as a tool for monitoring mucosal tissue ischemia and damage in the gut of critically ill patients resulting from shock and hypoperfusion. A specific device and system have been developed and tested for this specific application over the past 12 years by our research group. This paper reviews previously published studies as well as unpublished experimental results, and puts the whole in context and perspective to help understand this technology. Results presented include summaries of gastric reactance measurement understanding, in vivo measurements in animal models, clinical significance of the measurement, and future perspectives of clinical use of this technology. All of the experimental work done to date has been designed to determine the evolving device prototypes’ performance and limitations from an instrumentation point of view. Although there are still questions to be answered with regard to the IS measurement, we conclude that we have reached enough confidence in the measurement and the device’s performance and safety to begin clinically oriented research to learn how this technology may be useful in the diagnosis and management of different populations of the critically ill.