A novel application of Fourier-transformed infrared spectroscopy: classification of slime from staphylococci

Abstract

It has been proposed that the virulence of nosocomial Staphylococcus infections associated with indwelling medical devices is related to the ability of the bacterium to colonise these materials by forming a biofilm composed of multilayered cell clusters embedded in a slime matrix. However, the pathogenic role of exopolysaccharide biofilms is not fully understood. A new method was sought for differentiating the structure of slime from two closely related bacterial strains, Staphylococcus aureus and Staphylococcus epidermidis. Using PCR it was confirmed that these strains were positive for the icaA and icaD genes and the complete ica operon (2.7 kb). Monosaccharide analysis by thin-layer chromatography revealed an identical profile for both strains, with xylose and glucose present among the four visible bands. Using Fourier-transformed infrared spectroscopy and hierarchical cluster analysis, three of four S. aureus samples (75%), and four of five S. epidermidis samples were grouped according to species. A novel FTIR approach in classifying slime produced by S. aureus and S. epidermidis is reported.     

A novel application of Fourier-transformed infrared spectroscopy: classification of slime from staphylococci

It has been proposed that the virulence of nosocomial Staphylococcus infections associated with indwelling medical devices is related to the ability of the bacterium to colonise these materials by forming a biofilm composed of multilayered cell clusters embedded in a slime matrix. However, the pathogenic role of exopolysaccharide biofilms is not fully understood. A new method was sought for differentiating the structure of slime from two closely related bacterial strains, Staphylococcus aureus and Staphylococcus epidermidis. Using PCR it was confirmed that these strains were positive for the icaA and icaD genes and the complete ica operon (2.7 kb). Monosaccharide analysis by thin-layer chromatography revealed an identical profile for both strains, with xylose and glucose present among the four visible bands. Using Fourier-transformed infrared spectroscopy and hierarchical cluster analysis, three of four S. aureus samples (75%), and four of five S. epidermidis samples were grouped according to species. A novel FTIR approach in classifying slime produced by S. aureus and S. epidermidis is reported.     

Differentiation of Listeria monocytogenes serovars by using artificial neural network analysis of Fourier-transformed infrared spectra

A classification system based on Fourier transform infrared (FTIR) spectroscopy combined with artificial neural network analysis was designed to differentiate 12 serovars of Listeria monocytogenes using a reference database of 106 well-defined strains. External validation was performed using a test set of another 166 L. monocytogenes strains. The O antigens (serogroup) of 164 strains (98.8%) could be identified correctly, and H antigens were correctly determined in 152 (91.6%) of the test strains. Importantly, 40 out of 41 potentially epidemic serovar 4b strains were unambiguously identified. FTIR analysis is superior to PCR-based systems for serovar differentiation and has potential for the rapid, simultaneous identification of both species and serovar of an unknown Listeria isolate by simply measuring a whole-cell infrared spectrum.     

In vivo study of the state of order of the membranes of gram-negative bacteria by Fourier-transform infrared spectroscopy (FT-IR).

Temperature-induced order/disorder transition profiles were obtained from the membranes of intact Gram-negative bacterial cells by FT-IR analysis of the frequency shifts of the acyl chain methylene symmetric stretching band as a monitor. Cells grown at different temperatures yielded distinct transition profiles. At the individual growth temperatures, however, the nearly alike frequency values indicated a very similar 'state of order' of the bacterial membranes. The FT-IR data were complemented by GC analysis of whole cell fatty acid composition. The FT-IR data obtained in vivo gave direct evidence of the adaptation of the 'state of order' and 'fluidity' of bacterial membranes to varying growth temperatures.     

Ex vivo quantitative analysis of human corneal stroma dehydration by near‐infrared absorption spectroscopy

Corneal water content and hydrodynamics are critical indicators of eye health. In this work, a convenient method based on near‐infrared absorption spectroscopy (NIRA) was presented to measure the relative water content of the corneal stroma ex vivo, which paves the way to measure corneal water content in vivo. The relative water content of fresh corneal stroma during dehydration under natural conditions (temperature, 25.8 ± 0.3°C; humidity, 7.2% ± 0.9%) was monitored in real time, and the characteristic time τ when the relative water content dropped to 90% of the fresh corneal stroma was 140.1 ± 30.6 s. Furthermore, the change in the relative water content over time was found to be linear with a dehydration rate of 0.071% per second, consistent with indirect optical coherence pachymetry but with superior reproducibility and precision. Provided that the NIRA spectrometer is changed to a reflection structure from the current transmission configuration, the NIRA method proposed in this work has great potential for in vivo measurement with the advantages of non‐contact, high precision and low cost.     

In vivo estimation of water diffusivity in occluded human skin using terahertz reflection spectroscopy

Water diffusion and the concentration profile within the skin significantly affect the surrounding chemical absorption and molecular synthesis. Occluding the skin causes water to accumulate in the top layer of the skin (the stratum corneum [SC]) and also affects the water diffusivity. Scar treatments such as silicone gel and silicone sheets make use of occlusion to increase skin hydration. However with existing techniques, it is not possible to quantitatively measure the diffusivity of the water during occlusion: current methods determine water diffusivity by measuring the water evaporated through the skin and thus require the skin to breathe. In this work, we use the high sensitivity of terahertz light to water to study how the water content in the SC changes upon occlusion. From our measurements, we can solve the diffusion equations in the SC to deduce the water concentration profile in occluded skin and subsequently to determine the diffusivity. To our knowledge, this is the first work showing how the diffusivity of human skin can be measured during occlusion and we envisage this paper as being used as a guide for non‐invasively determining the diffusivity of occluded human skin in vivo.      

Quantitative analysis of cellulose nitrates by Fourier transform infrared spectroscopy

Quantitative express analysis of nitrogen content in cellulose nitrates by Fourier transform infrared spectroscopy has been developed. The slope of the dependence of the ratio of the band intensity (and area) to sample weight in a tablet, on the nitrogen content in a sample was used to find the reduced extinction coefficients for quantitative analysis of nitrogen content in cellulose nitrate samples by IR spectroscopy. The results were compared with the nitrogen content values in the same samples determined by the ferrosulfate method.     

In vivo generation of free radicals in the skin of live mice under ultraviolet light, measured by L-band EPR spectroscopy

Although free radicals may be involved in various types of UV-induced injuries, only a few in vivo studies of the generation of free radicals, including oxygen radicals, during exposure to ultraviolet light (UV) have been reported. In this study, the nitroxyl probe 3-carbamoyl-2,2,5,5-tetramethylpyrrolidine-N-oxyl was intravenously injected into hairless mice, and its decay was monitored in the skin with an in vivo EPR spectrometer equipped with a surface-coil-type resonator. The rate of decay of the EPR signal increased during UV (UVA+B) irradiation. This increase in signal decay was suppressed by preadministration of a spin trap, N-tert-butyl-alpha-phenylnitrone (PBN). PBN did not change the rate of signal decay in nonirradiated mice. The correlation between signal decay rate and physiological parameters such as blood velocity, blood mass, or skin temperature was low. The decay rate responded rapidly and reversibly to starting and stopping the UV illumination. Hydroxyl and peroxyl radicals caused reduction of the probe signal in vitro, and PBN inhibited only the peroxyl radical-induced signal reduction. These observations suggest that peroxyl radicals are generated in the skin of live mice during UVA+B irradiation.     

The in vivo toxicity of carbon tetrachloride and carrageenan on heart microsomes: analysis by Fourier transform infrared spectroscopy

We investigated the sensitivity of rat heart microsomes to free radical attack using Fourier transform infrared (FT-IR) spectroscopy. This physico-chemical method seemed a valuable technique: quite sensitive to changes in the vibrational spectra. The spectral variations observed between normal and treated rats were in great part due to reactive oxygen species that led to changes in protein conformation involving beta-sheets, aggregation of proteins, and modification of protein synthesis. Carrageenan-induced inflammation slightly enhanced the total lipid content; rearrangement of acyl chains and accumulation of cholesterol esters and phospholipids also occurred in the treated rats. Carbon tetrachloride induced a decrease in both lipid and protein contents. The level of glucidic substrates was diminished with carbon tetrachloride and enhanced with carrageenan; these changes were due to metabolic interactions between cell components and drugs. FT-IR spectroscopy provided an accurate means to monitor, in rat heart, the in vivo effects of inflammatory and peroxidative damages, to discriminate and classify the affected cells, and to correlate the findings with known physiological and biochemical data in close relationship with metabolic disruptions induced by the two xenobiotics.     

The quantitative analysis of uronic acid polymers by infrared spectroscopy.

I.r. absorption bands associated with the functional groups of carboxylic acid derivatives are useful for the analysis of alginates and pectins. The ester, amide, and uronate contents of pectins and the uronate content of alginates were determined, respectively, from the ester-carbonyl stretching band (1740 cm- minus 1), the amide I band (1650 cm- minus 1), and the carboxylate antisymmetric stretching band (1607 cm- minus 1) obtained from the spectra of solutions in D2O-phosphate buffer. The results are accurate to within plus or minus 2-4%, are self consistent, and agree well with the few reliable results that are available. The method should be applicable for the determination of carboxylic acid derivatives in other polysaccharides.     

Conformational analysis of hemopexin by fourier-transform infrared and circular dichroism spectroscopy

Hemopexin is a serum glyco-protein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptormediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% β-structure, 15% α-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme–hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the hemeprotein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis. © 1994 Wiley-Liss, Inc.     

Lipid-protein ratios by infrared spectroscopy

A method for measuring the ratio of diacyl phospholipid to protein in lipid-protein mixtures and membranes by infrared spectroscopy is described. Samples made of diacyl phospholipid and proteins mixed in known ratios were analyzed for lipid-protein ratio by the infrared (ir) method. Results had a standard deviation of less than +/- 4% over the lipid-protein molar ratio range of 9:1 to 320:1. Calculations of the ratio of total lipid to protein require that the diacyl phospholipid-to-protein ratio be divided by the mole fraction of diacyl phospholipid in the total lipid. Phospholipid-protein ratios for various sarcoplasmic reticulum membrane preparations (R1-washed, octylglucoside purified, deoxycholate treated) were determined by the ir method and compared to literature values. Also, phospholipid-protein ratios were determined for R1-washed sarcoplasmic reticulum by three chemical analyses using different protein assays and were compared with ratios obtained by the infrared method. The infrared results were closest to those of a chemical method designed specifically for membrane proteins.     

In vivo studies of sterol and squalene secretion by human skin

This work was aimed at studying the quantity and composition of sterols and squalene secreted by the human skin. Lipids secreted by the entire skin were recovered by Soxhlet extraction of the clothing worn by a patient for 24 hr with a chloroform-methanol azeotrope and by extracting the water of a shower taken by the patient at the end of the 24-hr period. Squalene and sterols were quantified by gas-liquid chromatography. Plant sterols were separated from total sterols by thin-layer chromatography. Free and esterified cholesterol were separated by digitonin precipitation. In eight adults, seven of them with hyperlipoproteinemia, the total skin secretion of cholesterol ranged from 59 to 108 mg/day, with a mean of 88 +/- 17 (SD) mg/day. There was no difference in cholesterol secretion between the normocholesterolemic individual and the hypercholesterolemic ones, nor were there any differences according to type of hyperlipoproteinemia. Free cholesterol amounted to 54 +/- 5% of the total cholesterol. The secretion of squalene ranged from 125 to 475 mg/day in five patients. The secretion of both squalene and cholesterol was quite constant for any individual on a given diet. Cholesterol constituted 95.6 +/- 0.5% of the digitonin-precipitable total body surface sterols of eight patients, and lathosterol, the next largest fraction, 3.4 +/- 0.4%. Total plant sterols formed only 0.65 +/- 0.38% and beta-sitosterol 0.35 +/- 0.23% of the skin surface sterols in six patients whose dietary beta-sitosterol intake ranged from 230 to 3400 mg/day.     

Structural analysis of DNA-chlorophyll complexes by Fourier transform infrared difference spectroscopy

Porphyrins and metalloporphyrins are strong DNA binders. Some of these compounds have been used for radiation sensitization therapy of cancer and are targeted to interact with cellular DNA. This study was designed to examine the interaction of calf thymus DNA with chlorophyll a (CHL) in aqueous solution at physiological pH with CHL/DNA(phosphate) ratios (r) of 1/160, 1/80, 1/40, 1/20, 1/10, and 1/5. Fourier transform infrared (FTIR) difference spectroscopy was used to characterize the nature of DNA-pigment interactions and to establish correlations between spectral changes and the CHL binding mode, binding constant, sequence selectivity, DNA secondary structure, and structural variations of DNA-CHL complexes in aqueous solution. Spectroscopic results showed that CHL is an external DNA binder with no affinity for DNA intercalation. At low pigment concentration (r = 1/160, 1/80, and 1/40), there are two major binding sites for CHL on DNA duplex: 1) Mg-PO2 and 2) Mg-N7 (guanine) with an overall binding constant of K = 1.13 x 10(4) M-1. The pigment distributions are 60% with the backbone PO2 group and 20% with the G-C base pairs. The chlorophyll interaction is associated with a major reduction of B-DNA structure in favor of A-DNA. At high chlorophyll content (r = 1/10), helix opening occurs, with major spectral alterations of the G-C and A-T bases. At high chlorophyll concentration (1/5), pigment aggregation is observed, which does not favor CHL-DNA complexation.     

Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy

Water from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance (ATR) accessory. However, when protein solutions are studied, ATR spectroscopy suffers from several drawbacks, the most severe being nonproportionality of the observed absorbance with the protein concentration and spectral distortions that vary from protein to protein and from sample to sample. In this study, we show (1) that the nonproportionality is due to adsorption of the protein on the ATR crystal surface; (2) that the contribution of the crystal-adsorbed protein can easily be taken into account, rendering the corrected absorbance proportional to the protein concentration; (3) that the observed variable base line distortions, likely due to changes in the penetration depth of the light beam in solutions with the refractive index that depends on the protein concentration, can be easily eliminated; and (4) that ATR IR spectra thus corrected for protein adsorption and light penetration can be used to properly analyze the secondary structure of proteins in solution.     

Fourier-transformed infrared assay for the determination of the positional specificity of non-specific and 1,3-specific lipases

A new fast infrared spectroscopy method for determination of the positional specificity of the lipase reaction is reported. This method is based on the analysis of specific infrared bands shown by the ester (1751 cm^–1) and thioester (1704 cm^–1) groups of the 2,3-dimercapto-1-propanol tributyrate.     

In vivo quantitative analysis of PKA subunit interaction and cAMP level by dual color fluorescence cross correlation spectroscopy

We employed dual color Fluorescence Cross Correlation Spectroscopy (FCCS) to measure the interaction between PKA regulatory (RII) and catalytic subunits (CAT) in living cells. Elevation of intracellular cAMP with forskolin decreased the cross-correlation amplitude between RFP-fused RII (RII-mRFP) and GFP-fused CAT (CAT-EGFP) by 50%, indicating that cAMP elevation leads to dissociation of RII-CAT complexes. Moreover, diffusion coefficient analysis showed that the diffusion rate of CAT-EGFP was significantly increased, suggesting that the decreased RII-CAT association caused by cAMP generated free CAT subunits. Our study demonstrates that in vivo FCCS measurements and their quantitative analysis permit one not only to directly quantify protein-protein interactions but also to estimate changes in the intracellular cAMP concentration.     

Chemical alterations of hyaluronic acid and dermatan sulfate detected in aging human skin by infrared spectroscopy

Age-mediated deacetylation of hyaluronic acid and dermatan sulfate, and shift of sulfate ester configuration were indicated by infrared spectroscopy. Hyaluronic acid and the three dermatan sulfates (DS₁₈, DS₁₈ and DS₃₅), sequentially precipitated from adult skin with 18%, 28% and 35% ethanol, were analyzed at varying ages. At age 75 years, loss of infrared bands in the 1650-1600 cm⁻¹ region, at 1380 cm⁻¹ and 1320 cm⁻¹ and appearance of a band at 1560 cm⁻¹ were characteristic of hyaluronic acid and DS₃₅,·moreover, in DS₂₈ and DS₃₅ the intensities of the bands at 840 cm⁻¹ and 860 cm⁻ were, respectively, decreased and increased. A low intensity band in the 805-785 cm⁻¹ region was observed in the spectra of DS₁₈ (19–35 years), DS₂₈ (70–80 years) and DS₃₅ (all ages). It intensified in DS₂₈ of the 80-years-olds. In the 75±5-year-old group. ninhydrin-positive material of hyaluronic acid and DS₃₅ increased, while reducing GlcNAc of hyaluronic acid decreased. The data demonstrated hyaluronic acid and DS₃₅ deacetylation and suggested a decrease of equatorial sulfates with infrared band at 840 cm⁻¹ and an incrase of axial sulfates with band at 860 cm⁻¹ in DS₂₈ and DS₃₅ of the 75±5-yearl-old set. Equatorial sulfates with band in the 805±785 cm⁻¹ region apparently decreased in DS₁₈ after 35 years and increased in DS₂₈ of the oldest group.