Radiation-induced apoptosis: a new approach using infrared microspectroscopy

PURPOSE: to characterize radiation-induced apoptosis in human cells using Fourier transform infrared microspectroscopy (FT-IRM) as a new analytical tool. MATERIAL AND METHODS: Normal human circulating lymphocytes were given a gamma ray dose of 6 Gy, or treated with t-butyl hydroperoxide (t-BuOH). HaCaT keratinocytes were given a dose of 20 Gy. Cells were deposited on ZnS windows for infrared spectral acquisition 2 days and 2 h after irradiation and 2 h after t-BuOH treatment. Apoptosis was simultaneously assessed by flow cytometry analysis of cells displaying annexin-V-positive staining. RESULTS: The flow cytometry study showed that about 90% of sham and irradiated cells were annexin-V negative 2 h after irradiation. Two days after irradiation, 68% of lymphocytes and 76% of HaCaT cells were apoptotic, as well as 43% of lymphocytes treated with t-BuOH. In infrared spectra of these apoptotic cells, qualitative and quantitative changes were observed. In the 960-1245 and 1690-1720 cm-1 ranges, mainly attributed to nucleic acids, changes corresponding to conformational changes in DNA were associated with a decrease in the amount of detectable DNA. Conformational changes were also observed in secondary protein structure, in particular an increase in the amount of beta structures. These DNA and protein changes were associated with an increase in the detectable amount of lipids in apoptotic HaCaT cells only. Two hours after irradiation, depending on the dose and (or) the cell type, qualitative and quantitative changes were observed in the IR spectra in the amide I and amide II bands, mainly attributed to proteins. These changes were associated with a significant decrease in the 1700-1750 cm-1 range, mainly attributed to the -C=O ester groups of DNA and phospholipids, in the irradiated HaCaT cells only. CONCLUSION: Our results are in agreement with biochemical published data on radiation-induced apoptosis, and show that DNA is the first cellular target of radiation-induced apoptosis, which, however, also requires conformational changes and synthesis of cell proteins. They also demonstrate that FT-IRM may be useful for assessing the early radiation damage at the molecular level in human cells.     

In situ examination of the time-course for secondary mineralization of Haversian bone using synchrotron Fourier transform infrared microspectroscopy.

At the tissue level it is well established that the rate of remodeling is related to the degree of mineralization. However, it is unknown how long it takes for an individual bone structural unit (BSU) to become fully mineralized during secondary mineralization. Using synchrotron Fourier transform infrared microspectroscopy (FTIRM) we examined the time required for newly formed bone matrix to reach a physiological mineralization limit. Twenty-six, four-month old female New Zealand white rabbits were administered up to four different fluorochrome labels at specific time points to evaluate the chemical composition of labeled osteons from the tibial diaphysis that had mineralized for 1, 8, 18, 35, 70, 105, 140, 175, 210, 245, 280, 315, 350, and 385 days. Interstitial bone from 505 day old rabbits was used as a reference value for the physiological limit to which bone mineralizes. Using synchrotron FTIRM, area integrations were carried out on protein (Amide I: 1688-1623 cm(-1)), carbonate (v(2)CO(3)(2-): 905-825 cm(-1)), and phosphate (v(4)PO(4)(3-): 650-500 cm(-1)) IR bands. IR spectral data are presented as ratios of phosphate/protein (overall matrix mineralization) and carbonate/protein. The rate of mineralization of osteonal bone proceeded rapidly between day 1 and 18, reaching 67% of interstitial bone levels. This was followed by a slower, more progressive accumulation of mineral up to day 350. By 350 days the rate of increase plateaued. The ratio of carbonate/protein also increased rapidly during the first 18 days, reaching 73% of interstitial bone levels. The ratio of carbonate/protein plateaued by day 315, reaching levels not significantly different to interstitial bone levels. In conclusion, our data demonstrate that bone accumulates mineral rapidly during the first 18 days (primary mineralization), followed by a more gradual increase in the accumulation of mineral (secondary mineralization) which we found to be completed in 350 days.     

Imaging of colorectal adenocarcinoma using FT-IR microspectroscopy and cluster analysis

In this paper, three different clustering algorithms were applied to assemble infrared (IR) spectral maps from IR microspectra of tissues. Using spectra from a colorectal adenocarcinoma section, we show how IR images can be assembled by agglomerative hierarchical (AH) clustering (Ward's technique), fuzzy C-means (FCM) clustering, and k-means (KM) clustering. We discuss practical problems of IR imaging on tissues such as the influence of spectral quality and data pretreatment on image quality. Furthermore, the applicability of cluster algorithms to the spatially resolved microspectroscopic data and the degree of correlation between distinct cluster images and histopathology are compared. The use of any of the clustering algorithms dramatically increased the information content of the IR images, as compared to univariate methods of IR imaging (functional group mapping). Among the cluster imaging methods, AH clustering (Ward's algorithm) proved to be the best method in terms of tissue structure differentiation.     

Determination of protein secondary structure using factor analysis of infrared spectra

A method is presented for determining the secondary structural composition of a protein in aqueous solution from its infrared spectrum. A factor analysis approach is used to analyze the infrared spectra of 18 proteins whose crystal structures are known from X-ray studies. Factor analysis followed by multiple linear regression identifies those eigenspectra that correlate with the variation in properties described by the calibration set. The properties of interest in this study are % alpha-helix, % beta-sheet, and % turns. In the analysis of an unknown, the factor loadings required to reproduce its spectrum are substituted in the regression equation for each property to predict its secondary structural composition. The accuracy of the method was determined by removing each standard, in turn, from the calibration set and using a calibration set generated from the remainder to predict its composition. By this method we obtain standard errors of prediction of 3.9% for alpha-helix, 8.3% for beta-sheet, and 6.6% for turns. The method may also be applied to the spectra of proteins in 2H2O. The method has important advantages over those currently in use for the quantitative analysis of the infrared spectra of proteins. Manipulation of the spectrum is kept to a minimum, no curve-fitting is necessary, and the several amide I band components need not be assigned.     

Ultrasound-assisted extraction of flaxseed oil using immobilized enzymes

An aqueous enzymatic process assisted by ultrasound extraction (AEP-UE) was applied to the extraction of oil from flaxseed (Linum usitatissimum L.). The highest oil recovery of 68.1% was obtained when ground flaxseed was incubated with 130 U/g of cellulase, pectinase, and hemicellulase for 12 h, at 45 °C and pH 5.0. The IC₅₀ values of oil obtained by AEP-UE and organic solvent extraction (OSE), as measured by DPPH scavenging activity essay, were 2.27 mg/mL and 3.31 mg/mL. The AEP-UE-derived oil had a 1.5% higher content of unsaturated fatty acids than the OSE-derived oil. AEP-UE is therefore a promising environmentally friendly method for large-scale preparation of flaxseed oil.     

Identifying two ancient enzymes in Archaea using predicted secondary structure alignment.

It is now possible to compare life forms at high levels of detail and completeness due to the increasing availability of whole genomes from all three domains. However, exploration of interesting hypotheses requires the ability to recognize a correspondence between proteins that may since have diverged beyond the threshold of detection by sequence-based methods. Since protein structure is far better conserved than protein sequence, structural information can enhance detection sensitivity, and this is the basis for the field of structural genomics. Demonstrating the effectiveness of this approach, we identify two important but previously elusive Archaeal enzymes: a homolog of dihydropteroate synthase and a thymidylate synthase. The former is especially noteworthy in that no Archaeal homolog of a bacterial folate biosynthetic enzyme has been found to date. Experimental confirmation of the deduced activity of both enzymes is described. Identification of two different proteins was attempted deliberately to help allay concern that predictive success is merely a lucky accident.     

Examination of bone chemical composition in osteoporosis using fluorescence-assisted synchrotron infrared microspectroscopy.

Although it is clear that osteoporosis is associated with a reduction in bone mass and a fragile skeleton, it is not understood whether the chemical composition of osteoporotic bone is different from normal bone. In this study, cynomolgus monkeys (Macaca fascicularis) were administered fluorochrome labels at one and two years after ovariectomy (Ovx) or Sham ovariectomy (intact), that were taken up into newly remodeled bone. Using fluorescence-assisted synchrotron infrared microspectroscopy, the chemical composition of bone from intact versus Ovx monkeys has been compared. Results from overall composition distributions (labeled + non-labeled bone) reveal similar carbonate/protein and phosphate/protein ratios, but increased acid phosphate content and different collagen structure in the Ovx animals. Analysis of the fluorochrome-labeled bone indicates similar degrees of mineralization in bone remodeled after one year, but decreased mineralization in Ovx bone remodeled two years after surgery. Thus, bone from monkeys with osteoporosis can be characterized as having abnormal collagen structure and reduced rates of mineralization. Coupled with factors such as trabecular architecture and bone shape and size, these ultrastructural factors may play a contributing role in the increased bone fragility in osteoporosis.     

Quantitation of secondary structure in ATR infrared spectroscopy

Polarized attenuated total reflection infrared spectroscopy of aligned membranes provides essential information on the secondary structure content and orientation of the associated membrane proteins. Quantitation of the relative content of different secondary structures, however, requires allowance for geometric relations of the electric field components (E(x), E(y), E(z)) of the evanescent wave, and of the components of the infrared transition moments, in combining absorbances (A() and A( perpendicular)) measured with radiation polarized parallel with and perpendicular to, respectively, the plane of incidence. This has hitherto not been done. The appropriate combination for exact evaluation of relative integrated absorbances is A() + (2E(z)(2)/E(y)(2) - E(x)(2)/E(y)(2))A( perpendicular), where z is the axis of ordering that is normal to the membrane plane, and the x-axis lies in the membrane plane within the plane of incidence. This combination can take values in the range approximately from A() - 0.4A( perpendicular) to A() + 2.7A( perpendicular), depending on experimental conditions and the attenuated total reflection crystal used. With unpolarized radiation, this correction is not possible. Similar considerations apply to the dichroic ratios of multicomponent bands, which are also treated.     

Mapping of nutrient-induced biochemical changes in living algal cells using synchrotron infrared microspectroscopy

High quality Fourier transform infrared (FTIR) spectra were acquired from living Micrasterias hardyi cells maintained in an IR transparent flow-through cell using a FTIR microscope coupled to a synchrotron light source. Spectral maps of living, nutrient-replete cells showed band intensities consistent with the known location of the nucleus and the chloroplasts. These were very similar to maps acquired from fixed, air-dried cells. Bands due to lipids were lowest in absorbance in the region of the nucleus and highest in the chloroplast region and this trend was reversed for the absorbance of bands attributed to protein. Spectra acquired in 10 microm steps across living phosphorus-starved (P-starved) cells, repeated approximately every 30 min, were consistent over time, and bands correlated well with the known position of the nucleus and the observed chloroplasts, corroborating the observations with replete cells. Experiments in which missing nutrients were re-supplied to starved cells showed that cells could be maintained in a functional state in the flow-through cell for up to one day. Nitrogen-starved cells re-supplied with N showed an increase in lipid in all positions measured across the cell over a 23 h period of re-supply, with the largest increases occurring in positions where the chloroplasts were observed. Re-supply of phosphorus to P-starved cells produced no changes in bands attributable to lipid or protein. Due to their thin cell body ( approximately 12 microm) and large diameter ( approximately 300 microm) Micrasterias sp. make an ideal spectroscopic model to study nutrient kinetics in algal cells.     

Effect of the structure of polymeric materials on the properties of immobilized enzymes

The relationship between the structure of triacetate cellulose fibres and films and properties of enzymes entrapped in these materials was investigated. Trypsin and penicillin amidase were entrapped in triacetate cellulose films and fibres during their formation. The effect of permeability of the films on the catalytic properties of entrapped trypsin was studied. The porous structure of triacetate cellulose fibres with entrapped penicillin amidase was studied, the fibres being produced by different methods. An increase of porosity and the specific surface of the fibre-biocatalyst reduced the Km value and the energy of activation of the hydrolytic decomposing of benzyl penicillin but increased the Vmax value.     

Improving the prediction of secondary structure of 'TIM-barrel' enzymes.

The information contained in aligned sets of homologous protein sequences should improve the score of secondary structure prediction. Seven different enzymes having the (beta/alpha)8 or TIM-barrel fold were used to optimize the prediction with regard to this class of enzymes. The alpha-helix, beta-strand and loop propensities of the Garnier-Osguthorpe-Robson method were averaged at aligned residue positions, leading to a significant improvement over the average score obtained from single sequences. The increased accuracy correlates with the average sequence variability of the aligned set. Further improvements were obtained by using the following averaged properties as weights for the averaged state propensities: amphipathic moment and alpha-helix; hydropathy and beta-strand; chain flexibility and loop. The clustering of conserved residues at the C-terminal ends of the beta-strands was used as an additional positive weight for beta-strand propensity and increased the prediction of otherwise unpredicted beta-strands decisively. The automatic weighted prediction method identifies greater than 95% of the secondary structure elements of the set of seven TIM-barrel enzymes.     

Protein analysis using enzymes immobilized to paramagnetic beads.

A new method combining protein chemistry with enzymes immobilized to paramagnetic beads is presented. The immobilized enzymes can substitute for regular enzymes in a number of protein chemistry protocols, resulting in faster reaction times, less sample contamination, and improved interfacing to modern procedures, like mass spectrometry. Trypsin was used as a model enzyme to test the amount of protein coupled to glass beads and the degree of autodigestion when analyzed by MALDI-MS and HPLC. Immobilization of trypsin resulted in digestions comparable with standard solution digestions using fetuin as a model substrate. Furthermore, fetuin was used to test the stability of the enzyme-coated beads. No apparent loss of enzyme activity was observed after 10 times reuse of trypsin-coated beads. Immobilization of exo- and endoglycosidases to paramagnetic beads resulted in high sensitivity, faster sequential glycosidase digestion of glycopeptides, and reduced sample contamination. All digestions could be performed in less than 24 h, when a tryptic glycopeptide from human lung proteinosis surfactant protein A was used as model compound.     

Sunflower oil transesterification with methanol using immobilized lipase enzymes

Bioprocess and Biosystems Engineering - The transesterification of sunflower oil with methanol, using immobilized lipase enzymes as catalysts, was studied. The process was carried out in a...     

Coated-wall microreactor for continuous biocatalytic transformations using immobilized enzymes

Microstructured flow reactors are emerging tools for biocatalytic process development. A compelling design is that of the coated-wall reactor where enzyme is present as a surface layer attached to microchannel walls. However, preparation of a highly active wall biocatalyst remains a problem. Here, a stainless steel microreactor was developed where covalent immobilization of the enzyme in multiple linear flow channels of the reaction plate was supported by a macroporous wash-coat layer of gamma-aluminum oxide. Using surface functionalization with aminopropyl triethoxysilane followed by activation with glutardialdehyde, the thermophilic beta-glycosidase CelB from Pyrococcus furiosus was bound with retention of half of the specific activity of the free enzyme (800 U/mg), yielding a high catalyst loading of about 500 U/mL. This microreactor was employed for the continuous hydrolysis of lactose (100 mM) at 80 degrees C, providing a space-time yield of 500 mg glucose/(mL h) at a stable conversion of > or =70%. The immobilized enzyme displayed a half-life of 15 days under the operational conditions. Due to the absence of hydrophobic solute-material interactions, which limit the scope of microstructures fabricated from poly(dimethylsiloxane) for biocatalytic applications, the new microreactor was fully compatible with the alternate enzyme substrate 2-nitro-phenyl-beta-D-galactoside and the 2-nitro-phenol product resulting from its hydrolysis catalyzed by CelB.     

Assessment of metabolic modulation in free-living versus endosymbiotic Symbiodinium using synchrotron radiation-based infrared microspectroscopy

The endosymbiotic relationship between coral hosts and dinoflagellates of the genus Symbiodinium is critical for the growth and productivity of coral reef ecosystems. Here, synchrotron radiation-based infrared microspectroscopy was applied to examine metabolite concentration differences between endosymbiotic (within the anemone Aiptasia pulchella) and free-living Symbiodinium over the light-dark cycle. Significant differences in levels of lipids, nitrogenous compounds, polysaccharides and putative cell wall components were documented. Compared with free-living Symbiodinium, total lipids, unsaturated lipids and polysaccharides were relatively enriched in endosymbiotic Symbiodinium during both light and dark photoperiods. Concentrations of cell wall-related metabolites did not vary temporally in endosymbiotic samples; in contrast, the concentrations of these metabolites increased dramatically during the dark photoperiod in free-living samples, possibly reflecting rhythmic cell-wall synthesis related to light-driven cell proliferation. The level of nitrogenous compounds in endosymbiotic cells did not vary greatly across the light-dark cycle and in general was significantly lower than that observed in free-living samples collected during the light. Collectively, these data suggest that nitrogen limitation is a factor that the host cell exploits to induce the biosynthesis of lipids and polysaccharides in endosymbiotic Symbiodinium.     

Quantitation of glycerophosphorylcholine by flow injection analysis using immobilized enzymes

A method for quantitating glycerophosphorylcholine by flow injection analysis is reported in the present paper. Glycerophosphorylcholine phosphodiesterase and choline oxidase, immobilized on controlled porosity glass beads, are packed in a small reactor inserted in a flow injection manifold. When samples containing glycerophosphorylcholine are injected, glycerophosphorylcholine is hydrolyzed into choline and sn-glycerol-3-phosphate. The free choline produced in this reaction is oxidized to betain and hydrogen peroxide. Hydrogen peroxide is detected amperometrically.Quantitation of glycerophosphorylcholine in samples containing choline and phosphorylcholine is obtained inserting ahead of the reactor a small column packed with a mixed bed ion exchange resin. The time needed for each determination does not exceed one minute.The present method, applied to quantitate glycerophosphorylcholine in samples of seminal plasma, gave results comparable with those obtained using the standard enzymatic- spectrophotometric procedure.An alternative procedure, making use of co-immobilized glycerophosphorylcholine phosphodiesterase and glycerol-3-phosphate oxidase for quantitating glycerophosphorylcholine, glycerophosphorylethanolamine and glycerophosphorylserine is also described.Abbreviations GPC sn-glycerol-3-phosphorylcholine - GPE sn-glycerol-3-phosphorylethanolamine - GPS sn-glycerol-3-phosphorylserine - GPA sn-glycerol-3-phosphoric acid - PDE glycerophosphorylcholine-phosphodiesterase - GPA-Ox glycerophosphate oxidase - Cho-Ox choline oxidase     

Fourier transform infrared analysis of bacteriorhodopsin secondary structure.

Fourier transform infrared spectroscopy at a resolution of 1 cm-1 has been used to study the conformation of dark-adapted bacteriorhodopsin in the native purple membrane, in H2O and D2O suspensions. A detailed analysis of the amide I bands was made using derivative and deconvolution techniques. Curve-fitting results of four independent experiments indicate, after estimation of the methodological errors, that native bacteriorhodopsin contains 52-73% alpha-helices, 13-19% reverse turns, 11-16% beta-sheets, and 3-7% unordered segments. Our analysis has enabled the identification of several components corresponding to alpha-helices, beta-sheets, and reverse turns. Besides the alpha I- and alpha II-helices (peaking at 1658 and 1665 cm-1), we propose that two more infrared bands arise from alpha-helical structures: one at 1650 cm-1 from alpha I and another one at 1642 cm-1 in H2O suspension, which could originate from type III beta-turns (i.e., one turn of 3(10)-helix). The relatively high content of reverse turns suggests the presence of one reverse turn per loop, plus another one in the C-terminal segment. On the other hand, several reasons argue that the calculated mean beta-sheet content of around 14% should be decreased somewhat. These beta-sheets could be located in the noncytoplasmatic links of the bacteriorhodopsin molecule.