bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of favourable sites for spin labelling of proteins
Authors: Polyhach Yevhen , Jeschke Gunnar
Published: April 2012

Electron paramagnetic resonance studies on diamagnetic proteins are based on site-directed spin labelling and require relatively much effort for engineering cystein point mutations as well as expressing and labelling the protein. Therefore, it is advantageous to predict those sites and pairs of sites that can provide the most precise and most reliable information on accessibility and distances. Systematic site scans based on a rotamer library approach for spin label side groups allow for such predictions. Figures of merit are defined that can be used to rank sites according to their potential suitability in studies of structure and structural changes. Such site scans can still provide useful results if only a backbone model and the amino acid sequence of the protein are known.
Fourier-Transform IR spectroscopic investigations of Cobalt(II)–dextran complexes by using D2O isotopic exchange
Authors: Mitic Žarko , Cakic Milorad , Nikolic Goran
Published: April 2012

Co(II) ion complexes with reduced low-molar dextran (RLMD) derivativesMw= 5000 − 6000 g/mol, their FTIR spectroscopic characterization, as well as the spectra-structure correlation was investigated in this work. The samples of Co(II) ion complexes with RLMD were deuterated (D2O, Merck) for 2 h, at room temperature, in vacuum. FTIR spectra as an average of 40 scans were recorded at room temperature in the range 4000 – 400 cm−1. FTIR investigation of Co(II)–RLMD complexes by D2O isotopic exchange proved to be a very sensitive method for determining OH group coordination and is related to the hydrogen bond strength. The results of our investigation point to the dextran and their complexes with Co(II) ion are crystalline hydrate molecules. The correlation of physicochemical, spectrophotometric and spectroscopic investigations of these complexes, coordination chemistry of Co(II) ion and the structure of an exopolysaccharide chain are proposed different model structures of the synthesized Co(II) complexes.
FTIR imaging and ATR-FT-Far-IR synchrotron spectroscopy of pig ear skin
Authors: Greve Tanja M. , Andersen Kristine B. , Nielsen Ole F. , Engdahl Anders
Published: April 2012

FTIR imaging was performed on pig ear skin samples cryo-sectioned perpendicular to the skin surface. The OH-stretch region revealed the distribution of water; the amide II band gave the protein distribution; the C═O stretch and C–H stretch regions showed the variation in lipids. Water and proteins were similarly distributed. Triglycerides were predominantly found in the deeper skin layers whereas free fatty acids and ceramides were more dominant in the upper layers. ATR-FT-Far-IR spectroscopy with synchrotron radiation was used on full thickness pig ear skin biopsies. The Far-IR spectra showed bands in the region from 100–150 cm–1due to hydrogen bonded proteins and a band around 180 cm–1arising from “free” water.
Different solid sample preparation methods affecting the spectral similarity of salmon calcitonin
Authors: Lin Shan-Yang , Lin Chih-Cheng , Lee Ting-Huei
Published: April 2012

Salmon calcitonin (sCT) was selected as a model protein drug for investigating its structural similarity in the solid state by four sample preparation methods, such as tape, smeared, CaF2and film methods. The conformational changes of sCT in the solid state were estimated by using a second-derivative Fourier transform infrared (FT-IR) microspectroscopy. The tape method was acted as a standard reference.

The value of correlation coefficient (r) for smeared method was higher than that of other method, indicating that a novel technique by smearing sCT powder on the surface of KBr pellet was the best optimal sample preparation method.
FTIR spectroscopy for detection and identification of fungal phytopathogenes
Authors: Salman A. , Tsror L. , Pomerantz A. , Moreh R. , Mordechai S. , Huleihel M.
Published: April 2012

Soil-borne fungi are considered as major pathogens to many plants and can cause a severe economic damage. Early detection and identification of these pathogens is very important and might be critical for their control. The available methods for identification of fungi like molecular biology, serological tests and PCRs tests (polymerase chain reaction) are time consuming and not always very specific. Fourier-transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy, is considered to be a comprehensive and sensitive method for detection of molecular changes in intact cells.

In the present study we used FTIR–ATR as a sensitive and effective assay for the detection and discrimination between different fungal genera. Our results showed significant spectral differences between the various examined fungi genera. These results proved the possibility of discrimination between these fungi on the genus level.
Accessing the distance range of interest in biomolecules: Site-directed spin labeling and DEER spectroscopy
Authors: Böhme Sabine , Steinhoff Heinz-Jürgen , Klare Johann P.
Published: April 2012

Investigations on the structure and function of biomolecules often depend on the availability of topological information to build up structural models or to characterize conformational changes during function. Electron paramagnetic resonance (EPR) spectroscopy in combination with site–directed spin labeling (SDSL) allow to determine intra- and intermolecular distances in the range from 4–70 Å, covering the range of interest for biomolecules. The approach does not require crystalline samples and is well suited also for molecules exhibiting intrinsic flexibility. This article is intended to give an overview on pulsed EPR in conjunction with SDSL to study protein interactions as well as conformational changes, exemplified on the tRNA modifying enzyme MnmE.
Interaction of alcohol with phospholipid membrane: NMR and XRD investigations on DPPC–hexanol system
Authors: Wanderlingh U. , D'Angelo G. , Nibali V. Conti , Crupi C. , Rifici S. , Corsaro C. , Sabatino G.
Published: April 2012

The investigations of the interaction between phospholipid bilayer and short-chain alcohols are relevant for the potential of lipid bilayer membranes to serve as model systems for studies of various biological processes including permeability of the plasma membrane and molecular mechanisms of anesthesia. Because the hydrophobic portion of an alcohol favorably interacts with lipid hydrocarbon chains, the polar hydroxyl group remains free to form hydrogen bonds with polar lipid atoms that are located near the water/lipid interface. Experiments on phospholipid membranes have shown that alcohols can induce an interdigitated phase and at high concentration even promote the assembly of some lipids into non-bilayer structures within the membrane interior. In this paper we have investigated the DPPC:hexanol system at high alcohol concentration (two molecules per phospholipid) by means of calorimetric, Nuclear Magnetic Resonance, X-ray diffraction and density measurements. We have found that the presence of a high alcohol concentration shifts the membrane transition temperature to lower values, and has a disordering effect on the phospholipid acyl chains in the gel phase. The bilayer spacing and the area of polar head have been also derived for the liquid phase.
A validated direct spectrofluorimetric method for quantification of mirtazapine in human whole blood
Authors: Saini Balraj , Kaushal Manjula , Bansal Gulshan
Published: April 2012

A spectrofluorimetric method for estimation of mirtazapine in human whole blood was developed and validated. The recovery efficiency of the processing method was 95–98%. The analytical method was linear over drug concentration of 10–200 ng/ml. The limit of quantification was 10 ng/ml. The method was precise with %RSD for intra-day and inter-day precision being <3.0 and 1.5, respectively. Excellent recoveries (97.87–99.69%) were achieved during accuracy studies. The method was robust to small changes in processing method and instrumental parameters. The present method can be employed for direct fluorimetric determination of mirtazapine in human whole blood during clinical studies.
From discrete multi-exponential model to lifetime distribution model and power law fluorescence decay function
Authors: Kierdaszuk Borys
Published: April 2012

Experimental and theoretical studies of the fluorescence intensity decays in biomolecular systems showed that under constraints of typical experiment fluorescence lifetime distribution is given by gamma function, which led to a power-like decay function. The latter well fits complex (heterogeneous) as well as simple mono-exponential decays. Fluorescence decay kinetics is described by mean value of lifetime distribution characterizing the average rate of the excited-state decay, and one new parameter of heterogeneity (1 < q < 3/2) describing the relative variance of distribution, and objectively reflecting physical heterogeneity of the system. In the classical limit, when q → 1, the gamma distribution becomes the Dirac delta function, and decay function converges from power-like form to the single-exponential form. Numerous examples illustrate successful applications of this model to rational analysis of complex fluorescence decays of biomacromolecules, e.g., complexes ofE. colipurine nucleoside phosphorylase (PNP-I) with formycin A (FA, inhibitor) and orthophosphate (Pi, cosubstrate), which led to identification of the mechanism of deactivation of excited state and the N(2)H tautomeric form of FA selectively bound by PNP-I. The latter is of great importance for the studies of the mechanism of protein (enzyme) action as well as for more rational drug design.
Interaction between linker histone H1 and non-histone chromatin protein HMGB1
Authors: Fonin Alexander V. , Stepanenko Olga V. , Kuznetsova Irina M. , Turoverov Konstantin K. , Kostyleva Elena I. , Vorobyev Vladimir I.
Published: April 2012

The possibility of interaction between linker histone H1 and non-histone chromatin protein HMGB1 was studied by intrinsic UV-fluorescence, far and near-UV CD and light scattering. The obtained data allow us to assume that the increase of histone H1 content in the HMGB1 solutions in a low ionic strength is accompanied by the destruction of HMGB1 associates. The interaction between proteins causes the increase of ordered regions in the protein molecules and the minor changes in their tertiary structure.
Simulation of IR, Raman and VCD amide I band profiles of self-assembled peptides
Authors: Schweitzer-Stenner Reinhard , Measey Thomas J.
Published: April 2012

Vibrational spectroscopy is a suitable and convenient tool to probe the self-assembly of peptides, a biomedically and biotechnologically relevant process. Theoretical efforts to quantitatively analyze vibrational spectra of peptide aggregates have thus far focused on exploring the IR and to a lesser extent the vibrational circular dichroism (VCD) spectra of rather small sized planar or nearly planarβ-sheet structure. The current study utilizes an algorithm based on an excitonic coupling model with experimentally or computationally determined parameters to simulate the amide I band profiles of the IR, isotropic Raman, anisotropic Raman and VCD spectra of two- and three-dimensionalβ-sheet structures. In agreement with earlier calculations we found that the splitting between the two prominent IR bands of an antiparallelβ-sheet increases with increasing number of strands until a saturation is reached at approximately eight strands. The dominant isotropic and anisotropic Raman bands of amide I are located between the two IR bands and downshift only slightly with increasing sheet length. The VCD signal is rather weak. We also investigated the influence of sheet stacking on amide I by calculating the respective IR, Raman and VCD profiles for two in-register, facially stackedβ-sheets with seven strands per sheet for an antiparallel arrangement of the sheets and six strands per sheet for a parallel arrangement. We found that stacking produces additional bands in the IR and Raman spectrum, in line with the reduced symmetry of the ideal unit cell of theβ-sheet. In addition, a more pronounced VCD signal is detected. A comparison with experimental IR, Raman and VCD spectra of gelated (AAKA)4reveals a good qualitative agreement between experimental and simulated amide I band profiles.
Cytochrome C as a benchmark system for a two-layer gold surface with improved surface-enhancement for spectro-electrochemistry
Authors: Nowak Christoph , Schach Denise , Grosserüschkamp Marc , Knoll Wolfgang , Naumann Renate L.C.
Published: April 2012

A two-layer gold surface is developed for use with electrochemistry followed by surface-enhanced infrared absorption spectroscopy (SEIRAS) consisting of a conducting underlayer onto which Au nanoparticles (AuNPs) are grown by self-catalyzed electroless deposition. AuNPs are grown on protruding substructures of the 25 nm thin underlayer. The enhancement factor of the two-layer gold surface is controlled by the growth conditions. Cytochrome c adsorbed to a self-assembled monolayer of mercaptoethanol is used as a benchmark system for the investigation of complex heme proteins from the respiratory chain such as cytochrome c oxidase and the bc1 complex. Under optimum conditions the absorbance of the amide I band of cytochrome c is increased by a factor of 5 vs. classical SEIRAS surface. Reversible reduction/oxidation of cytochrome c on the two-layer gold surface is shown to take place by cyclic voltammetry.
Analysis of spectroscopic diffuse reflectance plots for different skin conditions
Authors: Prince Shanthi , Malarvizhi S.
Published: April 2012

Optical means of characterizing tissues have gained importance due to its noninvasive nature. Spectral characteristics of the components provide useful information to identify the components, because different chromophores have different spectroscopic responses to electromagnetic waves of a certain energy band. The purpose of this study is to determine whether visible/near-infrared diffuse reflectance spectroscopy can be used to non-invasively characterize skin diseasesin vivo.

An optical fiber spectrometer is set up for obtaining diffuse reflectance spectra. The method involves exposure of skin surface to white light produced by an incandescent source. The back scattered photons emerging from various layers of tissue are detected by spectrometer resulting in diffuse reflectance spectra.

For the present study different skin conditions like – warts, vitiligo, thrombus (due to injury) and angioma are chosen. The spectral data obtained from the scan are plotted and compared. More or less, the shapes of the spectral curves for various skin conditions resemble. In order to characterize and differentiate different diseased state spectral analysis based on Ratio analysis, Student'st-tests and difference plot are carried out.

Based on the analysis the relative spectral intensity changes are quantified and the spectral shape changes are enhanced and more easily visualized on the spectral curves, thus assisting in differentiating the normal tissue from the one affected by disease.
Gastric ATPase phosphorylation/dephosphorylation monitored by new FTIR-based BIA–ATR biosensors
Authors: Goldsztein A. , Babar S. , Voué M. , De Coninck J. , Conti J. , Marchand-Brynaert J. , Devouge S. , Homblé F. , Goormaghtigh E.
Published: April 2012

Biosensors are composite devices suitable for the investigation of receptor–ligand interactions. In this paper we present the specific application to a membrane embedded protein of a new sensor device, so-called BIA–ATR, based on Attenuated Total Reflection–Fourier Transform Infrared (ATR–FTIR) spectroscopy. It consists in a functionalised ATR germanium crystal whose surface has been covalently modified to adsorb a biomembrane. Detection of the ligand–receptor interaction is achieved using FTIR spectroscopy. We report the specific detection of the phosphorylation/dephosphorylation of the H+/K+gastric ATPase. The H+, K+-ATPase is a particularly large protein entity. This glycosylated protein contains more than 1300 residues and is embedded in a lipid membrane. Yet we demonstrate that the BIA–ATR sensor is capable of monitoring the binding of a single phosphate on such a large protein entity. Furthermore, we also demonstrate the potential of the approach to monitor the kinetics of binding and dissociation of the ligand.
Translocation process of structured polypeptides across nanopores
Authors: Cecconi Fabio , Marconi Umberto Marini Bettolo , Vulpiani Angelo
Published: April 2012

The progress of molecular manipulation technology has made it possible to conduct controlled experiments on translocation of polynucleotide and polypeptide chains across alpha-Hemolysin channels and solid-state nanopores. To study the translocation process we combined Molecular Dynamics at coarse-grained level and appropriate drift-diffusion Smoluchowski equations as an integrated statistical physics approach. In particular, we performed simulations of the passage across a cylindrical nanopore of Ubiquitin described by a coarse-grained native-centric model to investigate the influence of protein structural properties on translocation mechanism. The kinetic characterization of the process is achieved by studying the statistics of blockage times, the mobility and translocation probability as a function of the pulling forceFacting in the pore. We find that the transport dynamics displays a thresholdFcdepending on a free-energy barrier that Ubiquitin overcomes to translocate. Our simulations show this barrier to be the result from competition of the unfolding energy and the entropy associated to the confinement effects of the pore.
Thermally Stimulated Depolarization Currents (TSDC): A sensitive technique for analyzing protein structure
Authors: Bedotti R. , Bridelli M. G. , Capelletti R. , Polverini E.
Published: April 2012

The water molecules surrounding proteins as a thin layer and those packaged in pockets and cavities shape and control their structure. Thermally Stimulated Depolarization Currents (TSDC) technique has been applied to investigate the hydration structure of six proteins with different structural motifs: pepsin,β-lactoglobulin,α-chymotrypsin, bovine serum albumin, human serum albumin and myoglobin, at very low hydration level (water vapor activity aw≈0.80) both in the native state and after treatment in trifluoroethanol/water mixture 80% (v/v). A combined approach based on the use of the TSDC technique, able to distinguish H2O dipoles belonging to the solvation shell in terms of their order degree and mobility, and of FTIR and CD spectroscopies has allowed us to reexamine the problem of conformational stability of macromolecules as a function of their hydration.
Primary events in the photodissociation of oxyhemoglobin
Authors: Yabushita Atsushi , Kobayashi Takayoshi
Published: April 2012

The growing number of data on heme proteins in the ultrafast time domain have revealed complicated photophysics of the heme that are sensitive both to the structure of the protein and to the ligand species. In this work, ultrafast time-resolved pump–probe in visible spectral range was performed using an ultrashort visible laser pulse. Broad spectral width of visible laser pulse enabled us to observe the pump–probe signal with a broadband range. A broadband multi-channel detector array coupled to a multi-channel lock-in amplifier was used to obtain the pump–probe signals at all of the probe frequencies simultaneously. In the simultaneous measurement at many probe wavelengths, we could obtain ultrafast spectral change after the photo-excitation of oxy-hemoglobin only with a short measurement time, avoiding laser damage on the sample. The time constant of the primary process was determined for the first time. Ultrafast spectral change observed in the early delay time region directly shows ultrafast photo-dissociation process of oxy-hemoglobin.
Raman spectroscopy of fingernails: A novel tool for evaluation of bone quality?
Authors: Cummins N. M. , Day J. C. C. , Wren A. , Carroll P. , Murphy N. , Jakeman P. M. , Towler M. R.
Published: April 2012

Raman data from human fingernails has been analysed to determine if a relationship exists between spectral features and bone quality. Previous work demonstrated a relationship between the manually determined intensity of the disulphide peak (Bone Quality Test; BQT) and osteoporotic fracture. A computer program is now described that automates the BQT determination for large sample-sets. In this study the ability of the automated BQT to discriminate between fractures and controls was compared to that of bone mineral density (BMD) and biomarkers of bone remodelling. Females aged 18–67 years participated in the study (n═ 159). Fingernails were analysed using Raman spectroscopy. Lumbar and Femoral BMD was measured by dual energy X-ray absorptiometry (DXA). Fasting venepuncture samples were analysed for osteocalcin and CTx (collagen C-telopeptides) by electrochemiluminescence. No correlation was found between the BQT and BMD or the biomarkers. The BQT and BMD were found to be equally accurate in identifying subjects with a history of fracture (p< 0.01) and both outperformed osteocalcin and CTx. It appears that keratin and collagen are related structural proteins that require disulphide bonding for stability. Therefore, these preliminary results suggest that Raman spectroscopy of keratin may have potential as a diagnostic tool for screening bone quality in large populations.
A study of [Au(ethylenediamine)Cl2]Cl interaction with L-methionine and DL-seleno-methionine by1H and13C NMR spectroscopy
Authors: Al-Maythalony Bassem A. , Wazeer Mohamed I. M. , Isab Anvarhusein A. , Ahmad Saeed
Published: April 2012

The interaction of [Au(en)Cl2]Cl with L-methionine (Met) and DL-seleno-methionine (Se-Met) was carried out in D2O solution at ∼pH 3.8.13C NMR spectra were interpreted by comparison with the spectra recorded after the reaction of Met or Se-Met with HAuCl4and also after oxidation by H2O2. Reactions of [Au(en)Cl2]Cl with Met and Se-Met were found to proceed through the exchange of chloride ligands from complex with Met or Se-Met. Gold(III) reduction takes place during the reaction andenligand was released from [Au(en)Cl2]Cl complex.
Comparison of molecular structure of alkali metal ortho substituted benzoates
Authors: Świsłocka R.
Published: April 2012

The influence of the amino-, nitro-, methoxy-, hydroxy- and chloro-substituents in the ortho position towards the carboxylic group as well as alkali metal on molecular structure of benzoates was estimated. Optimized geometrical structures were calculated by B3LYP/6-311++G** method. Experimental FT-IR, FT-Raman and NMR spectra of the title compounds were recorded and analyzed. Data of chemical shifts in1H and13C NMR as well as wavenumbers and intensities in IR and Raman spectra of studied benzoate derivatives were analyzed in comparison with benzoic acid and with alkali metal benzoates.
Laser Raman micro-spectroscopy of Proterozoic and Palaeozoic organic-walled microfossils (acritarchs and prasinophytes) from the Ghadamis Basin, Libya and Volta Basin, Ghana
Authors: Dhamelincourt Marie-Claire , Vecoli Marco , Mezzetti Alberto , Cesari Christian , Versteegh Gerard , Riboulleau Armelle
Published: April 2012

Laser Raman microspectroscopy was used as a microchemical analysis technique to characterize the wall chemistry of organic-walled microfossils (acritarchs and prasinophytes) extracted from Proterozoic (Tonian: ca. 900 Myr) and early Palaeozoic (Silurian: ca. 420 Myr) marine sediments in the Volta Basin of Ghana, and the Ghadamis Basin of Libya, respectively. Raman spectra of Proterozoic acritarchs show spectral features characteristic of kerogenous compounds at ~1350 and ~1600 cm−1, consistently with previously published reports. In addition, spectra from prasinophyte algae from the Silurian sample also show an interesting spectral feature at ~1707 cm−1indicative of carbonyl moieties.

Broadly speaking, shape and position of Raman bands appear to depend on the nature of the specimen considered, suggesting that laser micro-Raman analysis can potentially be used to establish phylogenetic relationships (high-rank taxonomy) among the main groups of pre-Cambrian to Palaeozoic palynomorphs.
Development of a quantitative and conformation-sensitive ATR-FTIR biosensor for Alzheimer's disease: The effect of deuteration on the detection of the Aβ peptide
Authors: Kleiren Emilie , Ruysschaert Jean-Marie , Goormaghtigh Erik , Raussens Vincent
Published: April 2012

Alzheimer's disease (AD) is the most common form of dementia worldwide and represents a growing socio-economical issue. To date, no reliable diagnosis can be obtained at an early-stage of the disease, though it is now recognized that the aggregation of the amyloid β (Aβ) peptide is responsible for the onset of the disease. Recent studies have shown that soluble amyloid oligomers present in the physiological fluids were the most neurotoxic species and correlated best with the first signs of cognitive decline, which makes them good biomarkers in the development of a diagnostic tool.

We describe here a new type of biosensor, based on attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, that would be able to specifically detect and quantify the presence of the different forms of the Aβ peptide in solution. The principle of the detection relies on the recognition of the peptides by specific antibodies that were previously grafted on the surface of an ATR element, consisting of a functionalized germanium crystal. We show that the BIA-ATR technology is able to detect the presence of Aβ if incubated in deuterated water and that this step is crucial in the development of our conformation-sensitive biosensor for AD.
Time-resolved EPR investigation of oxygen and temperature effects on synthetic eumelanin
Authors: Conti Fosca , Panzella Lucia , Napolitano Alessandra , d᾽Ischia Marco , Toffoletti Antonio
Published: April 2012

Synthetic eumelanin produced using 5,6-dihydroxyindole-2-carboxylic acid as precursor and H2O2/horseradish peroxidase as oxidative reagent, in form of dry powder, has been investigated under photoexcitation by TR-EPR spectroscopy. The formation of spin polarized radical pairs from triplet excited states of melanin has been observed both in absence and in presence of oxygen and has been followed as a function of the temperature in the range 140–290 K. The triplet mechanism explains the observed polarization pattern in net emission. In the presence of oxygen new radical pairs are formed by interaction of melanin with molecular oxygen.
Fluorescence study on the interaction of human serum albumin with loureirin B
Authors: Chen Xu , Ma Jia-Ming , Yong Ke-Lan , Lv Jing-Ci , Zhang Xia-Bing
Published: April 2012

The interaction between loureirin B (Lour B) and human serum albumin (HSA) was investigated by fluorescence and UV–vis absorption spectroscopy. Experimental results indicated that loureirin B had a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The fluorescence quenching data revealed that the quenching constants (KSV) 2.68×104, 3.30×104and 4.10×104l/mol at 300, 310 and 320 K, respectively. Based on the thermodynamic parameters obtained, the positive values of enthalpy change ΔH and entropy change ΔS suggested that hydrophobic forces played a major role in the interaction of Lour B with HSA. According to Förster theory of energy transfer, the distancerbetween HSA and Lour B was calculated to be 2.85 nm. Furthermore, the effect of Lour B on the conformation of HSA was analyzed by synchronous fluorescence and three-dimensional fluorescence spectra.
Monitoring of metabolism perturbation in prostate PC-3 cancer cells by sub-lethal concentrations of methotrexate
Authors: Derenne Allison , Gasper Régis , Goormaghtigh Erik
Published: April 2012

Infrared imaging was used to investigate the effect of sub-lethal concentration of methotrexate on prostate PC-3 cancer cells. Cells were exposed for 0, 24 and 48 h to 9 nM of methotrexate, the concentration that inhibits 50% of cell growth after 72 h. Sub-lethal concentrations of methotrexate induced a reproducible signature that can be measured by infrared spectroscopy. Student t-test revealed that the process occurs in at least two steps, the first one affecting the nucleic acid region of the spectrum and the second one, the protein region. Imaging of individual cells demonstrated that the recorded differences are not due to a specific subpopulation of cells but homogenously affects all the cells. Near perfect identification of treated cells could be obtained using a supervised classification.
Raman optical activity study of poly-L-proline chains of various lengths
Authors: Profant V. , Šafarík M. , Bour P. , Baumruk V.
Published: April 2012

Raman and Raman optical activity (ROA) spectra of several oligo- and poly-L-proline samples of various chain lengths were measured in a wide frequency range between 120 and 1800 cm−1and analysed with respect to the main peptide chain conformation. Specifically, formation of polyproline II (PPII) helical conformation was studied in dependence on the increasing chain lengthNof the (L-proline)Nsample. Due to high sensitivity of the ROA technique to the conformational stability and rigidity of peptide chain we were able to determine the characteristic spectral peaks associated with formation of stable PPII helical conformation in studied systems. The most relevant peaks are located at 405, 535 and 945 cm−1. Additionally, based on our data analysis, we were able to determine the minimal length of (L-proline)Nchain necessary for creation of the stable PPII conformation asN= 6.
ATR–FTIR, a new tool to analyze the oligomeric content of Aβ samples in the presence of apolipoprotein E isoforms
Authors: Cerf Emilie , Ruysschaert Jean-Marie , Goormaghtigh Erik , Raussens Vincent
Published: April 2012

Alzheimer̕s disease (AD) is a neurodegenerative disorder caused by the aggregation of the amyloid-beta peptide (Aβ), leading to amyloid plaques deposition in the brain. Although Aβaggregation pathway still remains unclear, recent studies point out the enhanced toxicity of oligomers compared to fibrils. The E4 isoform of apolipoprotein E (ApoE) is the major risk factor in AD as people carrying one ɛ4 allele have significantly higher chances to develop the disease. Nevertheless, this phenomenon is still poorly understood.

Our group has shown that attenuated total reflection Fourier-transform infrared spectroscopy (ATR–FTIR) could discriminate between Aβ42 oligomers and fibrils. Indeed, oligomers display anti-parallel β-sheet spectral components while fibrils are characterized by a parallelβ-sheet organization. Using those spectral features to analyze the oligomeric content of our samples, we studied the influence of ApoE on Aβ42 aggregation. Our experiments demonstrated that ApoE3 increased the amount of Aβ42 oligomers in the sample.

We can thus determine the proportion of Aβoligomers in the presence of another compound in the sample. We plan to use ATR–FTIR to assess the effects of the other isoforms of ApoE on Aβaggregation. Moreover, this could be extended to study the influence of other molecules or proteins on Aβaggregation.
Conformational analysis and vibrational spectroscopic investigation of L-alanyl-L-glutamine dipeptide
Authors: Kecel Serda , Ozel Aysen E. , Akyuz Sevim , Celik Sefa
Published: April 2012

In this study conformational behavior of anticancer chemotherapy dipeptide Ala-Gln and its dimers have been investigated by molecular mechanic and ab-initio calculations. The calculations on Ala-Gln dipeptide as a function of side chain torsion angles, enable us to determine their energetically preferred conformations. The relative positions of the side chain residues of the stable conformations of dipeptide were obtained, depending on the obtained conformational analysis results. The lowest energy conformation of the dipeptide has been determined by using the Ramachandran maps (Biopolymers6(1963), 1494;J. Mol. Biol.7(1963), 95) and compared with the quantum chemical ab-initio results. The geometry optimization, vibrational wavenumbers and intensity calculations of Ala-Gln dipeptide were carried out with theGaussian03program by using DFT with B3LYP functional and 6-31++G(d,p) basis set. The IR (4000–400 cm−1) and Raman spectra of the Ala-Gln dipeptide have been reported in solid phase, and compared with the theoretical vibrational data.
Pourous nanoparticles formation using a dendrimer template
Authors: Bonaccorsi L. , Lombardo D. , Longo A. , Proverbio E. , Calandra P.
Published: April 2012

We describe the synthesis of porous spherical nanoaggregates derived by the controlled growth of zeolite LTA on a poliamidoamine (Pamam) dendrimer acting as nano-template. The presence of a strong condensed cationic Na+charge all around the dendrimers, which is responsible for the intense electrostatic inter-particle interaction potential, stimulate the condensed growth of the zeolitic phase onto the dendrimer substrate. Moreover, the screening produced by the zeolite grown on the dendrimer surface promote the entanglement process between the primary units with the formation of large porous clusters. The main features of the self-assembly process has been characterised by means of different techniques such as Small Angle X-ray Scattering (SAXS), Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Energy Dispersive X-ray (EDX) microprobe spectroscopy. The finding of our results may open new perspectives in the synthesis of organic–inorganic nanostructured materials based on mesoporous frameworks with new characteristics and properties.
Non-invasive blood glucose measurement by near infrared spectroscopy: Machine drift, time drift and physiological effect
Authors: Lam Simon C. H. , Chung Joanne W. Y. , Fan K. L. , Wong Thomas K. S.
Published: April 2012

The aim of this paper is to evaluate development of the non-invasive blood glucose measurement of near infrared (NIR) spectroscopy. The results showed that NIR spectroscopy might obtain glucose concentration of up to 200% difference under a same environmental condition with two months apart due to time and machine drifts. These effects can restrict the development of the non-invasive blood glucose measurement. Partial least square (PLS) regression was used, which showed advantage over using simple absorbance for glucose concentration. Non-invasive blood glucose measurement of health subjects (non-diabetics) was also investigated. The results showed that R correlation coefficient of prediction (Rp) was 0.48 and root mean square of prediction (rmsep) was 1.34 mmol/l. The error was mainly due to the physiological effect of different subjects.
Denaturation of proteins with beta-barrel topology induced by guanidine hydrochloride
Authors: Stepanenko Olesya V. , Kuznetsova Irina M. , Verkhusha Vladislav V. , Staiano Maria , D'Auria Sabato , Turoverov Konstantin K.
Published: April 2012

The stability of the representatives of two protein classes withβ-barrel topology: porcine odorant-binding protein (OBP) and a number of fluorescent proteins (FPs), was studied. It was shown that both of them are significantly more stable than globular α-helical andα/βproteins. At the same time the value of energy barrier between native and unfolded state for FPs exceeds that for OBP. It was found that the small guanidine hydrochloride concentrations induce local structural disturbances in proteins: changes in microenvironment of tryptophan residue in the case of odorant-binding protein and decrease in chromophore non-planarity in the case of green fluorescent protein.
Quantitative analysis of perindopril erbumine in pharmaceutical preparations by spectrophotometry via ternary complex formation with Zn(II) and eosin and charge transfer complexation with iodine
Authors: Rahman Nafisur , Rahman Habibur
Published: April 2012

Two simple, sensitive and accurate spectrophotometric methods have been developed for the analysis of perindopril in pharmaceutical preparations. Method A is based on the formation of ternary complex between zinc(II), eosin and the perindopril, which is extractable with chloroform. The absorption spectrum exhibits a band peaking at 510 nm. Method B is based on the interaction of drug with iodine in dichloromethane resulting in the formation of charge transfer complex which absorbs maximally at 365 nm. Beer's law is obeyed in the concentration range 10–200 μg/ml and 10–180 μg/ml with molar absorptivity of 2.25×103and 3.71×103l/mol·cm for methods A and B, respectively. The detection limits for methods A and B are 0.49 and 0.90 μg/ml, respectively. The optimum experimental conditions for the proposed procedures are investigated. Statistical comparison of the results with the reference method shows excellent agreement and indicates no significant difference between the methods compared in terms of accuracy and precision.
Tissue classification in microscope imaging based on a discrete-band spectroscopy
Authors: Yoon Gilwon , Kim Hyejeong
Published: April 2012

Automatic classification of tissue types has a potential use in endoscopic or microscopic imaging. For this study, the microscope images from composite tissue samples were measured. Different shades of red meat such as beef and pork and bloodless tissues such as chicken breast and fat were chosen to provide with similar and contrasted colors. We applied a partial least squares discriminant analysis (PLS-DA) to classify the tissue type of the image pixels. With the RGB color images that are usually available in the hospital, we could classify beef, pork and chicken with an accuracy of only 85.7% and 80%, 60% and 11.4%, respectively. There was an apparent limitation in differentiating the tissue type due to the spectral overlapping of RGB colors. To increase the classification accuracy, band-pass filtered images were taken at the center frequencies of 414, 542, 655 and 832 nm without any spectral overlapping. Using these discrete-band spectral images, the classification accuracy reached to all 100% except for beef that was 96%. In capsule endoscopy where the amount of image data is prohibitively large, automatic detection of bleeding or cancerous region is of great interest and we believe that this method can be applicable in real time monitoring.
Automated diagnosis and treatment by lasers employing Raman spectroscopy and catheter with optical fibers
Authors: Lázaro João Carlos , de Paula Alderico Rodrigues , Moreira Leonardo Marmo , Lyon Juliana Pereira , Pacheco Marcos Tadeu T. , de Lima Carlos José
Published: April 2012

Raman spectroscopy is considered a very powerful tool for biochemical characterization, especially regarding biological samples. This technique allows the diagnosis of several diseases, such as cancer and atherosclerosis. In this context, the non invasive or minimally invasive character of the spectroscopic resources is an auspicious clinical advancement when compared with conventional procedures, which are associated to significant trauma and possible decrease in the quality of life of patients. Recently, the use of catheter with optical fibers associated to Raman spectroscopy has significantly minimized the invasive character of several clinical procedures. It is important to notice that this optical sensor already presents flexibility due to the employment of optical fibers to applications of lasers. Nowadays, this kind of device possesses autonomy of use and can be coupled to an optic fiber in order to permit the treatment with lasers. In this way, it is possible to develop an electronic automated optic system that achieves a diagnosis through catheter with optic fiber connected to a Raman spectrometer in order to analyze a certain organ and, considering the diagnosis obtained, to develop the adequate optical treatment can be automatically selected and applied to the respective organ. In the present work, the structure of this device will be presented with the more suitable optical techniques available to the laboratories. The minimum intervals of time involving each step of the sequence are evaluated and the efficiency of the spectroscopic system is discussed in details in agreement with the literature.
Optimizing electroporation assisted silver nanoparticle delivery into living C666 cells for surface-enhanced Raman spectroscopy
Authors: Yu Yun , Lin Juqiang , Wu Yanan , Feng Shangyuan , Li Yongzeng , Huang Zufang , Chen Rong , Zeng Haishan
Published: April 2012

Electroporation assisted metallic nanoparticle delivery has been shown by our previous work to significantly reduce the time of sample preparation for surface-enhanced Raman spectroscopy (SERS) measurements of biological cells. In this paper, we report our experimental work to optimize the electroporation parameters, including adjustment of the pulse pattern, operation temperature, and electroporation buffer, for fastest delivery of silver nanoparticles into living C666 cells (a human nasopharyngeal carcinoma cell line). The delivery efficiency was evaluated by the integrated intensity of whole cell SERS spectrum. Our work concluded that the silver nanoparticle delivery rate is best under the electroporation condition of using 4 consecutive 350 V (875 V/cm) rectangular electric pulses of 1, 10, 10 and 1 ms durations, respectively. Low temperature (0–4°C) is necessary for keeping cell viability during the electroporation process and it also improves the delivery efficiency of silver nanoparticles. The serum in the buffer has no obvious effect on the delivery efficiency.
Prooxidative and fluorescence properties of paracetamol during interactions with mitochondria
Authors: Tomečková Vladimíra , Gajová Alena , Veliká Beáta , Saxunová Lýdia , Hertelyová Zdenka
Published: April 2012

This study was carried out to investigate isolated liver mitochondrial functions after paracetamol administration by monitoring of liver mitochondrial fluorescence properties as well as prooxidative properties of paracetamol. Paracetamol was administered to rat (in subtoxic 500 mg·kg−1dose) invivo. The effect of this dose was compared with the subtoxic and toxic dose of paracetamol added to mitochondria invitro(1 and 1.5) mg paracetamol/mg mitochondrial protein. Subtoxic dose of paracetamol invitrodid not change mitochondrial fluorescence, but it significantly decreased mitochondrial fluorescence invivoin comparison with control mitochondrial group. Toxic dose of paracetamol invitrosignificantly decreased mitochondrial fluorescence. The enzymatic activity of superoxide dismutase (SOD) significantly decreased after paracetamol administration invitroand invivo. While both activities of glutathione peroxidase (GPx) and glutathione reductase (GR) significantly increased in dependence upon paracetamol doses. Our experiment showed, that paracetamol participates in formation of free radicals and confirms previous studies, in which paracetamol administration caused elevation of antioxidative enzymes activities in dependence on dose, which is considered therapeutically as subtoxic and toxic.
Rapid evaluation and quantitative analysis of eugenol derivatives in essential oils and cosmetic formulations on human skin using attenuated total reflectance–infrared spectroscopy
Authors: Wang Lai-Hao , Sung Wei-Chien
Published: April 2012

We studied the fragrances 4-allylbenzenes (eugenol, methyl eugenol, acetyl eugenol) as well as 4-propenylbenzenes (isoeugenol) in commercial essential oils using a fast and nondestructive attenuated total reflectance–infrared (ATR–IR) spectroscopy method. The method was based on ATR–IR utilizing partial least square regression. The calibrations were modeled in the characteristic region for eugenol (1430–1432 cm−1), isoeugenol (960–970 cm−1) and methyl eugenol (803–807 cm−1). The models were then applied to predict the percutaneous absorption process yield and to monitor the concentrations of eugenol derivatives on human skin.
Investigation of the mechanism of binding of thiacloprid to human serum albumin using spectroscopic techniques and molecular modeling methods
Authors: Wang Chuanxian , Chu Qinghua , Chen Changyun , Bo Zhao
Published: April 2012

Fluorescence spectroscopy, UV absorption, circular dichroism (CD) spectroscopy and molecular modeling methods were used to characterize the binding properties of thiacloprid (TL) with human serum albumin (HSA) at molecular level under physiological conditions. The fluorescence intensity of HSA decreased regularly with the gradually increasing concentration of thiacloprid. The binding constant K at three different temperatures (290, 300 and 310 K) were 3.07, 2.74 and 1.35 × 104M−1, respectively, for TL–HSA interaction have been calculated from the relevant fluorescence data. CD spectroscopic measurements have shown that the secondary structures of the protein have been changed by the interaction of thiacloprid with HSA. Furthermore, the study of molecular modeling indicated that thiacloprid could be located on the surface of the binding pocket of subdomains IIA in HSA. The hydrophobic interaction was the major acting force and there are H-bonds and electrostatic interactions between TL and HSA, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change ΔH0and the entropy change ΔS0were calculated to be -20.378 kJ/mol and 16.328 J/mol K according to the Van9t Hoff equation).
Effect of different doses of creatine on the bone in thirty days of supplementation in mice: FT-Raman study
Authors: Miranda Humberto , De Souza Renato Aparecido , Tosato Maira Gaspar , Simão Roberto , Oliveira Murilo Xavier , De Lima Flávia Mafra , Ferrari Erika , Ribeiro Wellington , Moreira Leonardo Marmo , Martin Airton Abrahão
Published: April 2012

In this study, Raman spectroscopy was employed in order to provide information about the effects of different doses of creatine on bone tissue composition of phosphate apatite (960 cm–1), carbonate apatite (1170 cm–1) representing the mineral content and collagen matrix (amide I, 1665 cm–1). The animals (27 Balb-C male) were divided into three groups (n═ per group): control (CON), supplemented with 0.5 g/kg (Cre-0.5) and with 2.0 g/kg (Cre-2.0) creatine. The experiment was carried out for thirty days. After this time, the right femur of each animal was harvested. The specimens were assessment by FT-Raman spectroscopy and in a total of 81 spectra were acquired in the medial diaphysis of the femur. The Raman data strongly suggest that only the creatine supplementation of 0.5 g/kg effective to the bone constitution. Furthermore, the present results demonstrate that creatine ingestion provokes decrease in the relative presence of carbonate in the chemical constitution of bones. The decrease in the carbonate content can be associated to a significantly bone resistance altered to several mammalians. The analysis evidenced that the mineral concentrations in the Raman spectroscopy could be a feasible method for non-invasive or minimally invasive assessment of bone tissue composition. Probably this high sensitivity can be employed to determine spectral profiles, such as wavelength of maximum absorption and maximum intensity of absorption of each wavelength, of several bone diseases.
Routine classification of food pathogensStaphylococcusandSalmonellaby ATR–FT-IR spectroscopy
Authors: Xu Shujun , Xie Yanping , Xu Chunxiang
Published: April 2012

Fourier-transform infrared equipped with attenuated total reflection (ATR–FT-IR) was used in combination with multivariate statistical analysis for classification and identification of food pathogensStaphylococcusandSalmonella. The goals of the present study were to validate the feasibility of ATR–FT-IR in collecting information for discriminating different bacteria, and to assess the merits of two routes for effectively identify target foodborne bacteria. The results showed that ATR–FT-IR was able to provide enough chemical information of each species. Cluster-analysis-test was able to identify target bacteria at the genus and species level using Pearson's product-moment correction coefficient and Ward's algorithm. Partial least squares regression discriminant analysis (PLS-DA) coupled with multiplicative scatter correction (MSC), standard normal variate (SNV) and their derivatives demonstrated the probable use of this routine method to differentiate food pathogens at the sub-species level.