bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis, spectroscopic characterization and antimicrobial studies of mercury(II) complexes of thiolates
Authors: Rabbani Ghulam , Isab Anvarhusein A. , Al-Arfaj Abdul Rahman , Ahmad Saeed , Saleem Muhammad , Hameed Abdul , Akbar Erum
Published: April 2012

Mercury(II) complexes of thiolates having the general formula [Hg(RS)Cl2]−and [Hg(RS)2] have been prepared and characterized by IR and NMR (1H and13C) spectroscopy (RSH = 2-aminoethanethiol hydrochloride (Aet), cysteine (Cys), thiosalicylic acid (Ts) and 2-mercaptonicotinic acid (Mnt)). The spectral data suggests that the coordination of thiolates to mercury(II) occurs through the sulfur as indicated by the absence of S–H vibrations in IR and significant downfield shifts in the C–S resonance in13C NMR. However, in Mnt complexes, coordination through both sulfur and nitrogen is indicated. Antimicrobial activities of the complexes were evaluated by minimum inhibitory concentration and the results showed that the complexes exhibited a wide range of activities against gram-negative bacteria (E. coli, P. aeruginosa), while moderate activity was observed against a mold,P. citrinum.
Raman spectroscopic study of bioactive silica-based glasses: The role of the alkali/alkali earth ratio on the Non-Bridging Oxygen/Bridging Oxygen (NBO/BO) ratio
Authors: Marsich Lucia , Moimas Loredana , Sergo Valter , Schmid Chiara
Published: April 2012

Raman spectra of bioactive glasses of the Na2O–K2O–MgO–CaO–B2O3–P2O5–SiO2to be used in bone reconstruction systems have been collected from samples with three different concentrations of alkali and alkali earth elements. Compositions were chosen with a constant total amount of modifiers and formers, with only minor changes among the formers. The ratio of Non-Bridging Oxygens to Bridging Oxygens (NBO/BO) has been obtained from the Raman spectra and reported as a function of the alkali/alkali earth ratio, showing a linear increase. Dissolution tests indicate also a linear dependence of the amount of Na+, K+and Ca++ions leached in water on the alkali/alkali earth ratio. Consequently a calibration plot correlating the NBO/BO ratio with the amount of Na+, K+and Ca++ions leached in water has been obtained, thus demonstrating the sensitivity of the method, given that the changes from one glass composition to the other are of the order of some points in percentage among the glass modifiers.
Dominant effect of ethanol in thermal destabilization of bovine serum albumin in the presence of sucrose
Authors: Sathya Devi V. , Chidi Obiora O. , Coleman Denis
Published: April 2012

The thermal melting of bovine serum albumin (BSA) in the presence of excipients like ethanol and sucrose was studied by circular dichroism spectroscopy at physiological pH in phosphate buffered saline. Calculated apparentTmvalues were used to assess the thermal stability using two state fitted experimental curves. 0.5 M sucrose stabilized the BSA indicated by the increase inTmof ∼8°C when compared to theTmof the same solution measured in the absence of sucrose. Conversely, in the presence of varying concentrations of ethanol (2–20%), the protein was destabilized by a decrease of ∽3–10°C ofTm. In the binary mixture of sucrose and ethanol, theTmvalues showed that ethanol dominantly destabilized BSA in the presence of sucrose, possibly by weakening the hydrophobic interactions in the protein.
Characterization ofBacillus subtilissporulation and bacteriophage infection via FT-IR spectroscopy
Authors: Mysliwiec Tami H. , Tierno Anthony F. , Aurentz David J.
Published: April 2012

A comparative analysis on cultures from wild-type and sporulation mutants ofBacillus subtilisinfected with pseudotemperate spore-converting bacteriophages was performed to discern differences in the chemical functionality of the cellular population. Variations in the cell surface chemistry ofB. subtiliscultures were analyzed using attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy of dried sample films on optical plates. Comparison of wild-type and phage infected cultures revealed an increase in the amount of aliphatic ester in the infected populations. Spectral analysis of cultures from bacteriophage infected sporulation mutants,spo0Kandspo0Jrevealed varying levels of ester linkages.
The application of two-dimensional fluorescence correlation spectroscopy on the interaction between bovine serum albumin and prulifloxacin
Authors: Xue Mao-Yun , Yang Ai-Ping , Ma Mei-Hua , Li Xiao-Hua
Published: April 2012

The interaction between bovine serum albumin (BSA) and prulifloxacin was investigated by ultraviolet spectrophotometer (UV) and fluorescence spectroscopy in this paper. Two-dimensional (2D) correlation spectroscopy was applied to the analysis of fluorescence spectra. The results of spectroscopic measurements suggested that prulifloxacin (PL) have a strong ability to quench the intrinsic fluorescence of bovine serum albumin through static quenching procedure. Thermodynamic parameter enthalpy changes (ΔH) and entropy changes (ΔS) were calculated. Owing to the spectral resolution enhancement in 2D correlation spectroscopy, the structure change of prulifloxacin can be observed.
ESI-MSnstudy on the fragmentation of protonated cyclic-dipeptides
Authors: Guo Yan-Chun , Cao Shu-Xia , Zong Xiang-Kun , Liao Xin-Cheng , Zhao Yu-Fen
Published: April 2012

Cyclic dipeptides are relatively simple compounds that can exhibit a great variety of important biological activities. The fragmentation pathways of protonated cyclic dipeptides have been studied by electrospray ionization multistage mass spectrometry (ESI-MSn). The mass spectra studies of the cyclic dipeptides showed that the cyclic dipeptides with the similar substituents, the side chains of amino acid residues at the diketopiperazine ring, followed the same fragmentation pathway. In the fragmentation spectra of protonated cyclic dipeptides, some characteristic fragment ions were observed and could be used to distinguish the cyclic dipeptides. The hydrogen/deuterium (H/D) exchange experiment and the high-resolution mass spectrometry (Q-TOF) were used to verify and rationalize the proposed fragmentation pathways. These observations may have some potential applications in the structural elucidation and interpretation of the mass spectra of homologous compounds.
Structural analysis of protein–DNA and protein–RNA interactions by FTIR, UV-visible and CD spectroscopic methods
Authors: Tajmir-Riahi H. A. , N'soukpoé-Kossi C. N. , Joly D.
Published: April 2012

In this chapter the fundamental question of how does protein–DNA or protein–RNA interaction affect the structures and dynamics of DNA, RNA and protein is addressed. Models for calf-thymus DNA and transfer RNA interactions with human serum albumin (HSA), ribonuclease A (RNase A) and deoxyribonuclease I (DNase I) are presented here, using Fourier Transform Infrared (FTIR) spectroscopy in conjunction with UV-visible and CD spectroscopic methods. In the models considered, the binding sites, stability and structural aspects of protein–DNA and protein–RNA are discussed and the effects of protein interaction on the secondary structures of DNA, RNA and protein were determined.
Discrimination of the binding mode of DNA ligands by single-photon timing
Authors: Nardo Luca , Bondani Maria , Andreoni Alessandra
Published: April 2012

We perform time-correlated single-photon counting measurements with 30-ps resolution of the fluorescence emitted by the donor fluorophores of donor–acceptor pairs covalently labeling DNA synthetic oligonucleotides by using a non-commercial single-photon avalanche diode. The measurements allow us to precisely assess the fluorescence resonant energy transfer efficiency of the pairs in solutions containing the oligonucleotides and DNA–ligands, for different ratios of the DNA base-pair to ligand concentrations. A quantitative evaluation of the deformations of DNA double strands following the ligand binding is obtained, as the transfer efficiency is a steep function of the donor-to-acceptor distance. The results lead to an easy and cheap method to discriminate between the binding modes of minor groove and base intercalating ligands.
The interaction of clenbuterol hydrochloride with bovine hemoglobin using spectroscopic techniques and molecular modeling methods
Authors: Wu Yun , Mao Hui , Zhao Bo , Shen Jian
Published: April 2012

The interaction of clenbuterol hydrochloride (CL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using UV-vis absorption, fluorescence, circular dichroism (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of CL. It is observed that there was a prominent interaction between CL and BHb. The fluorescence data revealed that the fluorescence quenching is a static process, and the thermodynamic parameters were calculated according to the Van't Hoff equation. The alternations of protein secondary structure in the presence of CL were determined by the evidence of CD. Molecular modeling study that corroborate our experimental results revealed that the binding mode of CL–BHb complex could be attributed to the hydrophobic interaction and hydrogen bonding, but electronic interaction cannot be excluded.
Wireless near-infrared spectroscopy of skeletal muscle oxygenation and hemodynamics during exercise and ischemia
Authors: Shadgan Babak , Reid W. Darlene , Gharakhanlou Reza , Stpublisher-ids Lynn , Macnab Andrew John
Published: April 2012

The majority ofin vivoapplications of near-infrared spectroscopic (NIRS) monitoring use continuous wave instruments that require a fiberoptic cable connection between the subject and the instrument during monitoring. In studies of muscle physiology where subjects are exercising, and particularly in those who are engaged in sports activity, a wireless instrument with telemetric capacity provides obvious advantages. Having access to reliable telemetric NIRS technology will also increase the practicality and scope of this biomedical monitoring technique in clinical settings.

We report the feasibility of using a wireless continuous wave NIRS instrument with light emitting diodes, spatially resolved configuration, and Bluetooth®capability to study skeletal muscle oxygenation and hemodynamics during isometric contraction and ischemia induction.

In ten healthy subjects comparable patterns of change in chromophore concentration (oxygenated and deoxygenated hemoglobin), total hemoglobin and muscle oxygen saturation were observed during 3 sets of isometric voluntary forearm muscle contraction at 10, 30 and 50% of maximum voluntary capacity (MVC), and a period of ischemia generated subsequently.

This small series indicates that data with good intra- and inter-subject reproducibility that is free of movement artifact can be obtained with the wireless NIRS instrument described. The validity of these muscle studies demonstrate a basis for applying wireless NIRS monitoring to publisher-id biomedical applications.
Detecting molecular changes in Vimy flaxseed protein structure using synchrotron FTIRM and DRIFT spectroscopic techniques: Structural and biochemical characterization
Authors: Doiron K. J. , Yu P. , Christensen C. R. , Christensen D. A. , McKinnon J. J.
Published: April 2012

Mid-IR techniques were used to characterize any changes that occurred on a molecular level in flaxseed that had been heated using an autoclave. The objectives were to investigate the effects of autoclave heating on differences in diffuse reflectance infrared Fourier transform (DRIFT) and synchrotron-based Fourier transform infrared microspectroscopy (SFTIRM) based measurements of the proteinα-helix toβ-sheet ratio for flaxseed (Linum usitatissimum), cv. Vimy. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were also conducted to identify molecular differences in the DRIFT spectra. Flaxseed samples were kept raw for the control or autoclaved in batches at 120°C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. DRIFT analysis of protein secondary structure ratios showed a decrease (P< 0.05) in theα-helix toβ-sheet ratio for the whole seed while the results from synchrotron SFTIRM spot data from the endosperm tissue in flaxseed showed autoclaving had the opposite effect (P> 0.05). CLA and PCA were successfully used to make distinctions between the different treatment spectra and showed enhanced sensitivity upon selection of a smaller spectral window to include only the amide I and II portion of the IR spectrum. Our results indicated that autoclaving had a great enough effect on the mid-IR spectrum of flaxseed to identify the alteredα-helix toβ-sheet ratio and subsequently differentiated between the treatments using PCA and CLA suggesting greater sensitivity of mid-IR spectral methods in identifying the effect of heat treatment on protein secondary structure. Future study is needed to quantify the relationship between protein secondary structure and protein functionality.
Unique spectral features of DNA infrared bands of some microorganisms
Authors: Ahmed M. Khalique , Amiama Frank , Sealy Earl A.
Published: April 2012

Half dozen microorganisms (Serratia marcescens, Klebsiella pneumonia, Staphylococcus aureus, Bacillus subtilis, Mycobacterium smegmatis and Saccharomyces cerevisiae) were cultivated, and their infrared spectra were recorded in the attenuated total reflection mode. Both the intensities and frequencies of the B-DNA and Z-DNA bands in the spectral region of 1250–900 cm–1were found to be different for different microorganisms. We suggest that characterization and identification of microorganisms may be possible through analysis of their DNA bands only without the analysis of the full range (4000–700 cm–1) of their infrared spectra.
Characterization of a novel LEDs device prototype for neonatal jaundice and its comparison with fluorescent lamps sources: Photpublisher-idapy treatment of hyperbilirubinemia in Wistar rats
Authors: Sebbe Priscilla Fróes , Villaverde Antônio Balbin , Moreira Leonardo Marmo , Barbosa Ana Maria , Veissid Nelson
Published: April 2012

This work describes experimental tests done using the LED-therapy equipment developed for neonatal jaundice treatment. Neonatal photpublisher-idapy consists in the irradiation of jaundice new-born with a high intensity light, in the spectral range of 400–500 nm, in order to promote the photochemical transformation of the bilirubin molecules in the areas exposed to the light. A convenient light source for jaundice treatment can be obtained employing blue LEDs, which are simple devices that present low cost, small heating production, narrow spectral band and long life-time. Equipment using an array with 88 blue LEDs (emission peak at 472 nm with 50 nm bandwidth) was constructed, optically characterized and then validated in comparison with a commercial equipment of photpublisher-idapy, i.e., the Fluorescent Conventional. For the device validation, experiments were undertaken employing male Wistar rats, to which the hyperbilirubinemia was induced by the obstruction of the billi duct. Using the LED-therapy equipment, it was obtained a reduction by 78% of the indirect bilirubin concentration against only 39% referent to the commercial Fluorescent Conventional, both for 8 h of treatment. For a period of 24 h, the reduction was 92% and 76%, respectively. Thus, the novel LED-therapy equipment was more efficient for photodegradation of the bilirubin molecules in animal model, when compared with the Conventional equipment. The novel prototype present requisites to be applied in clinical treatments, such as a large and uniform area of irradiation, efficient wavelength emission for jaundice treatment, high spectral irradiance, simplicity and low values of weight, heating and cost. Therefore, the new device is candidate to systematic applications in photpublisher-idapy treatments.
Synthesis, spectral characterization and antibacterial studies of palladium(II) complexes of heterocyclic thiones
Authors: Tirmizi Syed Ahmed , Nadeem Shafqat , Hameed Abdul , Wattoo Muhammad Hamid Sarwar , Anwar Aneela , Ansari Zameer Ahmed , Ahmad Saeed
Published: April 2012

Reactions of K2[PdCl4] with heterocyclic thiones in molar ratios of 1:2 and 1:4 in water-methanol medium yielded the palladium(II) complexes with the general formula of either [Pd(L)Cl2], [Pd(L)2]Cl2or [Pd(L)4]Cl2where L ═ Imidazolidine-2-thione (Imt), 2-Mercaptopyridine (Mpy), 2-Mercaptopyrimidine (Mpm), 6-Mercaptopurine (6-Mp) and Thionicotinamide (Tna). The complexes were characterized by elemental analysis and spectroscopic (IR,1H and13C NMR) methods. An upfield shift in the >C═S resonance of thiones in13C NMR and downfield shift in N–H or aromatic proton resonances in1H NMR are consistent with the sulfur coordination to palladium(II). The complexes were screened for antibacterial activity, and the results showed that the complexes exhibited moderate activities as compared to that of a standard drug.
Optimizing the Raman signal for characterizing organic samples: The effect of slit aperture and exposure time
Authors: Lázaro João Carlos , Pacheco Marcos Tadeu T. , Rodrigues Kátia Calligaris , de Lima Carlos José , Moreira Leonardo Marmo , Villaverde Antonio Balbin , Silveira Jr. Landulfo
Published: April 2012

The present work is focused on the influence of the slit aperture and time exposure of the infrared light on the Charge Coupled Device (CCD) in relation to their physical effects, in order to improve the Raman spectrum characteristics. Indeed, the alterations in slit aperture and CCD time exposure affect significantly important spectral properties, such as the spectral intensity, Signal to Noise Ratio (SNR) and band width resolution of the Raman spectra. Therefore, the present proposal has the aim of to found the optimum conditions of instrumental arrangement, involving the minimum collection time and maximum signal quality in dispersive Raman spectrometers. Samples of dehydrated human teeth and naphthalene were evaluated with a Raman dispersive spectrometer employing excitation wavelength of 830 nm in several integration times and spectrometer slit apertures. The analysis of the spectral intensity, SNR and band width of selected Raman peaks allowed to infer that these properties of a dispersive Raman spectrum depend directly of the exposure time on the detector as well as spectrograph slit aperture. It is important to register that the higher SNR was obtained with higher exposure time intervals. To the samples evaluated in the present article, the band width has lower values for slit apertures of 100–150 μm, i.e., in this aperture range the spectral resolution is maximum. On the publisher-id hand, the intensity and SNR of the Raman spectra becomes optimal for slit apertures of 150–200 μm, since this aperture does not affect significantly the integrity of the Raman signal. In this way, we can to propose that in approximately 150 μm, it is possible to obtain an optimum condition, involving spectral resolution as well as SNR and spectral intensity. In any case, depending of the priorities of each spectral measurement, the instrumental conditions can be altered according with the necessities of each specific chemical analysis involving a determined sample. The present data are discussed in details in agreement with recent data from literature.
Structural characterization and DNA-binding properties of Sm(III) complex with ofloxacin using spectroscopic methods
Authors: Chen Changyun , Chen Kai , Long Qi , Ma Meihua , Ding Fei
Published: April 2012

A novel complex Sm(III) complex with ofloxacin was synthesized and characterized on the basis of elemental analyses, molar conductivities, IR spectra, thermal analysis (TG-DSC),1H-NMR spectra. Then, spectrometric titration, ethdium bromide displacement experiments by UV spectroscopy, ionic influence, viscosity measurements and Circular Dichroism (CD) spectroscopic measurements were conducted to characterize the interaction between the complex and CT-DNA. Results obtained indicate that the complex bound with CT-DNA via an intercalation mechanism. The binding constants and binding sites number of the Sm(III) complex with CT-DNA were 1.80×105l·mol−1and 1, respectively.
Helical conformation of the AD1 peptide in the AML1-ETO–E-protein complex
Authors: Porumb Horea
Published: April 2012

The AML1-ETO fusion protein is responsible for 15% of the acute myeloid leukaemias due to its interference with transcription activation by E-proteins. The eTAFH region of the AML1-ETO competes for the AD1 domain of E-protein, thereby preventing wild-type transcription activation. The structural details concerning the eTAFH–bound AD1 domain are not known. We have previously shown that the eTAFH–AD1 interaction is strong (Kd=28 nM, H. Porumb,Spectroscopy22 (2008), 251–260). The secondary structure prediction algorithms are undecided as to the conformation of bound AD1 peptide. Here we demonstrate by circular dichroism that the bound AD1 peptide is fully helical. This will facilitate modeling of the interaction and launches a challenge as to using synthetic peptides to out compete the eTAFH–E-protein interaction.
FT-Raman study of the (sub)picosecond dynamics in genomic DNA from plant tissues
Authors: Muntean Cristina M. , Bratu Ioan
Published: April 2012

In this paper the Raman total half bandwidths of eight genomic DNAs from leaf tissues [potato (Solanum tuberosumL.), sword fern (Nephrolepis exaltataL.), scopolia (Scopolia carniolicaJacq.), redwood (Sequoia sempervirensD. Don. Endl.), orchids (Cymbidium × hybrida), chrysanthemum (Dendranthema grandifloraRamat.) and common sundew (Drosera rotundifoliaL.)] have been measured. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic plant DNA, are reported. It is shown that changes in the (sub)picosecond dynamics of molecular subgroups in genomic DNAs from leaf tissues can be monitored with Raman spectroscopy.

Particularly, the Raman band parameters for the vibrations at 879 cm−1(deoxyribose, dA), 1047 cm−1(CO stretching C‒O‒P‒O‒C, dG), 1089 cm−1(PO symmetric stretching of PO2‒), 1124 cm−1(dA), 1272 cm−1(dC, dG, dT), 1276 cm−1(dC), 1455 cm−1(deoxyribose, dA, dC, dT) and 1482 cm−1(dG, dA) of genomic leaf tissues DNAs are presented. In our study, the full widths at half-maximum (FWHM) of the bands in genomic DNAs from leaf tissues are typically in the wavenumber range from 7.8 to 23.1 cm−1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 1.36 ps and larger than 0.46 ps.

The fastest and the slowest relaxation processes of different DNA structural subgroups, for several types of genomic DNA extracted from leaf tissue, have been analyzed. Particularly, the slowest dynamics corresponding to the vibration near 1272 cm−1takes place in the case of DNA extracted from common sundew (global relaxation time 1.36 ps).

A comparison between different time scales of the vibrational energy transfer processes, characterizing several DNA complexes, has been given.

We have found that the bands at 879 cm−1(deoxyribose, phosphodiester, dA) and 1455 cm−1(deoxyribose, dA, dC, dT) are suitable for the study of dynamical behavior of molecular subgroups in genomic DNA extracted from leaf tissues.

Specific molecular relaxation processes, depending on the type of genomic DNA extracted from leaf tissues has been observed.
Flow injection chemiluminescence determination of levofloxacin in medicine and biological fluids based on its enhancing effect on luminol–H2O2reaction
Authors: Shao Xiaodong , Li Ying , Liu Yangqin , Song Zhenghua
Published: April 2012

Levofloxacin{(–)-(S)-9-fluoro-2,3-dihydro-3-methyl-10-(4-methyl-1-piperazinyl)-7-oxo-7H-pyrido[1,2,3-de]-1,4-benzoxazine-6-carboxylic acid} is a synthetic fluorinated quinolone derivative, having activity against both Gram (+) and Gram (–) bacteria (aerobic and anaerobic) through inhibition of their DNA gyrase. In this paper, a simple flow injection chemiluminescence with luminol–hydrogen peroxide system was described for determining levofloxacin. The chemiluminescence intensity in the presence of levofloxacin was remarkably enhanced compared with that in the absence of it. Under the optimum reaction conditions the chemiluminescence increment produced was proportional to the concentration of levofloxacin in the range of 1.0–700.0 ng ml–1(R2═0.9992), with a detection limit of 0.3 ng ml–1(3σ). At the flow rate of 2.0 ml min–1, the whole process including sampling and washing could be completed in 0.5 min offering the sampling efficiency of 120 times h–1accordingly, and the relative standard deviation (RSD) was less than 3.0% (n═5). The recovery for the levofloxacin samples was from 95.9% to 104.5%. It was satisfactory for the application to determine levofloxacin in pharmaceutical preparations, human urine and serum samples.
Spectroscopic studies of the inclusion compound of lisinopril withβ-cyclodextrin
Authors: Olaru Alexandra , Borodi Gh. , Kacsó Iren , Vasilescu M. , Bratu I. , Cozar O.
Published: April 2012

The inclusion compounds of lisinopril withβ-cyclodextrin, prepared by different methods: kneading, co-precipitation and freeze-drying were investigated by XRD, FTIR, DSC and solid-state NMR techniques. It was established by these methods that the complexation process was successfully. The degree of crystallinity for the product obtained by kneading was also determined. The kneaded product has a certain crystallinity degree, so it is possible that the inclusion process is less effective in this case. In the case of freeze-dried and co-precipitated products only amorphous phase exists, i.e. the complexation was produced with a higher efficiency.
Subpicosecond dynamics in calf-thymus DNA, in the presence of Zn2+ions: A Raman spectroscopic study
Authors: Muntean Cristina M. , Bratu Ioan , Nalpantidis Konstantinos , Purcaru Monica A. P.
Published: April 2012

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Zn2+ions concentration, in the presence of a constant concentration of Na+ions, respectively. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on Zn2+ions concentration, are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in ZnDNA complexes can be monitored with Raman spectroscopy.

Particularly, the Raman band parameters for the vibrations at 729 cm−1(dA), 792 cm−1(dC, dT and 5'-C–O–P–O–C-3' network), 1094 cm−1(DNA backbone PO2−symmetric stretching), 1377 cm−1(dA, dT, dC), 1489 cm−1(the guanine N-7 and adenine rings) and 1581 cm−1(dG, dA) of ZnDNA complexes, in the presence of Zn2+ions concentrations that varied between 0 and 250 mM, are presented. In our study, the full widths at half-maximum (FWHM) of the bands in calf-thymus DNA complexes are typically in the wavenumber range from 10 to 50 cm−1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.94 ps and larger than 0.21 ps. The limit values are characterizing the dA and dG residues, respectively (vibrations at 729 cm−1and 1489 cm−1).

Binding of Zn2+ions to double helical calf-thymus DNA results for some vibrations in smaller global relaxation times and larger bandwidths, respectively, possible as a consequence of the increased interaction of the base moieties with the solvent molecules in unstacked structures.

The fastest and the slowest dynamics for different DNA structural subgroups and different Zn2+ions concentrations, respectively, have been analyzed.

A comparison between different time scales of the vibrational energy transfer processes, characterizing the ZnDNA structural subgroups has been given.

We have found that metal ion's type and concentration are modulators for the (sub)picosecond dynamics of calf thymus DNA molecular subgroups.
Fourier transform infrared spectroscopy of dental unit water line biofilm bacteria
Authors: Liaqat Iram
Published: April 2012

Fourier transform-infrared (FT-IR) spectroscopy has become an important tool for rapid analysis of complex biological samples. The infrared absorbance spectrum could be regarded as a “fingerprint” which is a feature of biochemical substances. The FT-IR spectra of fresh and stored dried samples of six bacterial isolates (Klebsiellasp.,Bacillus cereus, Bacillus subtilis, Pseudomonas aeruginosa, Achromobacter xylosoxidans and Achromobactersp.) were observed by variation in sample preparation. The results indicated that variation in sample preparation did not affect the spectra of isolates. However, less promiment/absence of a small shoulder peak at 1738 cm−1was evident in fresh dried samples ofAchromobactersp. and A.xylosoxidanscompared to prominent and broad shoulder band at 1724 cm−1in stored dried samples of these two isolates. In addition to the established KBr pellet technique, attenuated total reflectance (ATR) spectroscopy was used to analyse the spectra of planktonic growth (−80°C liquid cultures) and biofilm growth of six isolates. ATR spectroscopy of −80°C planktonic and biofilm growth showed variation in absorption spectra in fingerprint (1200−900 cm−1) region. Two clear absorption bands were prominent in biofilm at 1175 and 1143 cm−1whereas, one prominent broad band at 1075 cm−1resulting from the overlapping of two band was noted in planktonic cultures. Biofilm forming capability of the six isolates was also determined by acridine orange staining method. The microscopic analysis of biofilms formed on glass slides revealed the presence of a matrix of exopolysaccharides and microcolonies typical of biofilm architecture. Maximum biofilm formation was observed after 175 h inP. aeruginosaandKlebsiellasp.
Quantitative determination of naltrexone by attenuated total reflectance – FTIR spectrometry using partial least squares (PLS) wavelength selection
Authors: Khanmohammadi Mohammadreza , Mobedi Hamid , Mobedi Elaheh , Kargosha Kazem , Bagheri Garmarudi Amir , Ghasemi Keyvan
Published: April 2012

A new method is presented for quantitative determination of naltrexone in aqueous solutions based up on the wavelength selection in mid-FTIR spectra using partial least squares (PLS) technique. The main aim is to find wavelengths which produce significant improvements in PLS prediction. PLS wavelength selection treatment is performed on the data obtained by attenuated total reflectance Fourier transform infrared spectrometry in 830–1800 cm−1wavenumber range. No separation or extraction steps are required prior to determination procedure and a simple pretreatment is performed. Absorbance spectra were employed for measurements using a set of 7 aqueous standard solutions of naltrexone. The method is applicable for pharmaceutical samples in aqueous solution in the presence of impurities, while it is simple, rapid and accurate. The results obtained from real samples were compared with those obtained using Ultra Violet spectrophotometry as a reference method. Statistical parameters such as R2, REP, RMSEC and RMSECV were evaluated, and number of factors, number of scans and resolution were also optimized. In this method R2and RMSEC for proposed procedure have been found to be 0.9983 and 0.1297, respectively.
Evaluation of anti-osteoporosis in ovariectomized Wistar rats treated with antler blood by synchrotron radiation X-ray fluorescence microprobe
Authors: Yang Jianhong , Wang Ruilin , Cao Yi , Fei Yurong , Huang Yuying , He Wei , Liu Jing
Published: April 2012

To evaluate the anti-osteoporotic effect of antler blood, the relationship between the change of element content and the bone mineral density (BMD) increase in femur was investigated. Female Wistar rats were randomly divided into three groups: sham-operated group (SHAM,n=5), ovariectomized group (OVX,n=5) and ovariectomized group with antler blood treatment (n=5). The femoral BMD was analyzed by dual-energy X-ray absorptiometry (DXA) and the element relative content was determined by synchrotron radiation X-ray fluorescence (SRXRF) microprobe. The results showed that the femoral BMD in ovariectomized rats was significantly lower than that of sham-operated rats (p<0.05) but reversed by antler blood treatment (p<0.05). A further study demonstrated that the relative contents of phosphorus (P), calcium (Ca), zinc (Zn) and strontium (Sr) were obviously lower in ovariectomized rats compared to sham-operated rats but only the relative contents of P, Ca and Zn were normalized by antler blood treatment (p<0.05). Our experiments revealed that loss of element Ca, P, Zn and Sr was closely related to the BMD reduction in ovariectomized rats and the anti-osteoporotic effect of antler blood was mediated by increasing the contents of P, Ca and Zn.
Abnormal shifts in Raman spectra of deuterated cytidine and 6-azacytidine
Authors: Garasevych S. , Iakhnenko M. , Slobodyanyuk O. , Vaskivskyi I.
Published: April 2012

It was revealed that some peaks in Raman spectra of cytidine, 6-azacytidine (6-azaC), and cytosine dissolved in D2O are shifted to high frequencies in respect to their positions in spectra of H2O solution. Such “blue shifts” occur due to deuteration of the nucleoside molecule itself but not due to effect of deuterated solvent. This conclusion is deduced from observation of blue (abnormal) shift in Raman spectra of cytidine and 6-azaC microcrystals recrystallized from D2O solution. Both normal and abnormal shifts close to the experimentally observed were obtained in the calculated spectra of 6-azaC and cytidine. We assume that abnormal shifts may be caused by substitution of intramolecular H-bonds with D-bonds.
Interactions of the β-blocker drug, propranolol, with detergents, β-cyclodextrin and living cells studied using fluorescence spectroscopy and imaging
Authors: Bisby R. H. , Botchway S. W. , Crisostomo A. G. , Karolin J. , Parker A. W. , Schröder L.
Published: April 2012

Interactions of theβ-blocker drug, propranolol, with amphipathic systems have been studied using fluorescence spectroscopy. The results show a strong binding of propranolol with micelles of sodium dodecyl sulfate revealed through changes in the fluorescence spectrum and an increase in fluorescence lifetime. Quenching of propranolol fluorescence by iodide is used to demonstrate interaction withβ-cyclodextrin. At high concentrations, self-quenching of propranolol fluorescence was also observed withκq=2.5×109dm3mol–1s–1. Two-photon excited (630 nm) fluorescence lifetime imaging of propranolol in cells showed propranolol to be widely distributed in the cell cytoplasm, with fluorescence lifetimes shorter than in solution. The results suggest that intracellular propranolol is mainly confined within the aqueous cytoplasm and rather than membrane associated.
SERS study on myeloperoxidase and its immunocomplex: Identification of binding interactions
Authors: Papazoglou Elisabeth S. , Babu Sundar , Hansberry David R. , Mohapatra Sakya , Patel Chirag
Published: April 2012

Surface Enhanced Raman Spectroscopy (SERS) has demonstrated significant benefit in the identification of biological molecules. In this paper we have examined how to identify and differentiate the 150 kDa protein myeloperoxidase (MPO) from its corresponding antibody (Ab) and their immunocomplex through the use of SERS. The SERS signal of these biological molecules was enabled by 40 nm gold nanoparticles. The SERS spectra for both MPO and the Ab (an IgG molecule) demonstrated results consistent with previous published work on the Raman spectra of MPO and IgG antibodies. The immunocomplex SERS spectra showed peak shifts and intensity variations that could be attributed to conformational changes that occur during immunocomplex formation. Several key spectral areas have been identified which correspond to specific amino acids being shielded from undergoing resonance while new amino acid residues are made visible in the SERS spectrum of the immunocomplex and could be a result of conformational binding. These results indicate that SERS can be used to identify binding events and distinguish an immunocomplex from its individual components.
Shape of the carbon monoxide infrared absorption band of carboxyheme proteins as a probe of the protein anharmonicity
Authors: Stavrov Solomon S.
Published: April 2012

Theory of the CO infrared absorption band of carbonmonoxyheme proteins is developed using results of the theory of optical absorption bandshape of impurity center in crystal. It is shown that the bandshape is controlled by electrostatic interaction to the polar or/and charged heme surrounding. Analysis of the CO bands of different heme proteins brings us to conclusion, that the CO band is broadened by very slow (τ > 10 ps) motions of the heme surrounding and this motion most probably corresponds to the slow collective motion of the protein molecule. Therefore the second moment of the band must depend linearly on temperature atT> 25 K if the heme surrounding moves harmonically. The motion of the protein formed surrounding of the heme is arrested by the glassy protein environment. It is shown that Gaussian is the only possible symmetric shape of the CO band, if the heme surrounding moves harmonically. Deviation from this bandshape is a manifestation of anharmonic character of the surrounding motion. In general, CO infrared absorption band is shown to be an excellent probe of the dynamics of the heme surrounding.
The comparison of aggregation and folding of enhanced green fluorescent protein (EGFP) by spectroscopic studies
Authors: Krasowska Joanna , Olasek Monika , Bzowska Agnieszka , Clark Patricia L. , Wielgus-Kutrowska Beata
Published: April 2012

GFP (Green Fluorescent Protein) is well known for its unique chromophore which is formed by autocatalytic cyclization of a polypeptide backbone of Ser65, Tyr66 and Gly67, and is able to emit green visible light. Due to unusual chromophore responsible for the fluorescence GFP and its mutants (e.g., EGFP) have become widely used reporter proteins in molecular biology and biotechnology. GFP can easily be fused to any protein of interest and co-expressed in cells; the GFP fluorescence is then used to visualize the distribution, transport and aggregation of the protein in the cell. However, GFP has a tendency to aggregate itself, and also formation of its chromophore critically depends on the presence of reducing agents. Therefore we have undertaken spectroscopic kinetic studies of EGFP folding and aggregation as a function of pH, and in the presence of various reducing agents, to study the competition between these two processes. The best conditions for folding of EGFP provides BME as a reducing agent. Aggregation of EGFP depends strongly on pH, and on the concentration of the protein. The careful control experiments must therefore be performed during investigations of proteins fused with EGFP, especially at pH lower than 7.
Self-distribution-function procedure in elastic incoherent neutron scattering for biosystems molecular motion characterization
Authors: Magazù Salvatore , Migliardo Federica , Benedetto Antonio , Gonzalez Miguel , Mondelli Claudia
Published: April 2012

In the present contribution we present a new procedure for the Mean Square Displacement (MSD) determination from Elastic Incoherent Neutron Scattering (EINS) where the connection between the Self-Distribution Function (SDF) and the measured EINS intensity profile is highlighted. We show how the SDF procedure allows both the total and the partial MSD evaluation, through the total and the partial SDFs. The procedure is applied on EINS data collected, by the IN13 backscattering spectrometer (ILL, Grenoble), on aqueous mixtures of sucrose and trehalose.
DNA photodamage: Study of cyclobutane pyrimidine dimer formation in a locked thymine dinucleotide
Authors: Schreier W. J. , Kubon J. , Clivio P. , Zinth W. , Gilch P.
Published: April 2012

The cyclobutane pyrimidine dimer (CPD) formed between two adjacent thymine bases is the most abundant DNA photolesion induced by UV radiation. The quantum yield of this reaction is on the order of ~1% in DNA. This small quantum yield hampers the study of damage formation in naturally occurring DNA. Investigations with increased accuracy become possible for a locked nucleotide model compound TLpTLwhich exhibits a quantum yield of about 10% for CPD formation. Time resolved IR spectroscopy on TLpTLand two other DNA model compounds (TpT and (dT)18) reveals that: (i) The absorption changes after ~1 ps are due to CPD photodamage. (ii) The quantum efficiency of CPD formation on the few picosecond time scale equals the quantum efficiency reported in stationary experiments. CPD photodamage formation in the investigated DNA constructs is thus predominantly formed from the primarily photoexcited singletππ*state, whereas the triplet channel does not play an essential role.
Analysis of a hybrid TATA box binding protein originating from mesophilic and thermophilic donor organisms
Authors: Kopitz Annette , Soppa Jörg , Hauser Karin
Published: April 2012

The TATA Box Binding Protein (TBP) is a 20 kD protein that is essential and universally conserved in eucarya and archaea. Especially among archaea, organisms can be found that live below 0°C as well as organisms that grow above 100°C. The archaeal TBPs show a high sequence identity and a similar structure consisting of α-helices andβ-sheets that are arranged in a saddle-shape 2-symmetric fold. In previous studies, we have characterized the thermal stability of thermophilic and mesophilic archaeal TBPs by infrared spectroscopy and showed the correlation between the transition temperature (Tm) and the optimal growth temperature (OGT) of the respective donor organism. In this study, a “new” mutant TBP has been constructed, produced, purified and analyzed for a deeper understanding of the molecular mechanisms of thermoadaptation. Theβ-sheet part of the mutant consists of the TBP fromMethanothermobacter thermoautotrophicus(OGT 65°C, MtTBP65) whose α-helices have been exchanged by those ofMethanosarcina mazei(OGT 37°C, MmTBP37). The Hybrid-TBP irreversibly aggregates after thermal unfolding just like MmTBP37 and MtTBP65, but theTm lies between that of MmTBP37 and MtTBP65 indicating that the interaction between the α-helical andβ-sheet part of the TBP is crucial for the thermal stability. The temperature stability is probably encoded in the variable α-helices that interact with the highly conserved and DNA bindingβ-sheets.
Data processing in FTIR imaging of cells: Towards protein secondary structure imaging
Authors: Goormaghtigh Erik , Derenne Allison , Bénard Audrey , Gasper Régis , Raussens Vincent
Published: April 2012

Focal plane arrays provide a rapid method for infrared imaging of cells and tissues. Beside statistical analyses designed to classify image features, insight into the structure of the molecules present in the sample can be obtained. The paper presents a simple way to retrieve complete information on protein secondary structure from the thousands of spectra obtained by imaging. Human PC-3 prostate cancer cells were shown here to present cell-to-cell variations in protein secondary structure which might be related to the cell cycle. Intracellular variations are small but intercellular variations can be quite significant. This observation could yield unanticipated insight in cell population analysis. Furthermore, the results demonstrate the robustness of secondary structure determination on individual pixels at a sub-cellular scale.
Unusual structural characteristics of theMycobacterium tuberculosispentapeptide repeat protein MfpA
Authors: Khrapunov S. , Cheng H. , Hegde S. , Blanchard J. , Brenowitz M.
Published: April 2012

The solution structure and refolding of theMycobacterium tuberculosispentapeptide repeat protein MfpA was explored by fluorescence and circular dichroism spectroscopy. Our results show that MfpA exists in two stable structural forms which exclusively favor dimer or oligomer formation. The structural malleability of MfpA may provide a novel target for drug discovery.
The role of Lys525 on the head-group anchoring of fatty acids in the highest affinity binding site of albumin
Authors: Rizzuti Bruno , Pantusa Manuela , Guzzi Rita
Published: April 2012

Human serum albumin provides the transport of long-chain fatty acids in the blood through three high-affinity and four low-affinity binding sites. Molecular dynamics simulations have been performed to investigate the anchoring of palmitic acid molecules to the protein. In the site with the highest affinity, Site 5, the key residue Lys525 not only binds the head-group of the palmitate ion by electrostatic interactions with its charged terminal group, but it also accommodates the first portion of the lipid chain by non-electrostatic interactions with the rest of its sidechain. The flexibility of Lys525, and in particular of the dihedral angleχ3, is suggested to account for a number of spectroscopic properties observed in correspondence with the entrance of the hydrophobic pocket constituting Site 5.
C-terminal domain of nonhistone protein HMGB1 as a modulator of HMGB1–DNA structural interactions
Authors: Chikhirzhina E. , Polyanichko A. , Leonenko Z. , Wieser H. , Vorob'ev V.
Published: April 2012

The HMGB1 protein (High Mobility Group protein 1) participates in the formation of functionally significant DNA-protein complexes. HMGB1 protein contains two DNA-binding domains and negatively charged C-terminal region. The latter consists of continuous sequence of dicarboxylic amino acids residues. Structural changes in DNA-protein complexes were studied by circular dichroism spectroscopy (CD) and atomic force microscopy (AFM). Natural HMGB1 and recombinant protein HMGB1(A + B) lacked negatively charged C-terminal region were used. The DNA–HMGB1(A + B) complexes demonstrate an unusually high optical activity in 150 mM NaCl solutions. AFM of the latter complexes shows, that at the low concentration of HMGB1 in the complex the protein is distributed along DNA in a random way. Increase of HMGB1 content leads to cooperative interaction and a redistribution of the bound protein molecules on DNA is observed. Based on the data obtained we conclude that protein–protein interactions play a key role in the formation of highly ordered DNA–HMGB1 complexes. It was shown that C-terminal domain modulate the interactions of DNA with HMGB1 protein. We suggest that the C-terminal domain of HMGB1 also modulates the “packing” of HMGB1 molecules on the DNA.
Raman spectroscopy methods for detecting and imaging supported lipid bilayers
Authors: Sweetenham Claire S. , Notingher Ioan
Published: April 2012

We have developed a Raman microspectroscopy system optimised for studying supported lipid bilayers (SLB). This system combines the benefits of Raman spectroscopy with the high spatial resolution of confocal microscopy. Furthermore, the additional incorporation of an atomic force microscope (AFM) makes it possible to directly correlate chemical information with spatial features of samples at the nanoscale. We focus on the limits of this system for detecting a single SLB and imaging its microdomains, and employ surface-enhanced Raman spectroscopy (SERS) to improve the sensitivity achieved with Raman microspectroscopy.