Spectroscopy - Volume 26, issue 3

Authors: Patti, Gary J. | Tautenhahn, Ralf | Fonslow, Bryan R. | Cho, Yonghoon | Deutschbauer, Adam | Arkin, Adam | Northen, Trent | Siuzdak, Gary

Article Type: Research Article

Abstract: Global metabolomics has emerged as a powerful tool to interrogate cellular biochemistry at the systems level by tracking alterations in the levels of small molecules. One approach to define cellular dynamics with respect to this dysregulation of small molecules has been to consider metabolic flux as a function of time. While flux measurements have proven effective for model organisms, acquiring multiple time points at appropriate temporal intervals for many sample types (e.g., clinical specimens) is challenging. As an alternative, meta-analysis provides another strategy for delineating metabolic cause and effect perturbations. That is, the combination of untargeted metabolomic data from multiple …pairwise comparisons enables the association of specific changes in small molecules with unique phenotypic alterations. We recently developed metabolomic software called metaXCMS to automate these types of higher order comparisons. Here we discuss the potential of metaXCMS for analyzing proteomic datasets and highlight the biological value of combining meta-results from both metabolomic and proteomic analyses. The combined meta-analysis has the potential to facilitate efforts in functional genomics and the identification of metabolic disruptions related to disease pathogenesis. Show more

Keywords: Metabolomics, meta-analysis, proteomics, untargeted, XCMS

DOI: 10.3233/SPE-2011-0534

Citation: Spectroscopy, vol. 26, no. 3, pp. 151-154, 2011

Authors: Hu, Tao | Lu, Yu-Hui | Cheng, Cun-Gui | Sun, Xiao-Chen

Article Type: Research Article

Abstract: This paper introduces a new method for the early detection of gastric cancer using a combination of feature extraction based on discrete wavelet transformation (DWT) for horizontal attenuated total reflectance–Fourier transform infrared spectroscopy (HATR–FT-IR) and classification using probability neural network (PNN). 344 FT-IR spectra were collected from 172 pairs of fresh normal and abnormal stomach tissue's samples. After preprocessing, 5 features were extracted with DWT analysis. Based on the PNN classification, all FT-IR spectra were classified into three categories. The accuracy of identifying normal gastric tissue, early gastric cancer tissue and gastric cancer tissue samples were 100.00, 97.56 and 100.00%, …respectively. This result indicated that FT-IR with DWT and PNN could effectively and easily diagnose gastric cancer in its early stages. Show more

Keywords: HATR–FT-IR, discrete wavelet transformation, probability neural network, earlier stage of gastric cancer, diagnose

DOI: 10.3233/SPE-2011-0535

Citation: Spectroscopy, vol. 26, no. 3, pp. 155-165, 2011

Authors: Tache, Andreia | Litescu, Simona-Carmen | Radu, Gabriel-Lucian

Article Type: Research Article

Abstract: Matrix assisted laser desorption–ionization time of flight (MALDI-ToF) and infrared techniques were used to study oxidative modification of low density lipoproteins (LDL), considered to have the key role in biological process that initiates and accelerates the development of cardiovascular disease. The early identification of lipoperoxidation products creates the opportunity of the efficient prevention of eventual oxidative damages. MALDI analysis of LDL subjected to in vitro oxidation process initiated by 2,2-azobis(2-amidinopropane) dihydrochloride revealed that some fragments of lipoprotein changed the molecular weight by 16 and 32 Da due to the oxygen or hydroxyl groups attachment, and peroxide or hydroperoxide formation, while …Fourier Transformed Infrared studies proved that lipoprotein changes its protein secondary conformation from predominantly α-helix in predominantly β-turn. The increase in free radicals concentration correlated to structural changes, and the presence of transitional metal ion, copper (II), in the oxidation process lead to an enhancing of the damaging effects of free radicals on lipoprotein substrate. It was shown that the toxic effects of oxidants are delayed by the presence of glutathione (10 mM), an endogenous antioxidant. Show more

Keywords: MALDI-ToF, FT-IR, lipoperoxidation, Cu^2+, glutathione

DOI: 10.3233/SPE-2011-0533

Citation: Spectroscopy, vol. 26, no. 3, pp. 167-178, 2011

Authors: Lin, Rui | Zhou, Lin | Lin, Yun | Wang, Ao | Zhou, Jia Hong | Wei, Shao Hua

Article Type: Research Article

Abstract: Tetra-tert-butyl zinc(II) phthalocyanine has attracted great attention as an effective photosensitizer in the field of photodynamic therapy. However, tetra-tert-butyl zinc(II) phthalocyanine is hydrophobic and trends to aggregate to form the inactive congeries in aqueous solution, which dramatically reduce its photodynamic activity. To solve this problem, tetra-tert-butyl zinc(II) phthalocyanine was encapsulated into silica nanoparticles using microemulsion method and its properties were studied using spectroscopic methods. After embedded inside the silica nanoparticles, the water-solubility, stability and monomer percent of phthalocyanine in water were greatly improved comparing with the free phthalocyanines, and therefore, its photo-induced singlet oxygen generation efficacy of drug-doped silica nanoparticles …was improved. The results indicated that encapsulation hydrophobic phthalocyanine into silica nanoparticles was an effective way to solve their problems and promote their clinical application. Show more

Keywords: Phthalocyanine, nanocomposites, photodynamic therapy, ceramics

DOI: 10.3233/SPE-2011-0536

Citation: Spectroscopy, vol. 26, no. 3, pp. 179-185, 2011

Authors: Huang, Hao | Chen, Weiwei | Pan, Jianji | Chen, Qisong | Feng, Shangyuan | Yu, Yun | Chen, Yanping | Su, Ying | Chen, Rong

Article Type: Research Article

Abstract: The intracellularly-grown-Au-nanoparticles (IGAuNs) technique was employed to analyze the surface-enhanced Raman scattering (SERS) spectra of nasopharyngeal carcinoma cells (CNE-1 cell line). There are only six obvious Raman bands (718, 1001, 1123, 1336, 1446, 1660 cm−1 ) in the normal Raman spectrum of living CNE-1 cells. However, over twenty SERS Raman bands have been detected in the SERS spectra of IGAuNs-induced cells, among which five bands are of the DNA backbone (673, 1097, 1306, 1336 and 1585 cm−1 ). There are four vibrations of the DNA backbone (1026, 1097, 1336 and 1585 cm−1 ) in the SERS spectra of living CNE-1 …cells induced by the passive uptake gold nanoparticles (PUAuNS), but one more DNA backbone and many nucleus Raman peaks appeared in the IGAuNs-induced SERS spectra. Many Raman peaks in the PUAuNs-induced SERS spectra are stronger than those in the IGAuNs-induced ones. This study has shown that the PUAuNs technique can achieve stronger Raman signals, and that the IGAuNs technique can enable the gold element to access to the nucleus more easily, which could help to obtain more surface-enhanced Raman signals of the intracellular biochemical molecules. Thus, the two techniques can work together to attain the Raman spectral information of the cytoplasm and the nucleus in a better way, which might provide a sensitive method for broad biomedical applications such as intracellular SERS analysis of living cells. Show more

Keywords: Surface-enhanced Raman scattering (SERS), intracellularly grown gold nanoparticles (IGAuNs), passively uptaken gold nanoparticles (PUAuNS), nasopharyngeal carcinoma cell

DOI: 10.3233/SPE-2011-0540

Citation: Spectroscopy, vol. 26, no. 3, pp. 187-194, 2011

Authors: Tian, Jing | Chen, Changyun | Xue, Mengwei

Article Type: Research Article

Abstract: The binding mechanism between protocatechuic aldehyde (PA) and human serum albumin (HSA) was investigated by fluorescence spectroscopy at different temperatures. It is proved that the fluorescence quenching of HSA by PA is not results of the formation of PA–HSA complex. The equilibrium constant K and the number of binding sites n were measured at different temperature by fluorescence quenching method. The standard enthalpy change (ΔH) and the standard entropy change (ΔS) of this interaction process were calculated to be 114.02 kJ·mol−1 , 541.92 J·mol−1 ·K−1 , respectively. According to the interaction between PA and HSA of thermodynamic parameters ΔH and …ΔS, the major acting force can be measured. The synchronous fluorescence spectra shows the microenvironment of tryptophan residue is changed and the hydrophobicity is increased. Through three-dimensional (3D) fluorescence spectra can get some valuable structure changing information. Show more

Keywords: Binding mechanism, protocatechuic aldehyde, human serum albumin, three-dimensional (3D) fluorescence spectra

DOI: 10.3233/SPE-2011-0539

Citation: Spectroscopy, vol. 26, no. 3, pp. 195-201, 2011

Authors: Rohman, Abdul | Che Man, Y.B.

Article Type: Research Article

Abstract: The purpose of this study was to optimize Fourier transform infrared (FTIR) spectroscopy in combination with multivariate calibrations (partial least square and principle component regression) for determination of extra virgin olive oil (EVOO) in quaternary mixture systems with grape seed oil (GSO), rice bran oil (RBO) and walnut oil (WO). FTIR spectra of EVOO in quaternary mixtures were subjected to several treatments including mean centering (MC), standard normal variate, and spectra derivatives. The combined frequency regions of 1200–900 and 2949–2885 cm−1 were used for determination of EVOO. Using partial least square calibration, FTIR normal spectra treated with MC model …give the highest values of coefficient of determination (R2 ) and the lowest values of root mean square error of calibration (RMSEC). The R2 value obtained for the relationship between actual and FTIR predicted value of EVOO was >0.99 with RMSEC value of 1.55% (v/v). The developed PLS model was further used to calculate EVOO in prediction samples, and the root mean square error of prediction obtained was 3.65% (v/v). Show more

Keywords: FTIR spectroscopy, extra virgin olive oil, partial least square, principle component regression, quaternary mixtures

DOI: 10.3233/SPE-2011-0538

Citation: Spectroscopy, vol. 26, no. 3, pp. 203-211, 2011