Three-way Principal Components Analysis for fluorescence spectroscopic classification of algae species

Excitation-emission matrices (EEM) from fluorescence spectroscopy may contain characteristic information about different algae species. As a result of measurements, one gets a whole stack of EEMs each of them corresponding to one species. Such a stack of matrices has to be understood as a cubic data array spanned by the dimensions ‘excitation’, ‘emission’ and ‘species’. The interpretation of higher dimensional data arrays requires efficient tools from multivariate data analysis. In this paper, it is illustrated how Three-way Principal Components Analysis as the appropriate generalization of conventional Principal Components Analysis may serve as a powerful method for classification of algae species. Received: 31 May 1996 / Revised: 1 July 1996 / Accepted: 4 Juli 1996     

Optical classification of algae species with a glass lab-on-a-chip

The identification of submillimetre phytoplankton is important for monitoring environmental and climate changes, as well as evaluating water for health reasons. Current standard methods for phytoplankton species identification require sample collection and ex situ analysis, an expensive procedure which prevents the rapid identification of phytoplankton outbreaks. To address this, we use a glass-based microchip with a microchannel and waveguide included on a monolithic substrate, and demonstrate its use for identifying phytoplankton species. The microchannel and the specimens inside it are illuminated by laser light from the curved waveguide as algae-laden water is passed through the channel. The intensity distribution of the light collected from the biochip is monitored with an external photodetector. Here, we demonstrate that the characteristics of the photodiode signal from this simple and robust system can provide significant and useful information as to the contents of the channel. Specifically, we show first that the signals are correlated to the size of algae cells. Using a pattern-matching neural network, we demonstrate the successful classification of five algae species with an average 78% positive identification rate. Furthermore, as a proof-of-concept for field-operation, we show that the chip can be used to distinguish between detritus in field-collected water and the toxin-producing cyanobacterium Cyanothece.     

Determination of elements in algae by different atomic spectroscopic methods

The chemistry of substances derived from plants has received a great deal of attention in the last several decades. Today, natural products and their synthetic analogs also play an important role in the pharmaceutical and food industry. Several interesting reviews on algae were published in the last 10 years. Algae, especially the red algae, are very helpful in every day practice in many fields, e.g. algal polysaccharides, agar, carrageenan and some algae extracts are used in agricultural, medicines and in food products, respectively (The Constituents of Red Algae, 1999; Gelling Hydrocolloids in Food Products Applications, 1979, p. 186; Marine Natural Products Chemistry, 1997, p. 337; Algae Polysaccharides, 1983, p. 195). The biological and pharmaceutical properties promote interest among chemists to focus their attention on algae, as yet, a wide open field (Synthesis and Proceedings of the Second EUMAC Workshop, Marine Eutrophication and Bentic Macrophytes, p. 2). The most extensively studied algal phyla are Chlorophyceae (green algae) (J. Phycol. 26 (1990) 670), Rhodophyceae (red algae) (J. Phycol. 25 (1989) 522) and Phaeophyceae (brown algae) (J. Phycol. 31 (1995) 325; J. Phycol. 32 (1996) 614). Concentrations of four elements (Ca, Mg, K, Na) were determined in the above-mentioned algal phyla by different atomic spectroscopic methods (F-AES, ICP-AES) after the digestion of algal samples with cc. HNO₃ in a microwave apparatus. Not only the Ca and Mg contents, but the ratio of the calcium to magnesium was calculated in every case. This ratio was lower (0.5–0.8) in green algae than in the red and brown algae (1.3–14.4). Therefore, the green algae are better magnesium sources than the red and brown. The elemental composition is of great importance in the ion system of human organism. It is usually characterized by the ion quotient ([Ca²⁺]+[Na⁺]:[Mg²⁺]+[K⁺]), which is approximately 1.0 under ideal conditions. However, in the human body this mole ratio generally varies between 2.5 and 4.0. The ion quotient was calculated by averaging between 1 and 2 in different algal phyla. This means that the 2.5–4.0 mole ratio can be decreased by different algal foods in the human organism.     

概率主成分分析联合支持向量机的前列腺SELDI-TOF质谱数据分析方法研究

基于前列腺癌检测中获取的表面增强激光解吸/离子化飞行时间质谱(SELDI-TOF-MS)数据,提出一种概率主成分分析(PPCA)联合支持向量机(SVM)的分类方法。对临床322例血清样本的质谱数据进行特征提取,以随机选取训练样本集(225例)构造SVM判别模型,对剩余样本集(97例)进行测试。采用均方根误差、识别率与预测率指标,将所构造的PPCA-SVM模型分别与偏最小二乘(Partial least squares,PLS)和PCA-SVM模型进行比较,发现PLS模型的识别率和预测率分别为90.92%和76.38%,PCA-SVM模型分别为99.23%和84.63%,而PPCA-SVM模型分别为99.01%和90.41%。因此SELDI-TOF-MS技术结合PPCA-SVM在样品分类中具有准确、重复性好等优点,为前列腺癌早期诊断提供了一种新方法。     

Synchronous fluorescence spectroscopic study of solvatochromic curcumin dye

Curcumin, the main yellow bioactive component of turmeric, has recently acquired attention by chemists due its wide range of potential biological applications as an antioxidant, an anti-inflammatory, and an anti-carcinogenic agent. This molecule fluoresces weakly and poorly soluble in water. In this detailed study of curcumin in thirteen different solvents, both the absorption and fluorescence spectra of curcumin was found to be broad, however, a narrower and simple synchronous fluorescence spectrum of curcumin was obtained at Δλ=10-20 nm. Lippert-Mataga plot of curcumin in different solvents illustrated two sets of linearity which is consistent with the plot of Stokes' shift vs. the ET30. When Stokes's shift in wavenumber scale was replaced by synchronous fluorescence maximum in nanometer scale, the solvent polarity dependency measured by λSFSmax vs. Lippert-Mataga plot or ET30 values offered similar trends as measured via Stokes' shift for protic and aprotic solvents for curcumin. Better linear correlation of λSFSmax vs. π* scale of solvent polarity was found compared to λabsmax or λemmax or Stokes' shift measurements. In Stokes' shift measurement both absorption/excitation as well as emission (fluorescence) spectra are required to compute the Stokes' shift in wavenumber scale, but measurement could be done in a very fast and simple way by taking a single scan of SFS avoiding calculation and obtain information about polarity of the solvent. Curcumin decay properties in all the solvents could be fitted well to a double-exponential decay function.     

Oxyammonolysis Products of Birch Wood and Its Principal Components

The composition of products from oxidative ammonolysis of the principal components of birch wood by mechanochemical treatment with atmospheric oxygen and ammonium persulfate in aqueous ammonia was studied.     

有机磷农药构效关系的主成分分析-人工神经网络研究

采用主成分分析法对样本数据集进行预处理，将得到的新的样本数据集输入人工神经网络，对有机磷农药的毒性参数进行预报。研究结果表明，主成分分析－人工神经网络的预报精度优于单纯的人工神经网络。     

Raman spectroscopic study on classification of cervical cell specimens

Cervix-cancer is the third most common female cancer worldwide. Papanicolaou (Pap) test, a well-recognized screening tool, is labor intensive, time consuming and prone to subjective interpretations. Optical spectroscopic methods, sensitive to molecular changes are being pursued as potential diagnostics tool. In this study we have explored Raman spectroscopic approach to differentiate exfoliated cell pellets using 94 cervical cell specimens (45-normal and 49-abnormal specimens). Study was carried out by two approaches. In the first approach, spectral data from 37 cell specimens were acquired and analyzed by Principal Component-Linear Discriminant Analysis (PC-LDA), which yielded classification efficiencies of 86% and 84% for normal and abnormal specimens, respectively. Mean and difference spectra suggest presence of blood in abnormal specimen as a major cause of discrimination. However, as tumor is vascular, bleeding was observed during abnormal sample collection. Hence, spectra of abnormal specimens show heme and fibrin features, and this can lead to false interpretations, as bleeding also occur in several non-cancerous conditions. Therefore, remaining 57 specimens were treated with Red Blood Corpuscles (RBC) lysis buffer in order to remove the RBC influence. PC-LDA resulted classification efficiency of about 79% and 78% for normal and abnormal smear, respectively – comparable to Pap test. Thus finding of the study suggests feasibility of Raman spectroscopic classification of normal and cancerous exfoliated cervical cell specimens.     

Principal component analysis: a chemometric aid for classification of polluted and unpolluted mussels

Ten trace elements (Al, Cr, Mn, Fe, Co, Ni, Cu, Zn, Cd and Pb) were determined in the dissolved ash of the edible part of wild mussels (28 samples) from a polluted site by electrothermal atomic absorption spectrometry. The distribution of the concentration of each element in the mussels was first investigated by means of a test of normality. The correlation matrix around the mean was used as a starting matrix for principal component analysis (PCA). Ten variables were reduced to two principal components, accounting for 77% of the total variance; Al, Cr, Mn, Fe, Zn, Cd and Pb are all positively associated with the first principal component and form a cluster of variables, indicating a common terrigenous origin. Comparison with 43 samples of unpolluted mussels from a nearby hatchery, on the basis of eight common variables (concentration of Mn, Fe, Co, Ni, Cu, Zn, Cd and Pb; 71 samples) by using a two-dimensional plot of PC scores, allows the mussels from the two sites to be differentiated.     

Lipids of two species of brown algae of the genusLaminaria

The compositions of the neutral lipids, glycolipids, phospholipids and fatty acids of the brown algaeLaminaria japonica andLaminaria cichoriodes have been studied. It has been found that the glycolipids are the main lipid classes in these algae. Palmitic, oleic, and polyunsaturated acids with 18 and 20 carbon atoms form the group of main acids. The lipids of both species of theLaminaria genus have a complex composition but they differ by the ratios of their fatty acids.Institute of Marine Biology, Far-eastern Scientific Center, Russian Academy of Sciences, Vladivostok, fax (4232) 310900, e-mail: lipid@biom.marine.su. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 22–26, January–February, 1999.     

UPLC-UV-MSE analysis for quantification and identification of major carotenoid and chlorophyll species in algae

A fast method for quantification and identification of carotenoid and chlorophyll species utilizing liquid chromatography coupled with UV detection and mass spectrometry has been demonstrated and validated for the analysis of algae samples. This method allows quantification of targeted pigments and identification of unexpected compounds, providing isomers separation, UV detection, accurate mass measurements, and study of fragment ions for structural elucidation in a single run. This is possible using parallel alternating low- and high-energy collision spectral acquisition modes, which provide accurate mass full scan chromatograms and accurate mass high-energy chromatograms. Here, it is shown how this approach can be used to confirm carotenoid and chlorophyll species by identification of key diagnostic fragmentations during high-energy mode. The developed method was successfully applied for the analysis of Dunaliella salina samples during defined red LED lighting growth conditions, identifying 37 pigments including 19 carotenoid species and 18 chlorophyll species, and providing quantification of 7 targeted compounds. Limit of detections for targeted pigments ranged from 0.01?ng/mL for lutein to 0.24?ng/mL for chlorophyll a. Inter-run precision ranged for of 3 to 24 (RSD%) while inter-run inaccuracy ranged from ?17 to 11.

Absorption and fluorescence spectroscopic characterization of cryptochrome 3 from Arabidopsis thaliana

The blue light photoreceptor cryptochrome 3 (cry3) from Arabidopsis thaliana was characterized at room temperature in vitro in aqueous solution by optical absorption and emission spectroscopic studies. The protein non-covalently binds the chromophores flavin adenine dinucleotide (FAD) and N5,N10-methenyl-5,6,7,8-tetrahydrofolate (MTHF). In the dark-adapted state of cry3, the bound FAD is present in the oxidized form (FAD(ox), ca. 38.5%), in the semiquinone form (FADH., ca. 5%), and in the fully reduced neutral form (FAD(red)H2) or fully reduced anionic form (FAD(red)H-, ca. 55%). Some amount of FAD (ca. 1.5%) in the oxidized state remains unbound probably caused by chromophore release and/or denaturation. F?rster-type energy transfer from MTHF to FAD(ox) is observed. Photo-excitation reversibly modifies the protein conformation causing a slight rise of the MTHF absorption strength and an increase of the MTHF fluorescence efficiency (efficient protein conformation photo-cycle). Additionally there occurs reversible reduction of bound FAD(ox) to FAD(red)H2 (or FAD(red)H-, FAD(ox) photo-cycle of moderate efficiency), reversible reduction of FADH. to FAD(red)H2 (or FAD(red)H-, FADH. photo-cycle of high efficiency), and modification of re-oxidable FAD(red)H2 (or FAD(red)H-) to permanent FAD(red)H2 (or FAD(red)H-) with low quantum efficiency. Photo-excitation of MTHF causes the reversible formation of a MTHF species (MTHF', MTHF photo-cycle, moderate quantum efficiency) with slow recovery to the initial dark state, and also the formation of an irreversible photoproduct (MTHF').     

Absorption and fluorescence spectroscopic characterisation of a phenothiazine–flavin dyad

The phenothiazine–phenylene–isoalloxazine dyad, 3-methyl-10-[4-(10-heptyl-10H-phenothiazin-3-yl)-phenyl]-10H-benzo[g]pteridine-2,4-dione, dissolved in either dichloromethane or acetonitrile is characterized by absorption and emission spectroscopy. Absorption cross-section spectra, stimulated emission cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and degrees of fluorescence polarisation are determined. The fluorescence decay is determined by time-resolved measurements. The dye photo-stability is investigated by observation of absorption spectral changes due to prolonged blue-light excitation. The absorption spectrum of the dyad resembles the superposition of the absorption of the isoalloxazine (flavin) moiety and of the phenylphenothiazine moiety. Photo-excitation of the flavin moiety causes fluorescence quenching by ground-state reductive electron transfer from phenylphenothiazine to isoalloxazine followed by charge recombination. Photo-excitation of the phenothiazine moiety causes (i) efficient excited-state oxidative electron transfer from phenothiazine to isoalloxazine with successive recombination, and (ii) moderate energy transfer followed by ground-state phenothiazine electron transfer and recombination.     

Micro-Raman and X-ray fluorescence spectroscopy data fusion for the classification of ochre pigments

Two different data-fusion strategies are evaluated for the combination of the outputs of combined Raman/X-Ray fluorescence instrument. The studied application deals with the classification of ochre pigments investigated in the field of cultural heritage. The two fusion strategies are: (1) first level fusion: combines raw signals obtained from each technique and (2) second level fusion: combines extracted features provided individually by each technique. Classification tool is partial least squares-discriminant analysis (PLS-DA). Classification results obtained performing different data-fusion strategies are compared with those results obtained performing a single classification model for each data source. The results show that the combination of signal features is the most suitable for a rapid and unique processing of both types of spectra. Benefits and drawbacks of each strategy are also discussed.     

Spectral signatures for the classification of microbial species using Raman spectra

In general, classification-based methods based on confocal Raman microscopy are focused on targeted studies under which the spectral libraries are collected under controlled instrument parameters, which facilitate analyses via standard multivariate data analysis methods and cross-validation. We develop and compare approaches to transform spectra collected at different spectral ranges and varying levels of resolution into a single lower-dimension spectral signature library. This will result in a more robust analysis method able to accommodate spectra accumulated at different times and conditions. We demonstrate these approaches on a relevant test case; the identification of microbial species from a natural environment. The training data were based on samples prepared for three unique species collected at two time points and the test data consisted of blinded unknowns prepared and analyzed at a later date with different instrument parameters. The results indicate that using reduced dimension representations of the spectral signatures improves classification accuracy over basic alignment protocols. In particular, utilizing the microbial species partial least squares discriminant analysis classifier on the blinded samples based on alignment achieved ~78 % accuracy, while both binning and peak selection approaches yielded 100 % accuracy.

啤酒主要成分的近红外光谱法测定

根据近红外光谱的振动吸收强度与有机分子官能团含量的线性关系,用偏最小二乘法,对啤酒的近红外光谱与其中的酒精度、原麦汁浓度以及总酸含量等3种主要成分进行了线性回归,并建立起相关的模型。用该模型对未知啤酒样品中的上述3种成分的含量进行预测,取得了令人非常满意的结果。可望作为啤酒厂的一种快捷而准确的检测方法予以推广。     

Interaction of acrylodan with human serum albumin. A fluorescence spectroscopic study

The binding of the fluorescent probe acrylodan (AC) to human serum albumin (HSA) was studied by fluorescence spectroscopy. The binding isotherms could be fitted to two types of sites. Competition experiments using iodoacetamide suggested that AC binds tightly on HSA by the cysteine-34. Attempts were made to find the location of the second site using high concentrations of warfarin, phenylbutazone, diazepam, indomethacin, palmitic acid or bilirubin in order to displace the bound AC to the HSA. Bilirubin was the only ligand able to displace the bound AC. This result suggests that AC, which is a very hydrophobic molecule also capable of labeling lysine residues, should also bind the human albumin in the primary site of bilirubin, but with less affinity than to the cysteine-34.     

Three-way Resolution of the Overlapping Ultrahigh-performance Liquid Spectrochromatograms for the Analysis of a Quaternary Mixture Using Parallel Factor Analysis

This paper presents a new application of three-way parallel factor analysis (3W-PARAFAC) model to the coeluting spectrochromatograms for the quantitative resolution of a quaternary mixture system consisting of paracetamol, propyphenazone, and caffeine with aspirin as an internal standard. Spectrochromatograms of calibration standards, validation sets, and unknown samples were recorded as a function of retention time and wavelength in the range of 0.0–2.5?min and 200–400?nm, respectively, using ultra-performance liquid chromatography with photodiode array detection (UPLC-PDA). Three-way UPLC-PDA data array X (retention time?×?wavelength?×?sample) was obtained from the data matrices of the spectrochromatograms. 3W-PARAFAC decomposition of three-way UPLC-PDA data array provided three loading matrices corresponding to chromatographic mode, spectral mode, and relative concentration mode. Quantitative estimation of paracetamol, propyphenazone, and caffeine in analyzed samples was accomplished using the relative concentration mode obtained by the deconvolution of the UPLC-PDA data set. The validity and ability of 3W-PARAFAC model were checked by analyzing independent test samples. It was observed from analyses that 3W-PARAFAC method has potential to uniquely resolve strongly overlapping peaks of analyzed compounds in a spectrochromatogram, which was obtained under experimental conditions consisting of the lower flow rate, short run time, and simple mobile phase composition. The proposed three-way chemometric approach was successfully applied to the simultaneous quantification of paracetamol, propyphenazone, and caffeine in tablets. Experiments showed that the determination results were in good agreement with label amount in commercial pharmaceutical preparation.     

Preparative, analytical and fluorescence spectroscopic studies of sulphonated aluminium phthalocyanine photosensitizers

Fluorescence spectroscopic studies were carried out on aluminium phthalocyanine with defined numbers (mono, di, tri and tetra) of sulphonate groups. Selective sulphonation was achieved using one of two synthetic methods to prepare a mixture of components which were separated using reverse-phase liquid chromatography. Fluorescence lifetimes were measured in methanol and buffer solution using time-correlated single-photon counting with picosecond laser excitation; the lifetime shows little variation with the number of sulphonate groups. Using steady state excitation, fluorescence quantum yields were determined for the tetrasulphonated component (phi F = 0.51) and, for comparison, unsulphonated aluminium phthalocyanine.