Rapid Quantification of Methamphetamine: Using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) and Chemometrics

In Australia and increasingly worldwide, methamphetamine is one of the most commonly seized drugs analysed by forensic chemists. The current well-established GC/MS methods used to identify and quantify methamphetamine are lengthy, expensive processes, but often rapid analysis is requested by undercover police leading to an interest in developing this new analytical technique. Ninety six illicit drug seizures containing methamphetamine (0.1%–78.6%) were analysed using Fourier Transform Infrared Spectroscopy with an Attenuated Total Reflectance attachment and Chemometrics. Two Partial Least Squares models were developed, one using the principal Infrared Spectroscopy peaks of methamphetamine and the other a Hierarchical Partial Least Squares model. Both of these models were refined to choose the variables that were most closely associated with the methamphetamine % vector. Both of the models were excellent, with the principal peaks in the Partial Least Squares model having Root Mean Square Error of Prediction 3.8, R² 0.9779 and lower limit of quantification 7% methamphetamine. The Hierarchical Partial Least Squares model had lower limit of quantification 0.3% methamphetamine, Root Mean Square Error of Prediction 5.2 and R² 0.9637. Such models offer rapid and effective methods for screening illicit drug samples to determine the percentage of methamphetamine they contain.     

Fourier Transform Infrared with Attenuated Total Reflectance Applied to the Discrimination of Freshwater Planktonic Coccoid Green Microalgae

Despite the recent advances on fine taxonomic discrimination in microorganisms, namely using molecular biology tools, some groups remain particularly problematic. Fine taxonomy of green algae, a widely distributed group in freshwater ecosystems, remains a challenge, especially for coccoid forms. In this paper, we propose the use of the Fourier Transform Infrared (FTIR) spectroscopy as part of a polyphasic approach to identify and classify coccoid green microalgae (mainly order Sphaeropleales), using triplicated axenic cultures. The attenuated total reflectance (ATR) technique was tested to reproducibility of IR spectra of the biological material, a primary requirement to achieve good discrimination of microalgal strains. Spectral window selection was also tested, in conjunction with the first derivative treatment of spectra, to determine which regions of the spectrum provided better separation and clustering of strains. The non-metric multidimensional scaling (NMDS), analysis of similarities (ANOSIM) and hierarchical clusters (HCA), demonstrated a correct discrimination and classification of closely related strains of chlorophycean coccoid microalgae, with respect to currently accepted classifications. FTIR-ATR was highly reproducible, and provided an excellent discrimination at the strain level. The best separation was achieved by analyzing the spectral windows of 1500–1200 cm⁻¹ and 900–675 cm⁻¹, which differs from those used in previously studies for the discrimination of broad algal groups, and excluding spectral regions related to storage compounds, which were found to give poor discrimination. Furthermore, hierarchical cluster analyses have positioned the strains tested into clades correctly, reproducing their taxonomic orders and families. This study demonstrates that FTIR-ATR has great potential to complement classical approaches for fine taxonomy of coccoid green microalgae, though a careful spectrum region selection is needed.     

Fourier Transform Infrared and Raman Spectroscopy for Characterization of Listeria monocytogenes Strains

The purpose of this study was to characterize the variation in biochemical composition of 89 strains of Listeria monocytogenes with different susceptibilities towards sakacin P, using Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. The strains were also analyzed using amplified fragment length polymorphism (AFLP) analysis. Based on their susceptibilities to sakacin P, the 89 strains have previously been divided into two groups. Using the FTIR spectra and AFLP data, the strains were basically differentiated into the same two groups. Analyses of the FTIR and Raman spectra revealed that the strains in the two groups contained differences in the compositions of carbohydrates and fatty acids. The relevance of the variation in the composition of carbohydrates with respect to the variation in the susceptibility towards sakacin P for the L. monocytogenes strains is discussed.     

Identification of Yersinia enterocolitica at the Species and Subspecies Levels by Fourier Transform Infrared Spectroscopy

Yersinia enterocolitica and other Yersinia species, such as Y. pseudotuberculosis, Y. bercovieri, and Y. intermedia, were differentiated using Fourier transform infrared spectroscopy (FT-IR) combined with artificial neural network analysis. A set of well defined Yersinia strains from Switzerland and Germany was used to create a method for FT-IR-based differentiation of Yersinia isolates at the species level. The isolates of Y. enterocolitica were also differentiated by FT-IR into the main biotypes (biotypes 1A, 2, and 4) and serotypes (serotypes O:3, O:5, O:9, and “non-O:3, O:5, and O:9”). For external validation of the constructed methods, independently obtained isolates of different Yersinia species were used. A total of 79.9% of Y. enterocolitica sensu stricto isolates were identified correctly at the species level. The FT-IR analysis allowed the separation of all Y. bercovieri, Y. intermedia, and Y. rohdei strains from Y. enterocolitica, which could not be differentiated by the API 20E test system. The probability for correct biotype identification of Y. enterocolitica isolates was 98.3% (41 externally validated strains). For correct serotype identification, the probability was 92.5% (42 externally validated strains). In addition, the presence or absence of the ail gene, one of the main pathogenicity markers, was demonstrated using FT-IR. The probability for correct identification of isolates concerning the ail gene was 98.5% (51 externally validated strains). This indicates that it is possible to obtain information about genus, species, and in the case of Y. enterocolitica also subspecies type with a single measurement. Furthermore, this is the first example of the identification of specific pathogenicity using FT-IR.The genus Yersinia belongs to the bacterial family Enterobacteriaceae and encompasses three well-known human pathogens: Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica. Pathogenic strains of Y. enterocolitica cause yersiniosis, an acute enteric disease. In Germany and Switzerland, strains of Y. enterocolitica belong to the most frequently isolated pathogens connected with bacterial gastroenteritis (27, 31). Y. enterocolitica also causes other clinical syndromes, such as enterocolitis, acute mesenteric lymphadenitis, mimicking appendicitis, postinfectious arthritis, and systemic infections (7, 21). It is assumed that the main contamination source is food of animal origin, especially pork meat or raw milk (8, 21, 27). Therefore, the focus of diagnosis for these bacteria as food-borne pathogens includes the examination of food samples in food inspection and veterinary controls of livestock.The species Y. enterocolitica sensu lato as described by Frederiksen (9) was recently subdivided into several species: Y. enterocolitica sensu stricto, Y. intermedia, Y. frederiksenii, Y. kristensenii, Y. aldovae, Y. mollaretii, Y. rohdei, and Y. bercovieri (20). The identification of Y. enterocolitica sensu stricto by traditional agar plate techniques (ISO standard 10273:2003) is complicated by the fact that on the commonly used selective agar plates, especially the cefsulodin-irgasan-novobiocin (CIN) agar, several unrelated bacteria also grow (1, 20). In addition, some Yersinia strains are inhibited by CIN agar (10). The differentiation of putative Yersinia strains isolated from the CIN agar is additionally impeded because the commonly used commercial identification systems (for example, API 20E or API Rapid 32IDE) do not include all Yersinia strains in their databases and usually misidentify them as Y. enterocolitica (12). Nevertheless, the biochemical test system API 20E is still used as an affordable tool for the identification of Y. enterocolitica. This probably results in a constant misidentification of certain Yersinia species, particularly Y. bercovieri, Y. rohdei, and Y. intermedia, as Y. enterocolitica (1, 12, 15).Y. enterocolitica sensu stricto comprises pathogenic and nonpathogenic members. The species can be grouped into various biotypes by biochemical tests and independently into different serotypes by immunological tests. Both types are connected with different pathogenic potential. The most common biotype-serotype combinations associated with human diseases were biotype 1B/serotype O:8, 2/O:5,27, 2/O:9, 3/O:3, and 4/O:3 (7). Biotype 1A is deemed to be non- or less pathogenic for humans. Biotype 1B is widespread in the United States and only rarely detected in Europe and Japan (11, 14, 26, 28). Based on different DNA-DNA hybridization values and 16S rRNA gene sequences, it was proposed to name the “American” strains Y. enterocolitica subsp. enterocolitica (19). Biotypes 2 and 4 are often isolated from yersiniosis patients, and biotype 3 seems to be pathogenic but rare (6, 21).Pathogenic strains of Y. enterocolitica harbor certain virulence factors, such as the plasmid-encoded yadA gene and the chromosomally encoded ail gene (17, 32). In contrast, apathogenic strains of Y. enterocolitica do not contain these two genes. However, the plasmid harboring the yadA gene can be lost under certain cultivation conditions in the laboratory (4). This may lead to false-negative results in any test system based on the presence of this plasmid. Therefore, the ail gene appears to be the best-suited marker for the detection of pathogenic Y. enterocolitica strains. The product of the ail gene is an adhesion and invasion factor (17). Therefore, the detection of the ail gene by PCR is used as an indication of the presence of pathogenic strains of Y. enterocolitica in selective enrichments or isolated pure cultures (33).Recently, Fourier transform infrared spectroscopy (FT-IR) has been established as a new method for identification of bacteria, yeasts, and other microorganisms (3, 16, 22, 24, 38). This method analyzes the total composition of all components of the cell using infrared spectroscopy (13, 18). The FT-IR method is rapid and reliable and therefore can be easily adapted to routine analysis. Furthermore, there accrue almost no costs for consumables during sample preparation and measurements. The technique offers a wide range of applications for differentiation at the species and subspecies levels. It has already been used for the differentiation of several food-borne pathogens, like Listeria monocytogenes (25), Escherichia coli (13), and Bacillus cereus (23, 29). Recently, promising results were obtained by combination of FT-IR and multivariate methods for data processing, in particular artificial neural networks (ANN) (25, 35).In the present work, FT-IR combined with ANN analysis was applied for classification of Yersinia strains at the species level and of Y. enterocolitica at the subspecies level. Furthermore, differentiation between pathogenic and apathogenic strains of Y. enterocolitica by FT-IR was attempted.     

Fourier Transform Infrared Reflection Absorption Spectroscopy (FT-IRAS) of fibrinogen adsorbed on metal and metal oxide surfaces

We have investigated the possibilities of using Infrared Reflection Absorption Spectroscopy in the study of the interaction of proteins with metal surfaces. Structural information can be obtained since the infrared radiation at the metal surface interacts only with dipole transition moments perpendicular to the metal surface. Fibrinogen spontaneously adsorbed from solution onto gold, titanium and aluminum was used as model systems. The infrared studies were carried out on dried protein films. The amide I bands of fibrinogen adsorbed on the metal surfaces shift towards higher frequencies (ca. 20 cm-1) relative to the same band in buffer solution. The magnitude of these shifts indicates that conformational change of the protein occurs upon adsorption on metal surfaces. The change in conformation of the fibrinogen also can partly be due to one week of drying at room temperature. The amide I and amide II bands show a slightly different behaviour in terms of frequency and intensity for each metal-protein system studied. The side chains appeared to be more substrate sensitive than the peptide group. Orientational effects were observed for a number of side-chain related groups.     

In Situ Monitoring of the Nascent Pseudomonas fluorescens Biofilm Response to Variations in the Dissolved Organic Carbon Level in Low-Nutrient Water by Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy

Drinking water quality management requires early warning tools which enable water supply companies to detect quickly and to forecast degradation of the microbial quality of drinking water during its transport throughout distribution systems. This study evaluated the feasibility of assessing, in real time, drinking water biostability by monitoring in situ the evolution of the attenuated total reflectance-Fourier transform infrared (ATR-FTIR) fingerprint of a nascent reference biofilm exposed to water being tested. For this purpose, the responses of nascent Pseudomonas fluorescens biofilms to variations in the dissolved organic carbon (DOC) level in tap water were monitored in situ and in real time by ATR-FTIR spectroscopy. Nascent P. fluorescens biofilms consisting of a monolayer of bacteria were formed on the germanium crystal of an ATR flowthrough cell by pumping bacterial suspensions in Luria-Bertani (LB) medium through the cell. Then they were exposed to a continuous flow of dechlorinated sterile tap water supplemented with appropriate amounts of sterile LB medium to obtain DOC concentrations ranging from 1.5 to 11.8 mg/liter. The time evolution of infrared bands related to proteins, polysaccharides, and nucleic acids clearly showed that changes in the DOC concentration resulted in changes in the nascent biofilm ATR-FTIR fingerprint within 2 h after exposure of the biofilm to the water being tested. The initial bacterial attachment, biofilm detachment, and regrowth kinetics determined from changes in the areas of bands associated with proteins and polysaccharides were directly dependent on the DOC level. Furthermore, they were consistent with bacterial adhesion or growth kinetic models and extracellular polymeric substance overproduction or starvation-dependent detachment mechanisms.     

High-Throughput Metabolic Fingerprinting of Legume Silage Fermentations via Fourier Transform Infrared Spectroscopy and Chemometrics

Silage quality is typically assessed by the measurement of several individual parameters, including pH, lactic acid, acetic acid, bacterial numbers, and protein content. The objective of this study was to use a holistic metabolic fingerprinting approach, combining a high-throughput microtiter plate-based fermentation system with Fourier transform infrared (FT-IR) spectroscopy, to obtain a snapshot of the sample metabolome (typically low-molecular-weight compounds) at a given time. The aim was to study the dynamics of red clover or grass silage fermentations in response to various inoculants incorporating lactic acid bacteria (LAB). The hyperspectral multivariate datasets generated by FT-IR spectroscopy are difficult to interpret visually, so chemometrics methods were used to deconvolute the data. Two-phase principal component-discriminant function analysis allowed discrimination between herbage types and different LAB inoculants and modeling of fermentation dynamics over time. Further analysis of FT-IR spectra by the use of genetic algorithms to identify the underlying biochemical differences between treatments revealed that the amide I and amide II regions (wavenumbers of 1,550 to 1,750 cm⁻¹) of the spectra were most frequently selected (reflecting changes in proteins and free amino acids) in comparisons between control and inoculant-treated fermentations. This corresponds to the known importance of rapid fermentation for the efficient conservation of forage proteins.     

Application of Fourier Transform Infrared Spectroscopy and Chemometrics for Differentiation of Salmonella enterica Serovar Enteritidis Phage Types

Fourier transform infrared (FT-IR) spectroscopy and chemometric techniques were used to discriminate five closely related Salmonella enterica serotype Enteritidis phage types, phage type 1 (PT1), PT1b, PT4b, PT6, and PT6a. Intact cells and outer membrane protein (OMP) extracts from bacterial cell membranes were subjected to FT-IR analysis in transmittance mode. Spectra were collected over a wavenumber range from 4,000 to 600 cm⁻¹. Partial least-squares discriminant analysis (PLS-DA) was used to develop calibration models based on preprocessed FT-IR spectra. The analysis based on OMP extracts provided greater separation between the Salmonella Enteritidis PT1-PT1b, PT4b, and PT6-PT6a groups than the intact cell analysis. When these three phage type groups were considered, the method based on OMP extract FT-IR spectra was 100% accurate. Moreover, complementary local models that considered only the PT1-PT1b and PT6-PT6a groups were developed, and the level of discrimination increased. PT1 and PT1b isolates were differentiated successfully with the local model using the entire OMP extract spectrum (98.3% correct predictions), whereas the accuracy of discrimination between PT6 and PT6a isolates was 86.0%. Isolates belonging to different phage types (PT19, PT20, and PT21) were used with the model to test its robustness. For the first time it was demonstrated that FT-IR analysis of OMP extracts can be used for construction of robust models that allow fast and accurate discrimination of different Salmonella Enteritidis phage types.Over the past 10 years there has been an increase in the incidence of gastrointestinal infections caused by Salmonella enterica serovar Enteritidis, which is now one of the leading S. enterica serotypes worldwide (21, 27). Poultry, poultry products, cattle, and dairy products are the predominant sources of Salmonella-contaminated food products that cause human salmonellosis (28). Large-scale infections continue to occur in developed countries (8). Unrestricted international movement of commercially prepared food and food ingredients and dissimilarities in government and industry food safety controls during the processing, distribution, and marketing of products have surely contributed to the increase in food-borne outbreaks. Salmonella is a tremendous challenge for the agricultural and food processing industries because of its ability to survive under adverse conditions, such as low levels of nutrients and suboptimal temperatures (4, 13).Salmonella Enteritidis isolates can be categorized for epidemiological purposes by using a variety of typing tools (13). These tools include typing techniques such as serological and phage typing (29) and antibiotic resistance patterns (25). These methods are now supplemented by molecular genetics techniques, such as DNA fingerprinting (23), plasmid profiling (16), and pulsed-field gel electrophoresis (26). Phage typing has been used to diagnose Salmonella outbreaks, including S. enterica serovar Typhi and S. enterica serovar Typhimurium outbreaks (29). It is useful to evaluate whether isolates obtained from different sources at different times are similar or distinct in terms of their reactions with a specific collection of bacteriophages used for typing. The correlation between phage type and the source of an epidemic is high (22). Although very effective, existing classification methods are time-consuming, laborious, and expensive, and they often require special training of personnel and expertise, which can prevent a rapid response to the presence of pathogenic bacterial species.Fourier transform infrared (FT-IR) spectroscopy has been successfully used for differentiation and classification of microorganisms at the species and subspecies levels (7, 9, 12, 15, 18, 19, 20). This technique has been shown to have high discriminatory power and allows identification of bacteria at distinct taxonomic levels based on differences in the infrared absorption patterns of microbial cells. FT-IR spectroscopy has been used to differentiate and characterize intact microbial cells based on outer membrane cell components, including lipopolysaccharides (LPS), lipoproteins, and phospholipids (24). Several studies in which S. enterica serotypes have been discriminated using multivariate data analysis and FT-IR spectroscopy have been performed (1, 2, 10, 11). Kim et al. (11) compared the FT-IR spectra of intact cells and the FT-IR spectra of outer membrane protein (OMP) extracts from S. enterica serotypes to discriminate serotypes. Analysis of spectra of OMP extracts in the 1,800- to 1,500-cm⁻¹ region resulted in 100% correct classification of the serotypes investigated.Previously, there have been no reports of differentiation of Salmonella Enteritidis phage types by FT-IR spectroscopy and chemometric methods. To discriminate closely related phage types of Salmonella Enteritidis in this study, intact cells and OMP extracts of bacterial cell membranes were subjected to FT-IR analysis. The isolates analyzed included isolates belonging to five of the phage types of Salmonella Enteritidis found most frequently in Portuguese hospitals in the period from 2004 to 2006, phage type 1 (PT1), PT1b, PT4b, PT6, and PT6a (5, 14). Chemometric models were used to discriminate between phage types based on infrared spectra.     

油菜籽含油量傅里叶变换近红外模型的修正

为了提高近红外模型的精确度与准确度,需要定期地对原模型进行修正。常用的方法是在原模型中添加一些包含新信息的新样品,因此,样品的选择成为模型维护过程中的关键因素之一。以利用近红外光谱分析法测定油菜籽含油量为例,向原模型中添加不同偏差的样品建立独立的近红外模型,并设计相应的验证集对各模型的预测性能进行全面评价。结果表明:不同偏差的样品对模型预测性能的改善效果有差异,只有当新样品的偏差与原模型的预测偏差相匹配时,添加的新样品才能更有效地对原模型进行修正。依据偏差选择样品的新思路为近红外模型的维护提供了一条有效地途径。     

Characterisation of Authentic Lignin Biorefinery Samples by Fourier Transform Infrared Spectroscopy and Determination of the Chemical Formula for Lignin

Efficient methods for lignin characterisation are increasingly important as the field of lignin valorisation is growing with the increasing use of lignocellulosic feedstocks, such as wheat straw and corn stover, in biorefineries. In this study, we characterised a set of authentic lignin biorefinery samples in situ with no prior purification and minimal sample preparation. Lignin chemical formulas and lignin Fourier transform infrared (FTIR) spectra were extracted from mixed spectra by filtering out signals from residual carbohydrates and minerals. From estimations of C, H and O and adjustment for cellulose and hemicelluloses contents, the average chemical formula of lignin was found to be C₉H_10.2O_3.4 with slight variations depending on the biomass feedstock and processing conditions (between C₉H_9.5O_2.8 and C₉H_11.1O_3.6). Extracted FTIR lignin spectra showed many of the same characteristic peaks as organosolv and kraft lignin used as benchmark samples. Some variations in the lignin spectra of biorefinery lignin residue samples were found depending on biomass feedstock (wheat straw, corn stover or poplar) and on pretreatment severity, especially in the absorbance of bands at 1267 and 1032 cm^?1 relative to the strong band at ~1120 cm^?1. The suggested method of FTIR spectral analysis with adjustment for cellulose and hemicellulose is proposed to provide a fast and efficient way of analysing lignin in genuine lignin samples resulting from biorefineries.     

人血清中胆固醇近红外光谱快速检测初步研究

以全自动生化分析仪测定结果为参考值,采用傅利叶变换近红外透射光谱技术,结合偏最小二乘法,建立人血清中胆固醇和甘油三酯的定标模型。利用内部交叉验证和自动优化功能对预测模型进行了优化,确定了最优建模参数。模型对人血清中胆固醇和甘油三酯定标样品集的预测值与参考值的相关系数r分别为0．9011、0．9593,预测校正标准误RMSECV分别为15．0mg／dL,21．6mg／dL。表明利用近红外光谱分析技术实现血清中胆固醇和甘油三酯快速检测是可行的。     

Molecular View by Fourier Transform Infrared Spectroscopy of the Relationship between Lactocin 705 and Membranes: Speculations on Antimicrobial Mechanism

Lactocin 705 is a bacteriocin whose activity depends upon the complementation of two peptides, termed Lac705α and Lac705β. Neither Lac705α nor Lac705β displayed bacteriocin activity by itself when the growth of sensitive cells was monitored. To obtain molecular insights into the lactocin 705 mechanism of action, Fourier transform infrared spectroscopy was used to investigate the interactions of each peptide (Lac705α and Lac705β) with dipalmitoylphosphatidylcholine liposomal membranes. Both peptides show the ability to interact with the zwitterionic membrane but at different bilayer levels. While Lac705α interacts with the interfacial region inducing dehydration, Lac705β peptide interacts with only the hydrophobic core. This paper presents the first experimental evidence that supports the hypothesis that Lac705α and Lac705β peptides could form a transmembrane oligomer. From the obtained results, a mechanism of action of lactocin 705 on membrane systems is proposed. The component Lac705α could induce the dehydration of the bilayer interfacial region, and the Lac705β peptide could insert in the hydrophobic region of the membrane where the peptide has adequate conditions to achieve the oligomerization.     

Resins for Combined Light and Electron Microscopy: A Half Century of Development

The last fifty years have seen enormous improvements in the way biological specimens are prepared for microscopy. The Fifties produced the essential groundwork upon which many of our current methodologies are based. Acrylic resin embedding was introduced in 1949, with subsequent publications seeking improvements to resin formulations, embedding protocols, and modes of polymerisation. Procedures for progressive lowering of temperature processing, cryosubstitution, freeze-drying and polymerisation by ultra-violet light at low temperatures, all had their genesis in this decade of great innovation. The Sixties marked the period when the acrylics were eclipsed by the more stable and reliable epoxy resins, and much of our present-day understanding of ultrastructure was elucidated. The Seventies carried on this work with advances in technical developments concerned mainly with freezing methodologies. The beginning of the Eighties saw a resurrection of the acrylic resins, with new formulations of these resins giving reliable and stable embeddings. The low temperature and freezing methodologies pioneered in the Fifties, backed up by recent improvements to low temperature technologies, were used to further our understanding of ultrastructure and breathe new life into the science of immunocytochemistry. The remainder of the Eighties and Nineties has seen the ever increasing application of these various microscopical techniques to a wide range of biological studies. The flexibility offered by the acrylic resins in choosing between different processing, embedding and polymerisation methods has provided the impetus for detailed studies to bring to the attention of microscopists the underlying trends governing specimen preparation. Therefore, looking forward to the new Millennium, this has allowed for a more reasoned choice in organising a strategy to deal with a variety of microscopical requirements and for planning an appropriate protocol.     

Phenotypic Characterization of Shewanella oneidensis MR-1 under Aerobic and Anaerobic Growth Conditions by Using Fourier Transform Infrared Spectroscopy and High-Performance Liquid Chromatography Analyses

Shewanella oneidensis is able to conserve energy for growth by reducing a wide variety of terminal electron acceptors during anaerobic respiration, including several environmentally hazardous pollutants. This bacterium employs various electron transfer mechanisms for anaerobic respiration, including cell-bound reductases and secreted redox mediators. The aim of this study was to develop rapid tools for profiling the key metabolic changes associated with these different growth regimes and physiological responses. Initial experiments focused on comparing cells grown under aerobic and anaerobic conditions. Fourier transform infrared (FT-IR) spectroscopy with cluster analysis showed that there were significant changes in the metabolic fingerprints of the cells grown under these two culture conditions. FT-IR spectroscopy clearly differentiated cells of S. oneidensis MR-1 cultured at various growth points and cells grown using different electron acceptors, resulting in different phenotypic trajectories in the cluster analysis. This growth-related trajectory analysis is applied successfully for the first time, here with FT-IR spectroscopy, to investigate the phenotypic changes in contrasting S. oneidensis cells. High-performance liquid chromatography (HPLC) was also used to quantify the concentrations of flavin compounds, which have been identified recently as extracellular redox mediators released by a range of Shewanella species. The partial least-squares regression (PLSR) multivariate statistical technique was combined with FT-IR spectroscopy to predict the concentrations of the flavins secreted by cells of S. oneidensis MR-1, suggesting that this combination could be used as a rapid alternative to conventional chromatographic methods for analysis of flavins in cell cultures. Furthermore, coupling of the FT-IR spectroscopy and HPLC techniques appears to offer a potentially useful tool for rapid characterization of the Shewanella cell metabolome in various process environments.Shewanella oneidensis, a Gram-negative dissimilatory metal-reducing bacterium, is able to conserve energy for growth by reducing a variety of terminal electron acceptors during aerobic and anaerobic respiration (24), including several environmentally hazardous pollutants (1). The terminal electron acceptors used during anaerobic respiration vary, ranging from nitrate, fumarate, trimethylamine N-oxide (TMAO), dimethyl sulfoxide (DMSO), and sulfur compounds to fuel cell anodes and various metals and metalloids, including insoluble metal oxides (5, 33, 34).There has been intense interest in the versatile metabolism of this bacterium and its potential to respire and bioremediate toxic environmental chemicals and metals, such as U(VI) and Cr(VI) (25, 43), under anoxic conditions. Riboflavin (RF), flavin mononucleotide (FMN), and flavin-adenine dinucleotide (FAD) were identified as the dominant electron shuttles secreted by a diversity of Shewanella cells and shown to mediate extracellular reduction of insoluble Fe(III) minerals and organic molecules, including azo dyes (23, 40). Field and Brady tested riboflavin and found that its presence during anaerobic reduction of azo dyes improves the overall kinetics of the reduction process (9). von Canstein et al. recently found that Shewanella cells are able to secrete flavins, FAD, FMN, and riboflavin as extracellular redox mediators and quantified these using high-performance liquid chromatography-mass spectrometry (HPLC-MS) (44). The experiments showed that the production profiles of these three chemicals were different under anaerobic and aerobic regimes, and this can be used to distinguish the two metabolic pathways with oxygen or fumarate as electron acceptors.Although we are gaining a deeper understanding of the genetic and biochemical basis of the diverse respiration pathways of this organism, supported by the recent availability of the complete genome sequence (14), complementary metabolomic approaches have not been used to identify or quantify the metabolic changes expected with major physiological shifts in this organism under contrasting growth regimes. Fourier transform infrared (FT-IR) spectroscopy was chosen for this study, as this method offers the advantage of minimal sample preparation, as well as being rapid, nondestructive, readily automatable, relatively inexpensive, and quantitative, compared with other metabolic profiling techniques (8, 12, 15, 35). The infrared absorbance spectra generated by FT-IR spectroscopy have been used to identify specific biochemical features and also provide a global biochemical “fingerprint” for mixed, complex samples (11, 27) in many research areas (10, 11). For instance, FT-IR spectroscopy has proved sensitive enough for analysis of the chemical composition of a single strain of Escherichia coli after exposure to ionic liquids (6), for functional genomics screening (22), for measuring abiotic perturbations in algae (39), and for characterization of microbial degradation pathways (16). We believe that this technique offers considerable potential for rapid differentiation of metabolic changes of bacteria responding to contrasting growth regimes in natural and engineered environments, although this remains to be demonstrated.The FT-IR spectra generated from microorganisms have very complex profiles that can be related back to biochemical components which one would expect to be detected in the samples. While some subtle quantitative differences can be observed between the spectra, there are few, if any, qualitative differences to be seen, and so it is almost impossible to interpret these data with the naked eye (19, 20, 45). Therefore, multivariate statistical techniques are needed to model the relationship between the phenotypic changes occurring in this organism during growth with the observations recorded by FT-IR spectroscopy.In the present study, we investigated the ability of FT-IR spectroscopy to analyze the S. oneidensis MR-1 cell metabolome and distinguish significant metabolic changes associated with anaerobic and aerobic growth conditions. Analyses were conducted directly on the cells for the endometabolome in assessing the metabolic fingerprint. Both unsupervised and supervised learning methods (viz., principal component analysis [PCA] [21] and discriminant function analysis [DFA] [26]) were used to identify any differences between the FT-IR spectra from cells grown under the two regimes, and the contributions of a range of biomolecules were elucidated. In addition to metabolic fingerprinting of whole cells by FT-IR, key components of the extracellular metabolome (the so-called exometabolome, or metabolic footprint) were also quantified by HPLC analysis. Here, riboflavin, FMN, and FAD in culture supernatants were quantified, and partial least-squares regression (PLSR) was used to identify correlations between the cell''s FT-IR spectra and flavin concentrations assessed using HPLC data. These studies show for the first time that FT-IR analyses can be used for rapid identification of metabolic shifts in both the intracellular and the extracellular metabolomes of S. oneidensis MR-1 cultures.     

Application of Fourier Transform Near-Infrared Spectroscopy Combined with High-Performance Liquid Chromatography in Rapid and Simultaneous Determination of Essential Components in Crude Radix Scrophulariae

A method is described using rapid and sensitive Fourier transform near-infrared spectroscopy combined with high-performance liquid chromatography–diode array detection for the simultaneous identification and determination of four bioactive compounds in crude Radix Scrophulariae samples. Partial least squares regression is selected as the analysis type and multiplicative scatter correction, second derivative, and Savitzky–Golay filter were adopted for the spectral pretreatment. The correlation coefficients (R) of the calibration models were above 0.96 and the root mean square error of predictions were under 0.028. The developed models were applied to unknown samples with satisfactory results. The established method was validated and can be applied to the intrinsic quality control of crude Radix Scrophulariae.KEY WORDS: crude Radix Scrophulariae, FT-NIRS, HPLC-DAD, quality control, quantification     

Epoxy Embedding, Sectioning and Staining of Plant Material for Light Microscopy

By using a formula which gives a relatively soft epoxy embedding medium, it is possible to cut sections of plant material with a sliding microtome equipped with a regular steel knife. Blocks having a cutting face of 10 × 10 mm, giving sections of 4-10 μm, can be used. Tissues are fixed in Karnovsky's fluid, postfixed in 1 or 2% OsO₄, embedded in Spurr's soft epoxy resin, Araldite, or Epon mixtures. 5% KMnO₄, followed by 5% oxalic acid, then neutralized in 1% LiCO₃, are used to mordant the sections. Some of the stains used are Mallory's phosphotungstic acid-hemotoxylin, acid fuchsin and toluidine blue, or toluidine blue. Mounting is done with whichever soft epoxy resin was used in casting the blocks.     

Conformations of hydrophobic peptides in trifluoroethanol, water and in solid state: a circular dichroism and Fourier Transform Infrared study

The conformations of peptides corresponding to KLLIALVLCFLPLAALG have been examined in trifluoroethanol (TFE), aqueous medium by circular dichroism spectroscopy and in the solid state by Fourier Transform Infra Red Spectroscopy (FTIR). The 17-residue parent peptide and peptides corresponding to shorter segments LVLCFLPLAALG and CFLPLAALG showed preference for helical conformation in TFE. Even the shorter hydrophobic peptides corresponding to KLLIA and LVL showed propensity for beta-turn conformations in TFE. However, peptides corresponding to the relatively polar segment FLPLAALG were unordered in TFE. In water, peptides that showed ordered conformation in TFE preferred beta-conformation. In solid-state, FTIR spectra indicated that the hydrophobic peptides adopt beta-structures with extensive hydrogen bonded network in the solid-state. The hydrophobic core segment thus appears to dictate the conformational propensity of the peptide.