Spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy are used to study interactions of light with biological materials. This interaction forms the basis of many analytical ...assays used in disease screening/diagnosis, microbiological studies, and forensic/environmental investigations. Advantages of spectrochemical analysis are its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, an urgent need exists for repetition and validation of these methods in large-scale studies and across different research groups, which would bring the method closer to clinical and/or industrial implementation. For this to succeed, it is important to understand and reduce the effect of random spectral alterations caused by inter-individual, inter-instrument and/or inter-laboratory variations, such as variations in air humidity and CO
levels, and aging of instrument parts. Thus, it is evident that spectral standardization is critical to the widespread adoption of these spectrochemical technologies. By using calibration transfer procedures, in which the spectral response of a secondary instrument is standardized to resemble the spectral response of a primary instrument, different sources of variation can be normalized into a single model using computational-based methods, such as direct standardization (DS) and piecewise direct standardization (PDS); therefore, measurements performed under different conditions can generate the same result, eliminating the need for a full recalibration. Here, we have constructed a protocol for model standardization using different transfer technologies described for FTIR spectrochemical applications. This is a critical step toward the construction of a practical spectrochemical analysis model for daily routine analysis, where uncertain and random variations are present.
Target organisms are continuously and variously exposed to contaminant mixtures in the environment. We noted that treatment with brominated diphenyl ether (BDE)47 or polychlorinated biphenyl (PCB)126 ...(toxic equivalency factor TEF = 0.1) induces similar alterations in MCF-7 cells when these were determined using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy with multivariate analysis. Because this method appears sensitive enough to signature low-dose effects, we examined how various test agents interact in binary mixtures to induce cell alterations. MCF-7 cells were exposed for 24 h to low concentrations (10−12 M) of polybrominated diphenyl ether (PBDE) congeners (47, 153, 183, or 209) with or without the coplanar PCB126 or nonplanar PCB153. Following treatment, ethanol-fixed cellular material was interrogated using ATR-FTIR spectroscopy; derived IR spectra in the biochemical-cell fingerprint region (1800 cm−1−900 cm−1) were then subjected to principal component analysis-linear discriminant analysis. Assuming that if two test agents independently induce the same cell alteration that in combination they’ll give rise to an additive effect, we examined predicted versus observed differences in induced alterations by binary mixtures. Compared to corresponding control clusters, treatment with PBDE congener plus PCB126 appeared to cancel out their respective induced alterations. However, treatment with binary mixtures including PCB153 gave rise to an enhanced segregation. Our findings suggest that test agents which mediate their cellular effects via similar mechanisms might result in inhibition within a binary mixture whereas independently acting agents could exacerbate induced alterations in overall cell status.
Full text
Available for:
IJS, KILJ, NUK, PNG, UL, UM
Nanotechnologies generate a wide range of engineered nanomaterials that enter into our ecosystem, especially carbon-based nanoparticles (CNPs). As these novel materials acquire ever increasing ...numbers of applications, they may pose a risk to organisms, including humans. However, our knowledge of nanoparticle-induced effects remains limited. We are yet to understand the interaction between nanoparticles and organisms, and classical toxicology fails to provide models for risk assessment. Biospectroscopy techniques were employed to identify the effects induced by real-world levels of a panel of CNPs. MCF-7 cells concentrated in S-phase or G0/G1-phase were treated for 24 h with short or long multiwalled carbon nanotubes (MWCNTs) or Fullerene (C60) at the following concentrations: 0.0025 mg/L, 0.005 mg/L, 0.01 mg/L, 0.025 mg/L, 0.05 mg/L, and 0.1 mg/L. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with computational analysis was then applied to interrogate the cells and significant dose-related effects were detected. From derived infrared spectra, distinct spectral biomarkers of cell alteration induced by each CNP type were identified. Additionally, Raman spectroscopy was applied and allowed us to determine that reactive oxygen species (ROS) were generated by CNPs. These observations highlight the potential of biospectroscopy techniques to determine CNP-induced alterations in target mammalian cells at ppb levels.
Full text
Available for:
IJS, KILJ, NUK, PNG, UL, UM
Subjective visual assessment of cervical cytology is flawed, and this can manifest itself by inter- and intra-observer variability resulting ultimately in the degree of discordance in the grading ...categorisation of samples in screening vs. representative histology. Biospectroscopy methods have been suggested as sensor-based tools that can deliver objective assessments of cytology. However, studies to date have been apparently flawed by a corresponding lack of diagnostic efficiency when samples have previously been classed using cytology screening. This raises the question as to whether categorisation of cervical cytology based on imperfect conventional screening reduces the diagnostic accuracy of biospectroscopy approaches; are these latter methods more accurate and diagnose underlying disease? The purpose of this study was to compare the objective accuracy of infrared (IR) spectroscopy of cervical cytology samples using conventional cytology vs. histology-based categorisation.
Within a typical clinical setting, a total of n = 322 liquid-based cytology samples were collected immediately before biopsy. Of these, it was possible to acquire subsequent histology for n = 154. Cytology samples were categorised according to conventional screening methods and subsequently interrogated employing attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy. IR spectra were pre-processed and analysed using linear discriminant analysis. Dunn's test was applied to identify the differences in spectra. Within the diagnostic categories, histology allowed us to determine the comparative efficiency of conventional screening vs. biospectroscopy to correctly identify either true atypia or underlying disease.
Conventional cytology-based screening results in poor sensitivity and specificity. IR spectra derived from cervical cytology do not appear to discriminate in a diagnostic fashion when categories were based on conventional screening. Scores plots of IR spectra exhibit marked crossover of spectral points between different cytological categories. Although, significant differences between spectral bands in different categories are noted, crossover samples point to the potential for poor specificity and hampers the development of biospectroscopy as a diagnostic tool. However, when histology-based categories are used to conduct analyses, the scores plot of IR spectra exhibit markedly better segregation.
Histology demonstrates that ATR-FTIR spectroscopy of liquid-based cytology identifies the presence of underlying atypia or disease missed in conventional cytology screening. This study points to an urgent need for a future biospectroscopy study where categories are based on such histology. It will allow for the validation of this approach as a screening tool.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell ...functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
Biospectroscopy is employed to derive absorbance spectra representative of biomolecules present in biological samples. The mid-infrared region (λ = 2.5 μm−25 μm) is absorbed to give a ...biochemical-cell fingerprint (ṽ = 1800−900 cm−1). Cellular material produces complex spectra due to the variety of chemical bonds present. The complexity and size of spectral data sets warrant multivariate analysis for data reduction, interpretation, and classification. Various multivariate analyses are available including principal component analysis (PCA), partial least-squares (PLS), linear discriminant analysis (LDA), and evolving fuzzy rule-based classifier (eClass). Interpretation of both visual and numerical results facilitates biomarker identification, cell-type discrimination, and predictive and mechanistic understanding of cellular behavior. Biospectroscopy is a high-throughput nondestructive technology. A comparison of biomarkers/mechanistic knowledge determined from conventional approaches to biospectroscopy coupled with multivariate analysis often provides complementary answers and a novel approach for diagnosis of disease and cell biology.
Full text
Available for:
IJS, KILJ, NUK, PNG, UL, UM
Environmental contaminants accumulate in many organisms and induce a number of adverse effects. As contaminants mostly occur in the environment as mixtures, it remains to be fully understood which ...chemical interactions induce the most important toxic responses. In this study, we set out to determine the effects of chemical contaminants extracted from Northern Gannet (Morus bassanus) eggs (collected from the UK coast from three sampling years (1987, 1990, and 1992) on cell cultures using infrared (IR) spectroscopy with computational data handling approaches. Gannet extracts were chemically analyzed for different contaminants, and MCF-7 cell lines were treated for 24 h in a dose-related manner with individual-year extracts varying in their polybrominated diphenyl ether (PBDE) to polychlorinated biphenyl (PCB) ratios. Treated cellular material was then fixed and interrogated using attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy; resultant IR spectra were computationally analyzed to derive dose-response relationships and to identify biomarkers associated with each contaminant mixture treatment. The results show distinct biomarkers of effect are related to each contamination scenario, with an inverse relationship with dose observed. This study suggests that specific contaminant mixtures induce cellular alterations in the DNA/RNA spectral region that are most pronounced at low doses. It also suggests alterations in the “biochemical-cell fingerprint” of IR spectra can be indicative of mixture exposures.
Full text
Available for:
IJS, KILJ, NUK, PNG, UL, UM
Applying Fourier-transform infrared (FTIR) spectroscopy (or related technologies such as Raman spectroscopy) to biological questions (defined as biospectroscopy) is relatively novel. Potential fields ...of application include cytological, histological and microbial studies. This potentially provides a rapid and non-destructive approach to clinical diagnosis. Its increase in application is primarily a consequence of developing instrumentation along with computational techniques. In the coming decades, biospectroscopy is likely to become a common tool in the screening or diagnostic laboratory, or even in the general practitioner's clinic. Despite many advances in the biological application of FTIR spectroscopy, there remain challenges in sample preparation, instrumentation and data handling. We focus on the latter, where we identify in the reviewed literature, the existence of four main study goals: Pattern Finding; Biomarker Identification; Imaging; and, Diagnosis. These can be grouped into two frameworks: Exploratory; and, Diagnostic. Existing techniques in Quality Control, Pre-processing, Feature Extraction, Clustering, and Classification are critically reviewed. An aspect that is often visited is that of method choice. Based on the state-of-art, we claim that in the near future research should be focused on the challenges of dataset standardization; building information systems; development and validation of data analysis tools; and, technology transfer. A diagnostic case study using a real-world dataset is presented as an illustration. Many of the methods presented in this review are Machine Learning and Statistical techniques that are extendable to other forms of computer-based biomedical analysis, including mass spectrometry and magnetic resonance.
Potential avenues in exploratory and diagnostic data analysis, biomarker identification and imaging for FTIR spectroscopy: towards a common tool in screening and diagnostics.
IRootLab is a free and open-source MATLAB toolbox for vibrational biospectroscopy (VBS) data analysis. It offers an object-oriented programming class library, graphical user interfaces (GUIs) and ...automatic MATLAB code generation. The class library contains a large number of methods, concepts and visualizations for VBS data analysis, some of which are introduced in the toolbox. The GUIs provide an interface to the class library, including a module to merge several spectral files into a dataset. Automatic code allows developers to quickly write VBS data analysis scripts and is a unique resource among tools for VBS. Documentation includes a manual, tutorials, Doxygen-generated reference and a demonstration showcase. IRootLab can handle some of the most popular file formats used in VBS. License: GNU-LGPL.
Official website: http://irootlab.googlecode.com/.
Supplementary data are available at Bioinformatics online.
Currently available screening tests do not deliver the required sensitivity and specificity for accurate diagnosis of ovarian or endometrial cancer. Infrared (IR) spectroscopy of blood plasma or ...serum is a rapid, versatile, and relatively non-invasive approach which could characterize biomolecular alterations due to cancer and has potential to be utilized as a screening or diagnostic tool. In the past, no such approach has been investigated for its applicability in screening and/or diagnosis of gynaecological cancers. We set out to determine whether attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy coupled with a proposed classification machine could be applied to IR spectra obtained from plasma and serum for accurate class prediction (cancer vs. normal). Plasma and serum samples were obtained from ovarian cancer cases (n = 30), endometrial cancer cases (n = 30) and non-cancer controls (n = 30), and subjected to ATR-FTIR spectroscopy. Four derived datasets were processed to estimate the real-world diagnosis of ovarian and endometrial cancer. Classification results for ovarian cancer were remarkable (up to 96.7%), whereas endometrial cancer was classified with a relatively high accuracy (up to 81.7%). The results from different combinations of feature extraction and classification methods, and also classifier ensembles, were compared. No single classification system performed best for all different datasets. This demonstrates the need for a framework that can accommodate a diverse set of analytical methods in order to be adaptable to different datasets. This pilot study suggests that ATR-FTIR spectroscopy of blood is a robust tool for accurate diagnosis, and carries the potential to be utilized as a screening test for ovarian cancer in primary care settings. The proposed classification machine is a powerful tool which could be applied to classify the vibrational spectroscopy data of different biological systems (e.g., tissue, urine, saliva), with their potential application in clinical practice.
PDF
