Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.
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ABSTRACT:
SUBMITTER: Mackie DM
PROVIDER: S-EPMC4781924 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Genomics-based population analysis of multidrug-resistant (MDR) Klebsiella pneumoniae motivated a renewed interest on the capsule as an evolutionary and virulence marker of clinically relevant strains. Whole-genome sequencing (WGS)-based approaches have provided great insights into the genetic variability of the capsular locus, but genotypic-biochemical capsular (K)-type correlations are lacking, hindering the establishment of a reliable framework for K-type characterization and typing. To fill this gap, we combined molecular, comparative genomics, and multivariate data analysis tools with biochemical data on the capsular locus to support the usefulness of Fourier transform infrared (FT-IR) spectroscopy as a reliable K typing tool. To validate our approach, we used a representative collection of well-defined MDR K. pneumoniae lineages involved in local or nationwide epidemics in multiple countries. With this, we demonstrate a high accuracy and resolution of our FT-IR-based spectroscopy approach for K-type discrimination that is even higher than that provided by WGS. Moreover, the specific associations established between certain K types and specific K. pneumoniae lineages with high clinical relevance, together with the accuracy, simplicity, short time to result, and inexpensive features of the method, support the value of the developed FT-IR-based approach for an easy, fast, and cost-effective strain typing. This fulfills a still unmet need for tools to support real-time monitoring and control of K. pneumoniae infections. In addition, the genotypic-biochemical correlations established provide insights on sugar composition/structure of newly defined K. pneumoniae capsular types.IMPORTANCE Klebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity.
| S-EPMC7093823 | biostudies-literature
Project description:Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.
| S-EPMC8473902 | biostudies-literature
Project description:We used diffuse reflectance Fourier-transform infrared (DR-FTIR) spectroscopy, X-ray diffraction (XRD), and chemical and isotopic analyses to characterize the light fraction of four contrasting soils (control and biocharamended soils) to determine changes in biochar properties after aging. Two Eucalyptus saligna Sm. wood biochars, produced at 450°C (B450) and 550°C (B550), were incubated separately in each of the four soils for up to 12 mo at 20, 40, and 60°C. Total C and isotopic (?13C) methods were used to quantify the amounts of biochar C and native C mineralized during incubation. The DR-FTIR spectra of the light fraction showed distinct absorption bands representing native soil organic C, biochar C, and mineral constituents present in the soils; the mineral bands were consistent with XRD data of the clay fraction of the four soils. Analysis of the DR-FTIR spectra in the ?(C-H) bands showed that the ratio of the aromatic ?(C-H) bands systematically increased relative to the aliphatic ?(C-H) bands with increasing mineralization of biochar C in the B550 amended soils, and this relationship was unique for each soil type. In contrast, this relationship was not observed for the B450 amended soils that contained a relatively smaller proportion of aromatic C.
| S-EPMC5898394 | biostudies-literature
Project description:According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R?0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R?0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc.
| S-EPMC5834390 | biostudies-literature
Project description:The normalized cross-correlation (NCC), usually its 2D version, is routinely encountered in template matching algorithms, such as in facial recognition, motion-tracking, registration in medical imaging, etc. Its rapid computation becomes critical in time sensitive applications. Here I develop a scheme for the computation of NCC by fast Fourier transform that can favorably compare for speed efficiency with other existing techniques and may outperform some of them given an appropriate search scenario.
| S-EPMC6147431 | biostudies-literature
Project description:This study focuses on developing a quantification method for phosphatidylcholine (PC) and total phospholipid (PL) in krill oil using Fourier-transform infrared (FT-IR) spectroscopy. Signals derived from the choline and phosphate groups were selected as indicator variables for determining PC and total PL content; calibration curves with a correlation coefficient of >0.988 were constructed with calibration samples prepared by mixing krill oil raw material and fish oil in different ratios. The limit of detection (LOD, 0.35-3.29%) of the method was suitable for the designed assay with good accuracy (97.90-100.33%). The relative standard deviations for repeatability (0.90-2.31%) were acceptable. Therefore, both the methods using absorbance and that using second-derivative were confirmed to be suitable for quantitative analysis. When applying this method to test samples, including supplements, the PC content and total PL content were in good agreement with an average difference of 2-3% compared to the 31P NMR method. These results confirmed that the FT-IR method can be used as a convenient and rapid alternative to the 31P NMR method for quantifying PLs in krill oil.
| S-EPMC8750116 | biostudies-literature
Project description:Conventional Fourier-transform infrared (FTIR) microspectroscopic systems are limited by an inevitable trade-off between spatial resolution, acquisition time, signal-to-noise ratio (SNR) and sample coverage. We present an FTIR imaging approach that substantially extends current capabilities by combining multiple synchrotron beams with wide-field detection. This advance allows truly diffraction-limited high-resolution imaging over the entire mid-infrared spectrum with high chemical sensitivity and fast acquisition speed while maintaining high-quality SNR.
| S-EPMC3877692 | biostudies-literature
Project description:Nowadays, Wolfiporia extensa as a popular raw material in food and medicine industry has received increasing interests. Due to supply shortage, this species of edible and medicinal mushroom has been cultivated in some provinces of China. In the present study, cultivated W. extensa collected from six regions in Yunnan Province of China were analyzed by an integrated method based on Fourier transform infrared (FT-IR) spectroscopy and ultra-fast liquid chromatography (UFLC) coupled with multivariate analysis including partial least squares discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) in order to investigate the differences and similarities in different origins and parts. In the tested mushroom samples, characteristic FT-IR spectra were obtained for acquiring comprehensive fuzz chemical information and pachymic acid was determinated as a biomarker in the meantime. From the results, the comparison of samples was achieved successfully according to their geographical regions and different parts. All the samples displayed regional dependence and the inner parts showed better quality consistency. In addition, the chemical constituents of cultivated W. extensa could be also affected by the cultivation methods. Meanwhile, there was an interesting finding that the soil properties of cultivation regions may have a relationship with the chemical constituents of the epidermis of soil-cultured W. extensa, rather than the inner parts. Collectively, it demonstrated that the present study could provide comprehensive chemical evidence for the critical complement of quality evaluation on the cultivated W. extensa. Moreover, it may be available for the further researches of complicated mushrooms in practice.
| S-EPMC5201297 | biostudies-literature
Project description:Macrohyporia cocos is a medicinal and edible fungi, which is consumed widely. The epidermis and inner part of its sclerotium are used separately. M. cocos quality is influenced by geographical origins, so an effective and accurate geographical authentication method is required. Liquid chromatograms at 242 nm and 210 nm (LC242 and LC210) and Fourier transform infrared (FTIR) spectra of two parts were applied to authenticate the geographical origin of cultivated M. cocos combined with low and mid-level data fusion strategies, and partial least squares discriminant analysis. Data pretreatment involved correlation optimized warping and second derivative. The results showed that the potential of the chromatographic fingerprint was greater than that of five triterpene acids contents. LC242-FTIR low-level fusion took full advantage of information synergy and showed good performance. Further, the predictive ability of the FTIR low-level fusion model of two parts was satisfactory. The performance of the low-level fusion strategy preceded those of the single technique and mid-level fusion strategy. The inner parts were more suitable for origin identification than the epidermis. This study proved the feasibility of the data fusion of chromatograms and spectra, and the data fusion of different parts for the accurate authentication of geographical origin. This method is meaningful for the quality control of food and the protection of geographical indication products.
| S-EPMC6479993 | biostudies-literature
Project description:Infrared nanospectroscopy enables novel possibilities for chemical and structural analysis of nanocomposites, biomaterials or optoelectronic devices. Here we introduce hyperspectral infrared nanoimaging based on Fourier transform infrared nanospectroscopy with a tunable bandwidth-limited laser continuum. We describe the technical implementations and present hyperspectral infrared near-field images of about 5,000 pixel, each one covering the spectral range from 1,000 to 1,900?cm-1. To verify the technique and to demonstrate its application potential, we imaged a three-component polymer blend and a melanin granule in a human hair cross-section, and demonstrate that multivariate data analysis can be applied for extracting spatially resolved chemical information. Particularly, we demonstrate that distribution and chemical interaction between the polymer components can be mapped with a spatial resolution of about 30?nm. We foresee wide application potential of hyperspectral infrared nanoimaging for valuable chemical materials characterization and quality control in various fields ranging from materials sciences to biomedicine.
| S-EPMC5316859 | biostudies-other