Simulating a reference medium for determining bacterial growth in hospital wastewater for Raman spectroscopic investigation

Wastewater is a very complex and diverse medium, which despite low nutrient density still harbors bacteria. Especially the wastewater from hospitals contains a high germ load. However, wastewater is also very variable and differs not only from day to day, but also from house to house. Since wastewater is always changing and medium has an impact on Raman spectra of bacteria, it is necessary to find a surrogate material in which bacteria can be cultured to mimic a real hospital wastewater sample. In this study, we investigate two different artificial wastewaters for their abilities as a good alternative to real wastewater from the Jena University Hospital and to serve as a reference material for bacterial cultivation with subsequent Raman measurement. Each of the artificial wastewater on its own was not suitable to be used as a reference medium. Only the combination of the two simulated wastewaters achieved satisfactory results in the Raman spectroscopic identification of bacteria from real wastewater. These results could be used later in new experiments as a reference dataset to identify bacteria from real hospital wastewater samples.

Changes in the mitochondrial membrane potential in endothelial cells can be detected by Raman microscopy

The role of mitochondria goes beyond their capacity to create molecular fuel and includes e.g. the production of reactive oxygen species and the regulation of cell death. In endothelial cells, mitochondria have a significant impact on cellular function under both healthy and pathological conditions. Endothelial dysfunction contributes to the development of various lifestyle diseases and the key players in their pathogenesis are among others vascular inflammation and oxidative stress. The latter is very closely related to mitochondrial dysfunction; however, it is not straightforward. First, because mitochondria are small cellular structures, and second, it requires a sensitive method to follow the subtle biochemical changes. For this purpose, Raman microscopy (RM) was used here, which is considered a high-resolution method and can be applied in situ, usually as a non-labeled technique. In this work, we show that RM can not only locate mitochondria in the cell but also track their functional changes. Moreover, we test if labeling cells with Raman probes (Rp) can improve the specificity and sensitivity of RM (compared to conventional labeled techniques such as fluorescence, and the non-labeled Raman technique). MitoBADY Rp was used to detect changes in mitochondrial membrane potential as an indicator of mitochondrial activity, e.g. hyperpolarization or distortion of the proton gradient in the intermembrane space (depolarization). Thus, we show and compare RM, in the form of a label and non-labeled, to such a subtle cellular analysis.

Raman microscopy tracks maturity of melanin intermediates in Botrytis cinerea, a plant pathogen

We use Raman microscopy to describe the structure and chemical composition of both conidiophore and hyphae of Botrytis cinerea, a common plant pathogen. To interpret experimental data, we use density functional theory (DFT) to compute Raman tensors specific to an important fungal glycopeptide, a segment of α-chitin, and several naphthalene-based precursors of increasing complexity, which we propose play a role in the melanin synthesis pathway. Using spectral interpretations based on quantum chemical validation, we review microscopy images reconstructed for specific Raman activities and describe differences in distributions of structural components, photo-protective secondary naphthalene-based pigments, and proteins in both spores and hyphal filaments. Comparison of our results with literature data on other fungi suggests an example of convergent evolution expressed at the level of secondary metabolites specific to plant pathogenic fungi. Our results indicate that pre-resonant Raman monitoring of melanin precursors may help assessment of local Botrytis population biology to aid agricultural production.

Raman Micro-spectroscopy and Imaging of Filamentous Fungi

Filamentous fungi grow by the elongation of tubular cells called hyphae and form mycelia through repeated hyphal tip growth and branching. Since hyphal growth is closely related to the ability to secrete large amounts of enzymes or invade host cells, a more detailed understanding and the control of its growth are important in fungal biotechnology, ecology, and pathogenesis. Previous studies using fluorescence imaging revealed many of the molecular mechanisms involved in hyphal growth. Raman microspectroscopy and imaging methods are now attracting increasing attention as powerful alternatives due to their high chemical specificity and label-free, non-destructive properties. Spatially resolved information on the relative abundance, structure, and chemical state of multiple intracellular components may be simultaneously obtained. Although Raman studies on filamentous fungi are still limited, this review introduces recent findings from Raman studies on filamentous fungi and discusses their potential use in the future.

Deuterium-labeled Raman tracking of glucose accumulation and protein metabolic dynamics in Aspergillus nidulans hyphal tips

Filamentous fungi grow exclusively at their tips, where many growth-related fungal processes, such as enzyme secretion and invasion into host cells, take place. Hyphal tips are also a site of active metabolism. Understanding metabolic dynamics within the tip region is therefore important for biotechnology and medicine as well as for microbiology and ecology. However, methods that can track metabolic dynamics with sufficient spatial resolution and in a nondestructive manner are highly limited. Here we present time-lapse Raman imaging using a deuterium (D) tracer to study spatiotemporally varying metabolic activity within the hyphal tip of Aspergillus nidulans. By analyzing the carbon-deuterium (C-D) stretching Raman band with spectral deconvolution, we visualize glucose accumulation along the inner edge of the hyphal tip and synthesis of new proteins from the taken-up D-labeled glucose specifically at the central part of the apical region. Our results show that deuterium-labeled Raman imaging offers a broadly applicable platform for the study of metabolic dynamics in filamentous fungi and other relevant microorganisms in vivo.

Extended Multiplicative Signal Correction for Infrared Microspectroscopy of Heterogeneous Samples with Cylindrical Domains

Optical scattering corrections are invoked to computationally distinguish between scattering and absorption contributions to recorded data in infrared (IR) microscopy, with a goal to obtain an absorption spectrum that is relatively free of the effects of sample morphology. Here, we present a modification of the extended multiplicative signal correction (EMSC) approach that allows for spectral recovery from fibers and cylindrical domains in heterogeneous samples. The developed theoretical approach is based on exact Mie theory for infinite cylinders. Although rigorous Mie theory implies utilization of comprehensive and time-consuming calculations, we propose to change the workflow of the original EMSC algorithm to minimize extensive calculations for each recorded spectrum at each iteration step. This makes the modified EMSC approach practical for routine use. First, we tested our approach using synthetic data derived from a rigorous model of scattering from cylinders in an IR microscope. Second, we applied the approach to Fourier transform IR (FT-IR) microspectroscopy data recorded from filamentous fungal and cellulose samples with pronounced fiber-like shapes. While the corrected spectra show greatly reduced baseline offsets and consistency, strongly absorbing regions of the spectrum require further refinement. The modified EMSC algorithm broadly mitigates the effects of scattering, offering a practical approach to more consistent and accurate spectra from cylindrical objects or heterogeneous samples with cylindrical domains.

Isolation matters-processing blood for Raman microspectroscopic identification of bacteria

Bacteremia with its high mortality is a frequent case in clinical health care. Further, bacteremia includes the considerable risk of progressing to a sepsis. Even in case of survival, sepsis still entails diminished quality of life for the survivors and high indirect cost for the society. The crucial factor in sepsis is time. Therefore, timely description of adequate antibiotics is vital to reduce mortality and improve quality of life after survival. Despite that, the current gold standard of clinical bacteria diagnostic is based on cultivation of bacteria, which requires an average of 13-h cultivation. Consequently, there is a necessity for culture free identification methods without sacrificing the range of bacteria strains which can be identified. Raman microspectroscopy in general requires only single bacteria cells and has proven to offer high identification accuracies. However, the prerequisite for Raman microspectroscopy is a suitable isolation strategy to obtain single unharmed bacteria cells free from matrix. Moreover, in blood, bacteria are outnumbered by billions of blood cells. In this study, we present an isolation strategy to recover single bacteria cells from blood and evaluate their suitability for Raman microspectroscopic identification. Graphical abstract.

Redox State of Cytochromes in Frozen Yeast Cells Probed by Resonance Raman Spectroscopy

Cryopreservation is a well-established technique used for the long-term storage of biological materials whose biological activity is effectively stopped under low temperatures (suspended animation). Since most biological methods do not work in a low-temperature frozen environment, the mechanism and details of the depression of cellular activity in the frozen state remain largely uncharacterized. In this work, we propose, to our knowledge, a new approach to study the downregulation of the redox activity of cytochromes b and c in freezing yeast cells in a contactless, label-free manner. Our approach is based on cytochrome photobleaching effects observed in the resonance Raman spectra of live cells. Photoinduced and native redox reactions that contributed to the photobleaching rate were studied over a wide temperature range (from -173 to +25 °C). We found that ice formation influences both the rate of cytochrome redox reactions and the balance between the reduced and oxidized cytochromes. We demonstrate that the temperature dependence of native redox reaction rates can be well described by the thermal activation law with an apparent energy of 32.5 kJ/mol, showing that the redox reaction rate is ∼10(15) times slower at liquid nitrogen temperature than at room temperature.

Classification and identification of pigmented cocci bacteria relevant to the soil environment via Raman spectroscopy

A soil habitat consists of a significant number of bacteria that cannot be cultivated by conventional means, thereby posing obvious difficulties in their classification and identification. This difficulty necessitates the need for advanced techniques wherein a well-compiled biomolecular database consisting of the already cultivable bacteria can be used as a reference in an attempt to link the noncultivable bacteria to their closest phylogenetic groups. Raman spectroscopy has been successfully applied to taxonomic studies of many systems like bacteria, fungi, and plants relying on spectral differences contributed by the variation in their overall biomolecular composition. However, these spectral differences can be obscured due to Raman signatures from photosensitive microbial pigments like carotenoids that show enormous variation in signal intensity hindering taxonomic investigations. In this study, we have applied laser-induced photobleaching to expel the carotenoid signatures from pigmented cocci bacteria. Using this method, we have investigated 12 species of pigmented bacteria abundant in soil habitats belonging to three genera mainly Micrococcus, Deinococcus, and Kocuria based on their Raman spectra with the assistance of a chemometric tool known as the radial kernel support vector machine (SVM). Our results demonstrate the potential of Raman spectroscopy as a minimally invasive taxonomic tool to identify pigmented cocci soil bacteria at a single-cell level.

Texture analysis and classification in coherent anti-Stokes Raman scattering (CARS) microscopy images for automated detection of skin cancer

Coherent anti-Stokes Raman scattering (CARS) microscopy is a powerful tool for fast label-free tissue imaging, which is promising for early medical diagnostics. To facilitate the diagnostic process, automatic image analysis algorithms, which are capable of extracting relevant features from the image content, are needed. In this contribution we perform an automated classification of healthy and tumor areas in CARS images of basal cell carcinoma (BCC) skin samples. The classification is based on extraction of texture features from image regions and subsequent classification of these regions into healthy and cancerous with a perceptron algorithm. The developed approach is capable of an accurate classification of texture types with high sensitivity and specificity, which is an important step towards an automated tumor detection procedure.

Quantification of plant surface metabolites by matrix-assisted laser desorption-ionization mass spectrometry imaging: glucosinolates on Arabidopsis thaliana leaves

The localization of metabolites on plant surfaces has been problematic because of the limitations of current methodologies. Attempts to localize glucosinolates, the sulfur-rich defense compounds of the order Brassicales, on leaf surfaces have given many contradictory results depending on the method employed. Here we developed a matrix-assisted laser desorption-ionization (MALDI) mass spectrometry protocol to detect surface glucosinolates on Arabidopsis thaliana leaves by applying the MALDI matrix through sublimation. Quantification was accomplished by spotting glucosinolate standards directly on the leaf surface. The A. thaliana leaf surface was found to contain approximately 15 nmol of total glucosinolate per leaf with about 50 pmol mm(-2) on abaxial (bottom) surfaces and 15-30 times less on adaxial (top) surfaces. Of the major compounds detected, 4-methylsulfinylbutylglucosinolate, indol-3-ylmethylglucosinolate, and 8-methylsulfinyloctylglucosinolate were also major components of the leaf interior, but the second most abundant glucosinolate on the surface, 4-methylthiobutylglucosinolate, was only a trace component of the interior. Distribution on the surface was relatively uniform in contrast to the interior, where glucosinolates were distributed more abundantly in the midrib and periphery than the rest of the leaf. These results were confirmed by two other mass spectrometry-based techniques, laser ablation electrospray ionization and liquid extraction surface analysis. The concentrations of glucosinolates on A. thaliana leaf surfaces were found to be sufficient to attract the specialist feeding lepidopterans Plutella xylostella and Pieris rapae for oviposition. The methods employed here should be easily applied to other plant species and metabolites.

Monitoring metabolites from Schizophyllum commune interacting with Hypholoma fasciculare combining LESA-HR mass spectrometry and Raman microscopy

Microbial competition for territory and resources is inevitable in habitats with overlap between niches of different species or strains. In fungi, competition is brought about by antagonistic mycelial interactions which alter mycelial morphology, metabolic processes, secondary metabolite release, and extracellular enzyme patterns. Until now, we were not able study in vivo chemical interactions of different colonies growing on the same plate. In this report, we developed a fast and least invasive approach to identify, quantify, and visualize co culture-induced metabolites and their location of release within Schizophyllum commune. The pigments indigo, indirubin, and isatin were used as examples to show secondary metabolite production in the interaction zone with Hypholoma fasciculare. Using a combinatory approach of Raman spectroscopy imaging, liquid extraction surface analysis (LESA), and high-resolution mass spectrometry, we identified, quantified, and visualized the presence of indigo and indirubin in the interaction zone. This approach allows the investigation of metabolite patterns between wood degrading species in competition to gain insight in community interactions, but could also be applied to other microorganisms. This method advances analysis of living, still developing colonies and are in part not destructive as Raman spectroscopy imaging is implemented.

Photobleaching of the resonance Raman lines of cytochromes in living yeast cells

The photobleaching of the resonance cytochrome Raman lines in living Saccharomyces cerevisiae cells was studied. The photobleaching rate versus the irradiation power was described by square function plus a constant in contrast to the linear dependence of the photoinjury rate. This difference distinguishes the cytochrome photooxidation from other processes of the cell photodamage. The square dependence is associated with the reaction involving two photogenerated intermediates while the constant with the dark redox balance rates. This work demonstrates a potential of Raman spectroscopy to characterize the native cytochrome reaction rates and to study the cell photodamage precursors.

Quantitative analysis of the redox states of cytochromes in a living L929 (NCTC) cell by resonance Raman microspectroscopy

Raman spectra and images of a living L929 (NCTC) cell have been measured with 532 nm excitation. Both reduced and oxidized forms of cytochromes b and c (cyt b and cyt c) have been observed in situ without any pretreatment. The redox states of cyts b and c have been assessed quantitatively with a spectral analysis. It has been found that reduced cyt c is more abundant than oxidized cyt c, while oxidized cyt b is slightly more abundant than reduced cyt b in a living cell.

Towards automated segmentation of cells and cell nuclei in nonlinear optical microscopy

Nonlinear optical (NLO) imaging techniques based e.g. on coherent anti-Stokes Raman scattering (CARS) or two photon excited fluorescence (TPEF) show great potential for biomedical imaging. In order to facilitate the diagnostic process based on NLO imaging, there is need for an automated calculation of quantitative values such as cell density, nucleus-to-cytoplasm ratio, average nuclear size. Extraction of these parameters is helpful for the histological assessment in general and specifically e.g. for the determination of tumor grades. This requires an accurate image segmentation and detection of locations and boundaries of cells and nuclei. Here we present an image processing approach for the detection of nuclei and cells in co-registered TPEF and CARS images. The algorithm developed utilizes the gray-scale information for the detection of the nuclei locations and the gradient information for the delineation of the nuclear and cellular boundaries. The approach reported is capable for an automated segmentation of cells and nuclei in multimodal TPEF-CARS images of human brain tumor samples. The results are important for the development of NLO microscopy into a clinically relevant diagnostic tool.

Spatially resolved investigation of the oil composition in single intact hyphae of Mortierella spp. with micro-Raman spectroscopy

Zygomycetes are well known for their ability to produce various secondary metabolites. Fungi of the genus Mortierella can accumulate highly unsaturated lipids in large amounts as lipid droplets. However, no information about the spatial distribution or homogeneity of the oil inside the fungi is obtainable to date due to the invasive and destructive analytical techniques applied so far. Raman spectroscopy has been demonstrated to be well suited to investigate biological samples on a micrometre scale. It also has been shown that the degree of unsaturation of lipids can be determined from Raman spectra. We applied micro-Raman spectroscopy to investigate the spatial distribution and composition of lipid vesicles inside intact hyphae. For Mortierella alpina and Mortierella elongata distinct differences in the degree of unsaturation and even the impact of growth conditions are determined from the Raman spectra. In both species we found that the fatty acid saturation in the vesicles is highly variable in the first 600 μm of the growing hyphal tip and fluctuates towards a constant composition and saturation ratio in all of the remaining mycelium. Our approach facilitates in vivo monitoring of the lipid production and allows us to investigate the impact of cultivation parameters on the oil composition directly in the growing hyphae without the need for extensive extraction procedures.

Combination of patch clamp and Raman spectroscopy for single-cell analysis

In this contribution we present the combination of patch clamp with Raman spectroscopy for a label-free quantitative detection of intracellular components. Patch clamp is used to gain controlled access to the cytosol and internalize water-soluble compounds into the cell. The presence and concentration of these substances inside the living mammalian cell are probed by means of Raman spectroscopy in a label-free manner. A proof of principle was given using the carotinoid crocin as a sample compound that does not show specific interaction with the cell. When the intracellular crocin concentration as determined from the Raman spectra was monitored, the kinetics of internalization/diffusion into the cell could be characterized by a single-exponential function. Furthermore, the technique was successfully applied to observe differences in the internalization of free and protein-bound heme into the living cell. Although the peptide-capped microperoxidase MP-11 did not show specific interactions, free heme accumulated in the cell by binding to cellular components.

Multimodal imaging to study the morphochemistry of basal cell carcinoma

Basal cell carcinoma is the most abundant malignant neoplasm in humans, the pathology of which is characterized by an abnormal proliferation of basal cells. Basal cell carcinoma can show a variety of different morphologies, which are based on different cellular biology. Furthermore, the carcinoma often grows invisibly to the eye imbedded in the surrounding skin. Therefore, in some cases its clinical detection is challenging. Thus, our work aims at establishing an unsupervised tissue classification method based on multimodal imaging and the application of chemometrics to discriminate basal cell carcinoma from non-diseased tissue. A case study applying multimodal imaging to ex-vivo sections of basal cell carcinoma is presented. In doing so, we apply a combination of various linear and non-linear imaging modalities, i.e. fluorescence, Raman and second-harmonic generation microscopy, to study the morphochemistry of basal cell carcinoma. The joint information content obtained by such multimodal approach in studying various aspects of the malignant tissue alterations associated with basal cell carcinoma is discussed.

Toward in vivo chemical imaging of epicuticular waxes

Epicuticular waxes, which are found on the outer surface of plant cuticles, are difficult to study in vivo. To monitor the growth, development, and structural alterations of epicuticular wax layers, coherent anti-Stokes Raman scattering (CARS) might be used. CARS, as a Raman-based technique, not only provides structural insight but also chemical information by imaging the spatial distribution of Raman-active vibrations. Here, we present a comparative study using CARS and scanning electron microscopy to characterize the structure of epicuticular waxes. The ability of CARS to provide detailed structural information on the biologically important wax layer was detailed on the examples of cherry laurel (Prunus laurocerasus), hoya (Hoya carnosa), and ceriman/Swiss cheese plant (Monstera sp. aff. deliciosa). We anticipate that the work presented will open a doorway for online monitoring of formation and alterations of epicuticular wax layers.

Separation of CARS image contributions with a Gaussian mixture model

Coherent anti-Stokes Raman scattering (CARS) gained a lot of importance in chemical imaging. This is due to the fast image acquisition time, the high spatial resolution, the non-invasiveness, and the molecular sensitivity of this method. By using the single-line CARS in contrast to the multiplex CARS, different signal contributions stemming from resonant and non-resonant light-matter interactions are indistinguishable. Here a numerical method is presented in order to extract more information from univariate CARS images: vibrational composition, morphological information, and contributions from index-of-refraction steps can be separated from single-line CARS images. The image processing algorithm is based on the physical properties of CARS process as reflected in the shape of the intensity histogram of univariate CARS images. Because of this the comparability of individual CARS images recorded with different experimental parameters is achieved. The latter is important for a quantitative evaluation of CARS images.