Inhomogeneous Molecular Distributions and Cytochrome Types and Redox States in Fungal Cells Revealed by Raman Hyperspectral Imaging Using Multivariate Curve Resolution–Alternating Least Squares

Exploring dynamic changes of fungal cellular components during nanoemulsion treatment by multivariate microRaman imaging

Recently, essential oils (EO) have gained a lot of interest for use as antifungal agent in food and agricultural industry and extensive research is ongoing to understand their mode of action. However, the exact mechanism is not yet elucidated. Here, we integrated spectral unmixing and Raman microspectroscopy imaging to unveil the antifungal mechanism of green tea EO based nanoemulsion (NE) against Magnaporthe oryzae. The dramatic change in protein, lipid, adenine, and guanine bands indicate that NE has a significant impact on the protein, lipid and metabolic processes of purine. The results also demonstrated that the NE treatment caused damage to fungal hyphae by inducing a physical injury leading to cell wall damage and loss of integrity. Our study shows that MCR-ALS (Multivariate Curve Resolution-Alternating Least Squares) and N-FINDR (N-finder algorithm) Raman imaging could serve as a suitable complementary package to the traditional methods, for revealing the antifungal mechanism of action of EO/NE.

Simultaneous Imaging and Characterization of Polyunsaturated Fatty Acids, Carotenoids, and Microcrystalline Guanine in Single Aurantiochytrium limacinum Cells with Linear and Nonlinear Raman Microspectroscopy

Thraustochytrids are heterotrophic marine protists known for their high production capacity of various compounds with health benefits, such as polyunsaturated fatty acids and carotenoids. Although much effort has been focused on developing optimal cultivation methods for efficient microbial production, these high-value compounds and their interrelationships are not well understood at the single-cell level. Here we used spontaneous (linear) Raman and multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy to visualize and characterize lipids (e.g., docosahexaenoic acid) and carotenoids (e.g., astaxanthin) accumulated in single living Aurantiochytrium limacinum cells. Spontaneous Raman imaging with the help of multivariate curve resolution-alternating least-squares enabled us to make unambiguous assignments of the molecular components we detected and derive their intracellular distributions separately. Near-IR excited CARS imaging yielded the Raman images at least an order of magnitude faster than spontaneous Raman imaging, with suppressed contributions of carotenoids. As the culture time increased from 2 to 5 days, the lipid amount increased by a factor of ∼7, whereas the carotenoid amount did not change significantly. Furthermore, we observed a highly localized component in A. limacinum cells. This component was found to be mixed crystals of guanine and other purine derivatives. The present study demonstrates the potential of the linear-nonlinear Raman hybrid approach that allows for accurate molecular identification and fast imaging in a label-free manner to link information derived from single cells with strategies for mass culture of useful thraustochytrids.

Quantitative Mass Spectrometry Imaging Using Multivariate Curve Resolution and Deep Learning: A Case Study

In the present contribution, a novel approach based on multivariate curve resolution and deep learning (DL) is proposed for quantitative mass spectrometry imaging (MSI) as a potent technique for identifying different compounds and creating their distribution maps in biological tissues without need for sample preparation. As a case study, chlordecone as a carcinogenic pesticide was quantitatively determined in mouse liver using matrix-assisted laser desorption ionization-MSI (MALDI-MSI). For this purpose, data from seven standard spots containing 0 to 20 picomoles of chlordecone and four unknown tissues from the mouse livers infected with chlordecone for 1, 5, and 10 days were analyzed using a convolutional neural network (CNN). To solve the lack of sufficient data for CNN model training, each pixel was considered as a sample, the designed CNN models were trained by pixels in training sets, and their corresponding amounts of chlordecone were obtained by multivariate curve resolution-alternating least-squares (MCR-ALS). The trained models were then externally evaluated using calibration pixels in test sets for 1, 5, and 10 days of exposure, respectively. Prediction R² for all three data sets ranged from 0.93 to 0.96, which was superior to support vector machine (SVM) and partial least-squares (PLS). The trained CNN models were finally used to predict the amount of chlordecone in mouse liver tissues, and their results were compared with MALDI-MSI and GC-MS methods, which were comparable. Inspection of the results confirmed the validity of the proposed method.

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.

Label-free third harmonic generation imaging and quantification of lipid droplets in live filamentous fungi

We report the utilization of Third-Harmonic Generation microscopy for label-free live cell imaging of lipid droplets in the hypha of filamentous fungus Phycomyces blakesleeanus. THG microscopy images showed bright spherical features dispersed throughout the hypha cytoplasm in control conditions and a transient increase in the number of bright features after complete nitrogen starvation. Colocalization analysis of THG and lipid-counterstained images disclosed that the cytoplasmic particles were lipid droplets. Particle Size Analysis and Image Correlation Spectroscopy were used to quantify the number density and size of lipid droplets. The two analysis methods both revealed an increase from 16 × 10^-3 to 23 × 10^-3 lipid droplets/µm² after nitrogen starvation and a decrease in the average size of the droplets (range: 0.5-0.8 µm diameter). In conclusion, THG imaging, followed by PSA and ICS, can be reliably used for filamentous fungi for the in vivo quantification of lipid droplets without the need for labeling and/or fixation. In addition, it has been demonstrated that ICS is suitable for THG microscopy.

Transient absorption spectroscopy and imaging of redox in muscle mitochondria

Mitochondrial redox is an important indicator of cell metabolism and health, with implications in cancer, diabetes, aging, neurodegenerative diseases, and mitochondrial disease. The most common method to observe redox of individual cells and mitochondria is through fluorescence of NADH and FAD+, endogenous cofactors serve as electron transport inputs to the mitochondrial respiratory chain. Yet this leaves out redox within the respiratory chain itself. To a degree, the missing information can be filled in by exogenous fluorophores, but at the risk of disturbed mitochondrial permeability and respiration. Here we show that variations in respiratory chain redox can be detected up by visible-wavelength transient absorption microscopy (TAM). In TAM, the selection of pump and probe wavelengths can provide multiphoton imaging contrast between non-fluorescent molecules. Here, we applied TAM with a pump at 520nm and probe at 450nm, 490nm, and 620nm to elicit redox contrast from mitochondrial respiratory chain hemeproteins. Experiments were performed with reduced and oxidized preparations of isolated mitochondria and whole muscle fibers, using mitochondrial fuels (malate, pyruvate, and succinate) to set up physiologically relevant oxidation levels. TAM images of muscle fibers were analyzed with multivariate curve resolution (MCR), revealing that the response at 620nm probe provides the best redox contrast and the most consistent response between whole cells and isolated mitochondria.

Nondestructive 3D imaging and quantification of hydrated biofilm matrix by confocal Raman microscopy coupled with non-negative matrix factorization

Biofilms are ubiquitous in natural and engineered environments and of great importance in drinking water distribution and biological wastewater treatment systems. Simultaneously acquiring the chemical and structural information of the hydrated biofilm matrix is essential for the cognition and regulation of biofilms in the environmental field. However, the complexity of samples and the limited approaches prevent a holistic understanding of the biofilm matrix. In this work, an approach based on the confocal Raman mapping technique integrated with non-negative matrix factorization (NMF) analysis was developed to probe the hydrated biofilm matrix in situ. The flexibility of the NMF analysis was utilized to subtract the undesired water background signal and resolve the meaningful biological components from Raman spectra of the hydrated biofilms. Diverse chemical components such as proteins, bacterial cells, glycolipids and polyhydroxyalkanoates (PHA) were unraveled within the distinct Pseudomonas spp. biofilm matrices, and the corresponding 3-dimensional spatial organization was visualized and quantified. Of these components, glycolipids and PHA were unique to the P. aeruginosa and P. putida biofilm matrix, respectively. Furthermore, their high abundances in the lower region of the biofilm matrix were found to be related to the specific physiological functions and surrounding microenvironments. Overall, the results demonstrate that our NMF Raman mapping method could serve as a powerful tool complementary to the conventional approaches for identifying and visualizing the chemical components in the biofilm matrix. This work may facilitate the online characterization of the biofilm matrix widely present in the environment and advance the fundamental understanding of biofilm.

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.

Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes

Accessing enormous uncultivated microorganisms (microbial dark matter) in various Earth environments requires accurate, nondestructive classification, and molecular understanding of the microorganisms in in situ and at the single-cell level. Here we demonstrate a combined approach of random forest (RF) machine learning and single-cell Raman microspectroscopy for accurate classification of phylogenetically diverse prokaryotes (three bacterial and three archaeal species from different phyla). Our RF classifier achieved a 98.8 ± 1.9% classification accuracy among the six species in pure populations and 98.4% for three species in an artificially mixed population. Feature importance scores against each wavenumber reveal that the presence of carotenoids and structure of membrane lipids play key roles in distinguishing the prokaryotic species. We also find unique Raman markers for an ammonia-oxidizing archaeon. Our approach with moderate data pretreatment and intuitive visualization of feature importance is easy to use for non-spectroscopists, and thus offers microbiologists a new single-cell tool for shedding light on microbial dark matter.

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Random forest models classify prokaryotic species with high accuracy of >98%

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Both bacteria and archaea are classified using minimally preprocessed Raman data

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Feature importance reveals what biomolecules contribute to species classification

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Raman marker bands for some archaeal species are discovered

DNA Fingerprint Analysis of Raman Spectra Captures Global Genomic Alterations in Imatinib-Resistant Chronic Myeloid Leukemia: A Potential Single Assay for Screening Imatinib Resistance

Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of blast crisis (BC). This study for the first time demonstrates the potential of Raman spectroscopy to sense the resistant phenotype. Currently recommended resistance screening strategy include detection of BCR-ABL1 transcripts, kinase domain mutations, complex chromosomal abnormalities and BCR-ABL1 gene amplification. The techniques used for these tests are expensive, technologically demanding and have limited availability in resource-poor countries. In India, this could be a reason for more patients reporting to clinics with advanced disease. A single method which can identify resistant cells irrespective of the underlying mechanism would be a practical screening strategy. During our analysis of imatinib-sensitive and -resistant K562 cells, by array comparative genomic hybridization (aCGH), copy number variations specific to resistant cells were detected. aCGH is technologically demanding, expensive and therefore not suitable to serve as a single economic test. We therefore explored whether DNA finger-print analysis of Raman hyperspectral data could capture these alterations in the genome, and demonstrated that it could indeed segregate imatinib-sensitive and -resistant cells. Raman spectroscopy, due to availability of portable instruments, ease of spectrum acquisition and possibility of centralized analysis of transmitted data, qualifies as a preliminary screening tool in resource-poor countries for imatinib resistance in CML. This study provides a proof of principle for a single assay for monitoring resistance to imatinib, available for scrutiny in clinics.

Preparation and characterization of a novel green tea essential oil nanoemulsion and its antifungal mechanism of action against Magnaporthae oryzae

Blast is one of the most devastating fungal diseases of rice caused by Magnaporthe oryzae. Plant essential oil (EO) can function as antifungal agents and are regarded as a safe and acceptable method for plant disease control. However, EOs are unstable and hydrophobic, which limits its use. In the present study, we aimed for the preparation and characterization of a nanoemulsion (NE) from green tea essential oil (GTO) by ultrasonication method and determined the antifungal activity of NE onM. oryzae. The particle size and zeta potential of the NE were 86.98 nm and -15.1 mV, respectively. The chemical composition and functional groups of GTO and NE were studied by using GC-MS analysis, portable Raman spectroscopy, and FTIR coupled with chemometric analysis. GC-MS analysis showed the major components in GTO and NE were n-Hexyl cinnamaldehyde and L-α-Terpineol. Both GTO and NE showed good antioxidant activity and total phenol content. Moreover, the NE showed good antifungal activity againstM. oryzae which was further confirmed by scanning electron microscopy (SEM) examination. Also, confocal Raman micro-spectroscopy (CRM) revealed the antifungal mechanism of GTO and NE on M. oryzae which proves the cell damage. To the best of our knowledge, this is the first study on the antifungal activity of GTO and NE against M. oryzae and also the use of CRM for the evaluation of the chemical changes in single fungal hyphae in a holistic approach. This study suggests that the prepared NE could be a potential candidate for use as a substitute for synthetic fungicides.

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.

An Application of Multivariate Data Analysis to Photoacoustic Imaging for the Spectral Unmixing of Gold Nanorods in Biological Tissues

Gold nanorods (GNRs) showed to be a suitable contrast agent in photoacoustics (PA), and are able to provide a tunable absorption contrast against background tissue, while a detectable PA signal can be generated from highly localized and targeted areas. A crucial issue for these imaging techniques is represented by the discrimination between exogenous and endogenous contrast and the assessment of the real PA signal magnitude. The application of image resolution/unmixing methods was implemented and optimized to recover the relative magnitude spectra and distribution maps of image constituents of the biological sample based on multivariate analysis (multivariate curve resolution-alternating least squares, MCR-ALS) in the presence of GNRs with tunable absorption properties. The proposed data analysis methodology is demonstrated on real PA images from experimental animal models and ex-vivo preparations.

Interactions of water confined in a metal-organic framework as studied by a combined approach of Raman, FTIR, and IR electroabsorption spectroscopies and multivariate curve resolution analysis

Water in nanoconfinement shows distinct properties that are markedly different from those of bulk water. These unique properties stem not only from the water-water interaction but also from the interactions between water and the surrounding confining environment. Here we used a combined approach of vibrational spectroscopies (Raman, FTIR, and IR electroabsorption) and a multivariate curve resolution technique to study the interactions of water in a heterogeneous confining environment within a prototype of pillared layer-type metal-organic frameworks (MOFs), CPL-1 ([Cu2(pzdc)2(pyz)]n, where pzdc = 2,3-pyrazinedicarboxylate, pyz = pyrazine). The OH stretching Raman spectrum of hydrated CPL-1 microcrystals revealed that the adsorbed water molecules resemble the subpopulation of bulk water whose hydrogen bond is weak. Multivariate curve resolution analysis of FTIR spectra monitoring water desorption from CPL-1 allowed for accurate assignments of the framework's carboxylate vibrational modes associated with water-filled and empty nanopores of the MOF, and for quantitative determination of the number fraction of these pores. Furthermore, building on the assignments so made, IR electroabsorption measurements showed that the hydrogen-bonding interaction with water adsorbed in CPL-1 has little impact on the response to electric fields of the framework vibrational modes. The present findings altogether provide a solid basis of elucidating water confined in CPL-1 and demonstrate the potential of the combined vibrational spectroscopic method for interrogating the interactions within MOFs.

Raman spectroscopic signatures of carotenoids and polyenes enable label-free visualization of microbial distributions within pink biofilms

Pink biofilms are multispecies microbial communities that are commonly found in moist household environments. The development of this pink stain is problematic from an aesthetic point of view, but more importantly, it raises hygienic concerns because they may serve as a potential reservoir of opportunistic pathogens. Although there have been several studies of pink biofilms using molecular analysis and confocal laser scanning microscopy, little is known about the spatial distributions of constituent microorganisms within pink biofilms, a crucial factor associated with the characteristics of pink biofilms. Here we show that Raman spectroscopic signatures of intracellular carotenoids and polyenes enable us to visualize pigmented microorganisms within pink biofilms in a label-free manner. We measured space-resolved Raman spectra of a pink biofilm collected from a bathroom, which clearly show resonance Raman bands of carotenoids. Multivariate analysis of the Raman hyperspectral imaging data revealed the presence of typical carotenoids and structurally similar but different polyenes, whose spatial distributions within the pink biofilm were found to be mutually exclusive. Raman measurements on individual microbial cells isolated from the pink biofilm confirmed that these distributions probed by carotenoid/polyene Raman signatures are attributable to different pigmented microorganisms. The present results suggest that Raman microspectroscopy with a focus on microbial pigments such as carotenoids is a powerful nondestructive method for studying multispecies biofilms in various environments.

Raman Scattering: From Structural Biology to Medical Applications

This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.