Experimental Evaluation of the Density of Water in a Cell by Raman Microscopy

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

Establishment of a Method for the Introduction of Poorly Water-Soluble Drugs in Cells and Evaluation of Intracellular Concentration Distribution Using Resonance Raman Imaging

Label-free measurement is essential to understand the metabolism of drug molecules introduced into cells. Raman imaging is a powerful method to investigate intracellular drug molecules because it provides in situ label-free observation of introduced molecules. In this study, we propose that Raman imaging can be used not only to observe the intracellular distribution of drug molecules but also to quantitatively visualize the concentration distribution reflecting each organelle in a single living cell using the Raman band of extracellular water as an intensity standard. We dissolved poorly water-soluble all-trans-retinoic acid (ATRA) in water using a cytocompatible amphiphilic phospholipid polymer, poly[2-methacryloyloxyethyl phosphorylcholine-co-n-butyl methacrylate] (PMB) as a solubilizing reagent, introduced it into cells, and obtained the intracellular concentration distribution of ATRA. ATRA was concentrated in the cells and mainly localized to mitochondria and lipid droplets, interacting strongly with mitochondria and weakly with lipid droplets. Poorly water-soluble β-carotene was also introduced into cells using PMB but was not concentrated intracellularly, indicating that β-carotene does not interact specifically with intracellular molecules. We established a protocol for the solubilization and intracellular uptake of poorly water-soluble molecules using PMB and obtaining their concentration distribution using Raman microscopy.

Water bend-libration as a cellular Raman imaging probe of hydration

Water is a ubiquitous and vital component of living systems. Hydration, which is the interaction between water and intracellular biomolecules, plays an important role in cellular processes. However, it is technically challenging to study water structure within cells directly. Here, we demonstrate the utility and power of the water bend-libration combination band as a unique Raman spectral imaging probe of cellular hydration. Hydration maps reveal distinct water environments within subcellular compartments (e.g., nucleolus and lipid droplet) due to the spectral sensitivity of this coupled vibrational band. Spectroscopic studies using the water bend-libration are broadly applicable, offering the potential to capture the chemical complexity of hydration in numerous systems.

Correction for Extrinsic Background in Raman Hyperspectral Images

Raman hyperspectral microscopy is a valuable tool in biological and biomedical imaging. Because Raman scattering is often weak in comparison to other phenomena, prevalent spectral fluctuations and contaminations have brought advancements in analytical and chemometric methods for Raman spectra. These chemometric advances have been key contributors to the applicability of Raman imaging to biological systems. As studies increase in scale, spectral contamination from extrinsic background, intensity from sources such as the optical components that are extrinsic to the sample of interest, has become an emerging issue. Although existing baseline correction schemes often reduce intrinsic background such as autofluorescence originating from the sample of interest, extrinsic background is not explicitly considered, and these methods often fail to reduce its effects. Here, we show that extrinsic background can significantly affect a classification model using Raman images, yielding misleadingly high accuracies in the distinction of benign and malignant samples of follicular thyroid cell lines. To mitigate its effects, we develop extrinsic background correction (EBC) and demonstrate its use in combination with existing methods on Raman hyperspectral images. EBC isolates regions containing the smallest amounts of sample materials that retain extrinsic contributions that are specific to the device or environment. We perform classification both with and without the use of EBC, and we find that EBC retains biological characteristics in the spectra while significantly reducing extrinsic background. As the methodology used in EBC is not specific to Raman spectra, correction of extrinsic effects in other types of hyperspectral and grayscale images is also possible.

Measurement of cellular thermal properties and their temperature dependence based on frequency spectra via an on-chip-integrated microthermistor

To understand the mechanism of intracellular thermal transport, thermal properties must be elucidated, particularly thermal conductivity and specific heat capacity. However, these properties have not been extensively studied. In this study, we developed a cellular temperature measurement device with a high temperature resolution of 1.17 m °C under wet conditions and with the ability to introduce intracellular local heating using a focused infrared laser to cultured cells on the device surface. Using this device, we evaluated the thermal properties of single cells based on their temperature signals and responses. Measurements were taken using on-chip-integrated microthermistors with high temperature resolution at varying surrounding temperatures and frequencies of local infrared irradiation on cells prepared on the sensors. Frequency spectra were used to determine the intensities of the temperature signals with respect to heating times. Signal intensities at 37 °C and a frequency lower than 2 Hz were larger than those at 25 °C, which were similar to those of water. The apparent thermal conductivity and specific heat capacity, which were determined at different surrounding temperatures and local heating frequencies, were lower than and similar to those of water at 37 °C and 25 °C, respectively. Our results indicate that the thermal properties of cells depend on both temperatures and physiological activities in addition to local heating frequencies.

Label-Free Tracking of Nanoprodrug Cellular Uptake and Metabolism Using Raman and Autofluorescence Imaging

Nano-DDS, a drug delivery system using nanoparticles, is a promising tool to reduce adverse drug reactions and maximize drug efficiency. Understanding the intracellular dynamics following the accumulation of nanoparticles in tissues, such as cellular uptake, distribution, metabolism, and pharmacological effects, is essential to maximize drug efficiency; however, it remains elusive. In this study, we tracked the intracellular behavior of nanoparticles of a prodrug, cholesterol-linked SN-38 (CLS), in a label-free manner using Raman and autofluorescence imaging. Bright autofluorescent spots were observed in cells treated with CLS nanoparticles, and the color tone of the bright spots changed with incubation time. The Raman spectra of the bright spots showed that the autofluorescence came from the nanoparticles taken into cells, and the change in color of bright spots indicated that CLS turned into SN-38 via hydrolysis inside a cell. It was found that most of the SN-38 were localized in small regions in the cytoplasm even after the conversion from CLS, and only a small amount of SN-38 was dissolved and migrated into other cytoplasm regions and the nucleus. The massive size growth of cells was observed within several tens of hours after the treatment with CLS nanoparticles. Moreover, Raman images of cells using the cytochrome c band and the fluorescence images of cells stained with JC-1 showed that cellular uptake of CLS nanoparticles efficiently caused mitochondrial damage. These results show that the combination of Raman and autofluorescence imaging can provide insight into the intracellular behavior of prodrug nanoparticles and the cell response and facilitate the development of nano-DDSs.

Crystal optics simulations for delineation of the three-dimensional cellular nuclear distribution using analyzer-based refraction-contrast computed tomography

Refraction-contrast computed tomography (RCT) using a refractive angle analyzer of Si perfect crystal can reconstruct the three-dimensional structure of biological soft tissue with contrast comparable to that of stained two-dimensional pathological images. However, the blurring of X-ray beam by the analyzer has prevented improvement of the spatial resolution of RCT, and the currently possible observation of tissue structure at a scale of approximately 20 µm provides only limited medical information. As in pathology, to differentiate between benign and malignant forms of cancer, it is necessary to observe the distribution of the cell nucleus, which is approximately 5-10 µm in diameter. In this study, based on the X-ray dynamical diffraction theory using the Takagi-Taupin equation, which calculates the propagation of X-ray energy in crystals, an analyzer crystal optical system depicting the distribution of cell nuclei was investigated by RCT imaging simulation experiments in terms of the thickness of the Laue-case analyzer, the camera pixel size and the difference in spatial resolution between the Bragg-case and Laue-case analyzers.

New "HOPE" laser for photoacoustic imaging of water

A hybrid optical parametrically-oscillating laser at 1930 nm enables photoacoustic mapping of water content in deep tissue with good sensitivity and high spatial resolution.

Raman microscopy-based quantification of the physical properties of intracellular lipids

The physical properties of lipids, such as viscosity, are homeostatically maintained in cells and are intimately involved in physiological roles. Measurement of the physical properties of plasma membranes has been achieved primarily through chemical or genetically encoded fluorescent probes. However, since most probes target plasma membranes, physical properties of lipids in intracellular organelles, including lipid droplets (LDs) are yet to be analyzed. Here, we present a novel Raman microscopy-based approach for quantifying the physical properties of intracellular lipids under deuterium-labeled fatty acid treatment conditions. Focusing on the fact that Raman spectra of carbon-deuterium vibration are altered depending on the surrounding lipid species, we quantitatively represented the physical properties of lipids as the gauche/trans conformational ratio of the introduced labeled fatty acids, which can be used as an indicator of viscosity. Intracellular Raman imaging revealed that the gauche/trans ratio of cytosolic regions was robustly preserved against perturbations attempting to alter the lipid composition. This was likely due to LDs functioning as a buffer against excess gauche/trans ratio, beyond its traditional role as an energy storage organelle. Our novel approach enables the observation of the physical properties of organelle lipids, which is difficult to perform with conventional probes, and is useful for quantitative assessment of the subcellular lipid environment.

Regulation of Cell Volume by Nanosecond Pulsed Electric Fields

Stimulation of cells by nanosecond pulsed electric fields (nsPEFs) has attracted attention as a technology for medical applications such as cancer treatment. nsPEFs have been shown to affect intracellular environments without significant damage to cell membranes; however, the mechanism underlying the effect of nsPEFs on cells remains unclear. In this study, we constructed electrodes for applying nsPEFs and analyzed the change in volume of a single cell due to nsPEFs using fluorescence and Raman microscopy. It was shown that the direction of the change depended on the applied electric field; expansion due to the influx of water was observed at high electric field, and cell shrinkage was observed at low electric field. The change in cell volume was correlated to the change in the intracellular Ca²⁺ concentration, and nsPEFs-induced shrinking was not observed when the Ca²⁺-free medium was used. This result suggests that the cell shrinkage is related to the regulatory volume decrease where the cell adjusts the increase in intracellular Ca²⁺ concentration, inducing the efflux of ions and water from the cell.

A Comprehensive Review on Raman Spectroscopy Applications

Raman spectroscopy is a very powerful tool for material analysis, allowing for exploring the properties of a wide range of different materials. Since its discovery, Raman spectroscopy has been used to investigate several features of materials such carbonaceous and inorganic properties, providing useful information on their phases, functions, and defects. Furthermore, techniques such as surface and tip enhanced Raman spectroscopy have extended the field of application of Raman analysis to biological and analytical fields. Additionally, the robustness and versatility of Raman instrumentations represent a promising solution for performing on-field analysis for a wide range of materials. Recognizing the many hot applications of Raman spectroscopy, we herein overview the main and more recent applications for the investigation of a wide range of materials, such as carbonaceous and biological materials. We also provide a brief but exhaustive theoretical background of Raman spectroscopy, also providing deep insight into the analytical achievements.

Predicting the Refractive Index of Tissue Models Using Light Scattering Spectroscopy

In this work, we report the application of Raman microspectroscopy for analysis of the refractive index of a range of tissue phantoms. Using both a custom-developed setup with visible laser source and a commercial microspectrometer with near infrared laser, we measured the Raman spectra of gelatin hydrogels at various concentrations. By building a calibration curve from measured refractometry data and Raman scattering intensity for different vibrational modes of the hydrogel, we were able to predict the refractive indices of the gels from their Raman spectra. This work highlights the importance of a correlative approach through Brillouin-Raman microspectroscopy for the mechano-chemical analysis of biologically relevant samples.

Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy

Liquid-liquid phase separation (LLPS) plays an important role in a variety of biological processes and is also associated with protein aggregation in neurodegenerative diseases. Quantification of LLPS is necessary to elucidate the mechanism of LLPS and the subsequent aggregation process. In this study, we showed that ataxin-3, which is associated with Machado-Joseph disease, exhibits LLPS in an intracellular crowding environment mimicked by biopolymers, and proposed that a single droplet formed in LLPS can be quantified using Raman microscopy in a label-free manner. We succeeded in evaluating the protein concentration and identifying the components present inside and outside a droplet using the O-H stretching band of water as an internal intensity standard. Only water and protein were detected to be present inside droplets with crowding agents remaining outside. The protein concentration in a droplet was dependent on the crowding environment, indicating that the protein concentration and intracellular environment should be considered when investigating LLPS. Raman microscopy has the potential to become a powerful technique for clarifying the chemical nature of LLPS and its relationship with protein aggregation.

Multivariate probing of antitumor metal-based complexes damage on living cells through Raman imaging

Intracellular modifications caused by two metal-based antitumor compounds were assessed by confocal Raman imaging assisted by multivariate curve resolution method, a very powerful deconvolution tool that can be used to extract the characteristic spectral profile of the individual or "purest" components from an image dataset. The use of this Raman methodology has the advantage of being non-invasive and totally label-free. Four main different intracellular processes were observed under the Raman imaging and multivariate approach combination, and even, significant differences could be identified between the treatments with both metallodrugs. Leakage of the nucleus and nucleolus content into the cytoplasm, along with releasing of cytochrome c were observed for the treatment with the Cu-based complex. At the same time, changes of hydrogen-bonding network were also evidenced, indicating an apoptotic cellular death process, consistent with complementary Total Reflection X-Ray fluorescence (TXRF) and fluorescence experiments attesting mitochondria and DNA as main targets after uptake of the complex by cells. For treatment with the Zn-based complex, changes associated with cytochrome c were not detected, neither a rapid leakage of nucleus content upon 24 h treatment. The hydrogen-bonding network also followed a quite different pattern, suggesting that with this metallodrug, the cellular death follows a different mechanism.

The Relative Densities of Cytoplasm and Nuclear Compartments Are Robust against Strong Perturbation

The cell nucleus is a compartment in which essential processes such as gene transcription and DNA replication occur. Although the large amount of chromatin confined in the finite nuclear space could install the picture of a particularly dense organelle surrounded by less dense cytoplasm, recent studies have begun to report the opposite. However, the generality of this newly emerging, opposite picture has so far not been tested. Here, we used combined optical diffraction tomography and epi-fluorescence microscopy to systematically quantify the mass densities of cytoplasm, nucleoplasm, and nucleoli of human cell lines, challenged by various perturbations. We found that the nucleoplasm maintains a lower mass density than cytoplasm during cell cycle progression by scaling its volume to match the increase of dry mass during cell growth. At the same time, nucleoli exhibited a significantly higher mass density than the cytoplasm. Moreover, actin and microtubule depolymerization and changing chromatin condensation altered volume, shape, and dry mass of those compartments, whereas the relative distribution of mass densities was generally unchanged. Our findings suggest that the relative mass densities across membrane-bound and membraneless compartments are robustly conserved, likely by different as-of-yet unknown mechanisms, which hints at an underlying functional relevance. This surprising robustness of mass densities contributes to an increasing recognition of the importance of physico-chemical properties in determining cellular characteristics and compartments.

Automatic Determination of the Sequential Order of Dynamic Data and Its Application to Vibrational Spectroscopy

For over the past 30 years, generalized two-dimensional correlation spectroscopy has formed an active and widespread research area. One of the most attractive properties of this method is that one can determine the sequential order of signal changes. But the determination of the sequential order has only been done manually for several arbitrarily chosen bands. In this paper, we develop a method to automatically determine the sequential order of all of the band intensity changes, and we applied this method to band changes of vibration spectra. This method will open a door to analyze more complicated signals often seen in life phenomena.

Observation of the changes in the chemical composition of lipid droplets using Raman microscopy

We report the dynamics of lipid droplet formation induced by introducing cis- and/or trans-fatty acids into cells. Raman imaging allows the chemical analysis of each droplet, showing that exogenous fatty acids initially enter original endogenous droplets, then induce additional droplets containing endogenous lipids, and finally form their droplets.

Shot-Noise-Limited Two-Color Stimulated Raman Scattering Microscopy with a Balanced Detection Scheme

Stimulated Raman scattering (SRS) microscopy has been considered a useful technique for investigating chemical components by selectively targeting the vibration mode of chemical structures. Its practical application to the observation of molecular structures and dynamics in complicated biological environments requires broad spectral coverage with both high resolution and a high signal-to-noise ratio. Here, we demonstrate a two-color SRS microscopy employing a balanced detection scheme and a spectral focusing method. Two different SRS signals are generated with pump and Stokes laser pulse pairs in perpendicular polarization, where each of them acts as an intensity reference for the other, significantly reducing the background noise level close to the shot-noise limit even with a fiber-based femtosecond laser system. The high spectral resolution comparable to that of spontaneous Raman scattering spectroscopy is achieved with the spectral focusing method. The two-color SRS images are obtained for a mixture of polymer beads and for the distributions of lipids and proteins in U2OS cells.

Optical mapping of biological water in single live cells by stimulated Raman excited fluorescence microscopy

Water is arguably the most common and yet least understood material on Earth. Indeed, the biophysical behavior of water in crowded intracellular milieu is a long-debated issue. Understanding of the spatial and compositional heterogeneity of water inside cells remains elusive, largely due to a lack of proper water-sensing tools with high sensitivity and spatial resolution. Recently, stimulated Raman excited fluorescence (SREF) microscopy was reported as the most sensitive vibrational imaging in the optical far field. Herein we develop SREF into a water-sensing tool by coupling it with vibrational solvatochromism. This technique allows us to directly visualize spatially-resolved distribution of water states inside single mammalian cells. Qualitatively, our result supports the concept of biological water and reveals intracellular water heterogeneity between nucleus and cytoplasm. Quantitatively, we unveil a compositional map of the water pool inside living cells. Hence we hope SREF will be a promising tool to study intracellular water and its relationship with cellular activities.

Label-free diagnostics and cancer surgery Raman spectra guidance for the human colon at different excitation wavelengths

Raman spectroscopy and imaging are highly structure-sensitive methods that allow the characterization of biological samples with minimal impact. In this paper, Raman spectra and imaging of noncancerous and cancerous human colon tissue samples were measured at different excitation wavelengths: 355, 532, and 785 nm. Intra-patient variability in the analyzed spectra showed colon sample heterogeneity for both noncancerous and cancerous human sample types. The lowest inter-patient variability of Raman spectra was observed for the fingerprint region of noncancerous samples for the 532 nm excitation laser line. The bands of principal biochemical constituents (proteins, lipids, nucleic acids) predominate in VIS and NIR-Raman spectra (excitation: 532, 785 nm), with the special role of the bands of intrinsic tissue chromophores—carotenoids for VIS excitation due to resonance enhancement. At 355 nm excitation, high autofluorescence of colon tissues were observed. Our studies proved high potential of Raman spectroscopy and Raman imaging in differentiation of noncancerous and cancerous human colon tissues and that the wavelengths 532 and 785 nm offer wide possibilities for the detection of human colon tissue pathology for ex vivo and in vivo measurements and prevail over 355 nm excitation.

Raman spectroscopy and imaging are highly structure-sensitive methods that allow the characterization of biological samples with minimal impact.

Raman Spectroscopic Analysis of Signaling Molecules-Dopamine Receptors Interactions in Living Cells

The selective interaction of signaling compounds including neurotransmitters and drugs with the dopamine receptors (DARs) is extremely important for the treatment of neurodegenerative diseases. Here, we report a method to probe the selective interactions of signaling compounds with D1 and D2 DARs in living cells using the combined approach of theoretical calculation and surface-enhanced Raman spectroscopy (SERS). When signaling compounds such as DA, amphetamine, methamphetamine, and methylenedioxypyrovalerone interact with D1 dopamine receptors (DRD1), the intracellular cyclic adenosine monophosphate (cAMP) level is increased. However, the intracellular level of cAMP is decreased when D2 dopamine receptors (DRD2) interact with the abovementioned signaling compounds. In our experiments, we have internalized the silica-coated silver nanoparticles (AgNP@SiO₂) in living cells to adsorb biologically generated cAMP which was probed by using SERS. Besides adsorptions of cAMP, AgNP@SiO₂ has a crucial role for the enhancement of Raman cross section of the samples. We observed the characteristic SERS peaks of cAMP when DRD1-overexpressed cells interact with the signaling compounds; these peaks were not observed for other cells including DRD2-overexpressed and DRD1-DRD2-coexpressed cells. Our experimental approach is successful to probe the intracellular cAMP and characterize the selectivity of signaling compounds to different types of DARs. Furthermore, our experimental approach is highly capable for in vivo studies because it can probe intracellular cAMP using a low input power of incident laser without significant cell damage. Our experimental results and density functional theory calculations showed that 780 and 1503 cm^-1 are signature Raman peaks of cAMP. The SERS peak at 780 cm^-1 is associated with C-O, C-C, and C-N stretching and symmetric and asymmetric bending of two O-H bonds of cAMP, whereas the SERS peak at 1503 cm^-1 is contributed by the O₉-H₃ bending mode.

Live Cell Microscopy: A Physical Chemistry Approach

Probing dynamics of intracellular components using physical chemistry techniques is a remarkable bottom-up approach for understanding the structures and functions of a biological cell. In this "Feature Article", we give an overview on local polarity, solvation, viscosity, acid-base property, red-ox processes (thiol-disulfide exchange), and gene silencing at selected intracellular components inside a live cell. Significant differences have been observed between cancer cells and their noncancer counterparts. We demonstrate that thiol-disulfide exchange, calcium oscillation, and gene silencing are manifested in time dependence of fluorescence intensity. We show that fluorescent gold nanoclusters may be used in drug delivery (e.g., doxorubicin) and selective killing of cancer cells. Further, we discuss dynamics and structural changes of DNA quadruplexes and i-motifs, induced by different external conditions (e.g., pH) and additives (e.g., K⁺ and other target specific small molecules). We demonstrate that peptidomimetic analogues have high specificity over double-stranded DNA for binding with i-motifs and G-quadruplexes. These results may have significant biological implications.