Optical imaging of metabolic dynamics in animals

Monitoring Enzymatic Reactions through Probing Chemical Bond Changes by the CD3 Group Using Multiplex Coherent Anti-Stokes Raman Scattering

We propose a method to measure enzymatic reactions using the C-D stretching vibrational spectra of CD3 groups that exist next to the site where a chemical bond changes. In the proposed method, temporal changes in the concentrations of the substrate and product are measured from changes in the C-D stretching spectra of the CD3 groups. Vibrational spectra are obtained using multiplex coherent anti-Stokes Raman scattering (CARS) spectroscopy, which can obtain vibrational spectra much faster than spontaneous Raman spectroscopy. We tested the proposed method by examining the dehydrogenation reaction of isopropyl alcohol-1,1,1,3,3,3-D6 (IPA-D6) catalyzed by alcohol dehydrogenase and found that the change in concentrations of the substrate and product, IPA-D6 and acetone-D6, respectively, was successfully measured from the C-D stretching spectra.

Temporal and spatial omics technologies for 4D profiling

Cells have distinct molecular repertoires on their surfaces and unique intracellular biomolecular profiles that play pivotal roles in orchestrating a myriad of biological responses in the context of growth, development and disease. A persistent challenge in the deep exploration of these cues has been in our inability to effectively and precisely capture the temporal and spatial characteristics of living cells. In this Perspective, we delve into techniques for temporal and two- and three-dimensional spatial omics analyses and underscore how their harmonious fusion promises to unlock insights into the dynamics and diversity of individual cells within biological systems such as tissues and organoids. We then explore four-dimensional profiling, a nascent but promising frontier that adds a temporal (fourth-dimension) component to three-dimensional omics; highlight the advancements, challenges and gaps in the field; and discuss potential strategies for further technological development.

Raman Microspectroscopy to Trace the Incorporation of Deuterium from Labeled (Micro)Plastics into Microbial Cells

The ubiquitous use of plastics demands thoughtfulness about their fate in the environment. Biodegradability is, therefore, a prerequisite for the future use of plastics in many applications, including agriculture. Here, we bring forward stable isotope (resonance) Raman microspectroscopy at the single-cell level to broaden the mechanistic understanding of microbial degradation of (micro)plastics in natural systems. We selected perdeuterated d-polylactic acid (dPLA) as model plastic, synthesized from d-lactic acid-d4, via enantioselective, biocatalytic reduction of pyruvate-d3. With dPLA in hand, we traced the deuterium label during incubation experiments into microbial biomass using C-D vibrations (appear in the Raman-silent region of undeuterated biomass, 2050-2300 cm-1). The 2068 cm-1 C-D band was indicative of strongly deuterated lipids enabling the detection of metabolic differences during incubation with dPLA (i.e., stronger lipid and weaker protein deuteration) compared to glucose-d12 and D2O as alternative D sources. Single-cell analysis was the key to detecting phenotypic heterogeneity and classifying cells of the naturally occurring bacterium Sphingomonas koreensis in two clusters: one showed a significantly stronger deuteration level than the Escherichia coli control, whereas the other was nonlabeled. The deuterium label could even be detected in the strong resonance Raman signal of carotenoids, highlighting the potential for high throughput technologies like imaging and cell sorting. To further demonstrate the transferability to environmental samples, the experiment was repeated with soil bacteria isolates, and deuterium uptake from dPLA into microbial biomass was observed after 2 weeks.

The optimization of sample preparation on zebrafish larvae in vibrational spectroscopy imaging

The zebrafish (Danio rerio) larvae are widely used in biomedical, pharmaceutical, and ecotoxicological studies. Their transparency and translational potential make them particularly valuable for fluorescence imaging. In addition to fluorescence imaging, microspectroscopy, which combines vibrational spectroscopy: Raman or Fourier transform infrared (FT-IR) with microscopy, allows the collection of spatially resolved, label-free information. According to available literature, it was the first application of FT-IR imaging in zebrafish larvae. This study aims to compare different fixation methods for 10-day post-fertilization (dpf) zebrafish larvae using vibrational spectroscopy imaging. Paraformaldehyde (PFA), glutaraldehyde (GA), low temperature, and embedding in gelatin and agarose were investigated. Amides, lipids, and phosphates distribution were more informative in embedded samples but with challenging handling of the sample due to stiffness at -20 °C. FT-IR and Raman mapping revealed that frozen samples had better-preserved tissue structure than chemical fixation. PFA showed uniform amide distribution, while GA treatment exhibited tissue disruptions and denser protein networks in both. Handling of embedded samples is challenging for an operator, but provides more reliable results in developmental biology or disease modeling, compared to chemical treatment.

Lipid Metabolic Heterogeneity during Early Embryogenesis Revealed by Hyper-3D Stimulated Raman Imaging

Studying embryogenesis is fundamental to understanding developmental biology and reproductive medicine. Its process requires precise spatiotemporal regulations in which lipid metabolism plays a crucial role. However, the spatial dynamics of lipid species at the subcellular level remains obscure due to technical limitations. To address this challenge, we developed a hyperspectral 3D imaging and analysis method based on stimulated Raman scattering microscopy (hyper-3D SRS) to quantitatively assess lipid profiles in individual embryos through submicrometer resolution (x-y), 3D optical sectioning (z), and chemical bond-selective (Ω) imaging. Using hyper-3D SRS, individual lipid droplets (LDs) in single cells were identified and quantified. Our findings revealed that the LD profiles within a single embryo are not uniform, even as early as the 2-cell stage. Notably, we also discovered a dynamic relationship between the LD size and unsaturation degree as embryos develop, indicating diverse lipid metabolism during early development. Furthermore, abnormal LDs were observed in oocytes of a progeria mouse model, suggesting that LDs could serve as a potential biomarker for assessing oocyte/embryo quality. Overall, our results highlight the potential of hyper-3D SRS as a noninvasive method for studying lipid content, composition, and subcellular distribution in embryos. This technique provides valuable insights into lipid metabolism during embryonic development and has the potential for clinical applications in evaluating oocyte/embryo quality.

Shedding new light on the hidden complexity of seeds: chemically selective imaging of seed coats with stimulated Raman scattering microscopy

The seed coat plays a pivotal role in seed development and germination, acting as a protective barrier and mediating interac-tions with the external environment. Traditional histochemical techniques and analytical methods have provided valuable insights into seed coat composition and function. However, these methods often suffer from limitations such as indirect chemical signatures and lack of spatial resolution. Here, we introduce stimulated Raman scattering (SRS) microscopy as a novel analytical tool for non-destructive, label-free, high-resolution mapping of biopolymers, water and applied active ingre-dients (AIs) in intact seed coats. We demonstrate the capability of SRS microscopy to perform depth-resolved, chemically selective imaging of major seed coat biopolymers (pectin, tannin, and suberin). By comparing wild type arabidopsis thali-ana seeds with genetically modified mutants deficient in suberin and tannin, we illustrate the potential for semi-quantitative analysis of biopolymer content. Furthermore, we show that SRS microscopy can track the permeability of seed coats to wa-ter using deuterated water (D2O) uptake studies. Real-time imaging reveals differences in water permeation between wild type and suberin deficient seeds, highlighting the importance of seed coat composition in regulating water uptake during germina-tion. Additionally, we extend the application of SRS microscopy to large seeds, such as brassica oleracea, utilizing epi-detected imaging for surface studies. Finally, using a deuterated insecticide (clothianidin-d3), we demonstrate the capability of SRS microscopy to visualize the incorporation of AIs into seed coats. Our study presents SRS microscopy as a powerful tool for characterizing seed coat composition and understanding the diffusion of low molecular weight compounds into seeds. This technique offers new opportunities for designing seeds with tailored properties for improved germination and resilience to environmental stressors.

Probing metabolism in mouse embryos using Raman spectroscopy and deuterium tags

The use of deuterated compounds is an interesting opportunity to expand the capabilities of Raman spectroscopy to study metabolism in living cells. Different biological objects have different tolerances to different deuterated compounds, and their metabolic chains may differ. Here, we explore the potential of this approach to probe metabolism in early mouse embryos. We investigated the Raman spectra of mouse embryos at different developmental stages cultured with deuterated amino acids, phenylalanine-d8 and leucine-d10, glucose-d7, and D2O. Embryos after in vitro culture with 20 % v/v D2O demonstrate Raman peak at 2186 cm-1 corresponding to newly synthesized proteins. Deuterated amino acids can slow down the development rate in 4-8 cell stage embryos, and deuterated glucose can be used at 2 mM concentration. For blastocyst, it was possible to achieve 75 % fraction of deuterated phenylalanine, when cultured with glucose, the maximal intensity ratio between CD and CH bands was 13.7 %. To demonstrate the capabilities of Raman spectroscopy reinforced by deuterium labeling, we investigated the short-term effect of cryopreservation and revealed that cryopreservation decreases the amount of saccharides in embryos and does not affect the activity of protein de novo synthesis.

Multimodal Imaging Unveils the Impact of Nanotopography on Cellular Metabolic Activities

Nanoscale surface topography is an effective approach in modulating cell-material interactions, significantly impacting cellular and nuclear morphologies, as well as their functionality. However, the adaptive changes in cellular metabolism induced by the mechanical and geometrical microenvironment of the nanotopography remain poorly understood. In this study, we investigated the metabolic activities in cells cultured on engineered nanopillar substrates by using a label-free multimodal optical imaging platform. This multimodal imaging platform, integrating two photon fluorescence (TPF) and stimulated Raman scattering (SRS) microscopy, allowed us to directly visualize and quantify metabolic activities of cells in 3D at the subcellular scale. We discovered that the nanopillar structure significantly reduced the cell spreading area and circularity compared to flat surfaces. Nanopillar-induced mechanical cues significantly modulate cellular metabolic activities with variations in nanopillar geometry further influencing these metabolic processes. Cells cultured on nanopillars exhibited reduced oxidative stress, decreased protein and lipid synthesis, and lower lipid unsaturation in comparison to those on flat substrates. Hierarchical clustering also revealed that pitch differences in the nanopillar had a more significant impact on cell metabolic activity than diameter variations. These insights improve our understanding of how engineered nanotopographies can be used to control cellular metabolism, offering possibilities for designing advanced cell culture platforms which can modulate cell behaviors and mimic natural cellular environment and optimize cell-based applications. By leveraging the unique metabolic effects of nanopillar arrays, one can develop more effective strategies for directing the fate of cells, enhancing the performance of cell-based therapies, and creating regenerative medicine applications.

Metabolic nanoscopy enhanced by experimental and computational approaches

The advances in microscopy techniques have led to new findings in biology. The recent advances in super-resolution microscopy technologies revealed precise molecular distribution. The techniques to visualize the distributions of multiple molecules in biological samples from experimental techniques to computational approaches are reviewed. By summarizing the techniques, the future direction of collaborative research of the techniques is highlighted to show the nanoscopic chemical details of biological samples.

An Activity-Based Sensing Approach to Multiplex Mapping of Labile Copper Pools by Stimulated Raman Scattering

Molecular imaging with analyte-responsive probes offers a powerful chemical approach to studying biological processes. Many reagents for bioimaging employ a fluorescence readout, but the relatively broad emission bands of this modality and the need to alter the chemical structure of the fluorophore for different signal colors can potentially limit multiplex imaging. Here, we report a generalizable approach to multiplex analyte imaging by leveraging the comparably narrow spectral signatures of stimulated Raman scattering (SRS) in activity-based sensing (ABS) mode. We illustrate this concept with two copper Raman probes (CRPs), CRP2181 and CRP2153.2, that react selectively with loosely bound Cu(I/II) and Cu(II) ions, respectively, termed the labile copper pool, through copper-directed acyl imidazole (CDAI) chemistry. These reagents label proximal proteins in a copper-dependent manner using a dye scaffold bearing a 13C≡N or 13C≡15N isotopic SRS tag with nearly identical physiochemical properties in terms of shape and size. SRS imaging with the CRP reagents enables duplex monitoring of changes in intracellular labile Cu(I) and Cu(II) pools upon exogenous copper supplementation or copper depletion or genetic perturbations to copper transport proteins. Moreover, CRP imaging reveals reciprocal increases in labile Cu(II) pools upon decreases in activity of the antioxidant response nuclear factor-erythroid 2-related factor 2 (NRF2) in cellular models of lung adenocarcinoma. By showcasing the use of narrow-bandwidth ABS probes for multiplex imaging of copper pools in different oxidation states and identifying alterations in labile metal nutrient pools in cancer, this work establishes a foundation for broader SRS applications in analyte-responsive imaging in biological systems.

Solvent-mediated analgesia via the suppression of water permeation through TRPV1 ion channels

Activation of the ion channel transient receptor potential vanilloid 1 (TRPV1), which is integral to pain perception, leads to an expansion of channel width, facilitating the passage of cations and large organic molecules. However, the permeability of TRPV1 channels to water remains uncertain, owing to a lack of suitable tools to study water dynamics. Here, using upconversion nanophosphors to discriminate between H2O and D2O, by monitoring water permeability across activated TRPV1 at the single-cell and single-molecule levels, and by combining single-channel current measurements with molecular dynamics simulations, we show that water molecules flow through TRPV1 and reveal a direct connection between water migration, cation flow and TRPV1 functionality. We also show in mouse models of acute or chronic inflammatory pain that the administration of deuterated water suppresses TRPV1 activity, interrupts the transmission of pain signals and mitigates pain without impacting other neurological responses. Solvent-mediated analgesia may inspire alternative options for pain management.

Imaging Metabolic Flow of Water in Plants with Isotope-Traced Stimulated Raman Scattering Microscopy

Water plays a vital role in the life cycle of plants, participating in various critical biochemical reactions during both non-photosynthetic and photosynthetic processes. Direct visualization of the metabolic activities of water in plants with high spatiotemporal resolution is essential to reveal the functional utilization of water. Here, stimulated Raman scattering (SRS) microscopy is applied to monitor the metabolic processes of deuterated water (D2O) in model plant Arabidopsis thaliana (A. thaliana). The work shows that in plants uptaking D2O/water solution, proton-transfer from water to organic metabolites results in the formation of C-D bonds in newly synthesized biomolecules (lipid, protein, and polysaccharides, etc.) that allow high-resolution detection with SRS. Reversible metabolic pathways of oil-starch conversion between seed germination and seed development processes are verified. Spatial heterogeneity of metabolic activities along the vertical axis of plants (root, stem, and tip meristem), as well as the radial distributions of secondary growth on the horizontal cross-sections are quantified. Furthermore, metabolic flow of protons from plants to animals is visualized in aphids feeding on A. thaliana. Collectively, SRS microscopy has potential to trace a broad range of matter flows in plants, such as carbon storage and nutrition metabolism.

Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D

Kidney disease, the ninth leading cause of death in the United States, has one of the poorest diagnostic efficiencies of only 10% 1 . Conventional diagnostic methods often rely on light microscopy analysis of 2D fixed tissue sections with limited molecular insight compared to omics studies. Targeting multiple features in a biopsy using molecular or chemical reagents can enhance molecular phenotyping but are limited by overlap of their spatial and chromatic properties, variations in quality of the products, limited multimodal nature and need additional tissue processing. To overcome these limitations and increase the breadth of molecular information available from tissue without an impact on routine diagnostic workup, we implemented label-free imaging modalities including stimulated Raman scattering (SRS) microscopy, second harmonic generation (SHG), and two photon fluorescence (TPF) into a single microscopy setup. We visualized and identified morphological, structural, lipidomic, and metabolic biomarkers of control and diabetic human kidney biopsy samples in 2D and 3D at a subcellular resolution. The label-free biomarkers, including collagen fiber morphology, mesangial-glomerular fractional volume, lipid saturation, redox status, and relative lipid and protein concentrations in the form of Stimulated Raman Histology (SRH), illustrate distinct features in kidney disease tissues not previously appreciated. The same tissue section can be used for routine diagnostic work up thus enhancing the power of cliniopathological insights obtainable without compromising already limited tissue. The additional multimodal biomarkers and metrics are broadly applicable and deepen our understanding of the progression of kidney diseases by integrating lipidomic, fibrotic, and metabolic data.

Abstract Figure

Metabolic light absorption, scattering, and emission (MetaLASE) microscopy

Optical imaging of metabolism can provide key information about health and disease progression in cells and tissues; however, current methods have lacked gold-standard information about histological structure. Conversely, histology and virtual histology methods have lacked metabolic contrast. Here, we present metabolic light absorption, scattering, and emission (MetaLASE) microscopy, which rapidly provides a virtual histology and optical metabolic readout simultaneously. Hematoxylin-like nucleic contrast and eosin-like cytoplasmic contrast are obtained using photoacoustic remote sensing and ultraviolet reflectance microscopy, respectively. The same ultraviolet source excites endogenous Nicotinamide adenine dinucleotide (phosphate), flavin adenine dinucleotide, and collagen autofluorescence, providing a map of optical redox ratios to visualize metabolic variations including in areas of invasive carcinoma. Benign chronic inflammation and glands also are seen to exhibit hypermetabolism. MetaLASE microscopy offers promise for future applications in intraoperative margin analysis and in research applications where greater insights into metabolic activity could be correlated with cell and tissue types.

High Sensitivity Stimulated Raman Scattering Microscopy with Electronic Resonance Enhancement

Raman microscopy is an important tool for labelfree microscopy. However, spontaneous Raman microscopy suffers from slow image acquisition rates and susceptibility to fluorescence background. Coherent Raman microsocopy techniques such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microscopy, by contrast, offer fast imaging capability and robustness against sample fluorescence. Yet, their rather low sensitivity impedes their broader application. This review discusses sensitivity enhancement of SRS microscopy to μ ${\mu }$ M detection levels by using electronically pre-resonant excitation. We present the foundations of this approach, discuss its technological implementation, and show first successful applications. A special emphasis is given to outlining new experimental developments allowing novel types of investigations.

Electrocatalytic reductive deuteration of arenes and heteroarenes

The incorporation of deuterium in organic molecules has widespread applications in medicinal chemistry and materials science1,2. For example, the deuterated drugs austedo3, donafenib4 and sotyktu5 have been recently approved. There are various methods for the synthesis of deuterated compounds with high deuterium incorporation6. However, the reductive deuteration of aromatic hydrocarbons-ubiquitous chemical feedstocks-to saturated cyclic compounds has rarely been achieved. Here we describe a scalable and general electrocatalytic method for the reductive deuteration and deuterodefluorination of (hetero)arenes using a prepared nitrogen-doped electrode and deuterium oxide (D2O), giving perdeuterated and saturated deuterocarbon products. This protocol has been successfully applied to the synthesis of 13 highly deuterated drug molecules. Mechanistic investigations suggest that the ruthenium-deuterium species, generated by electrolysis of D2O in the presence of a nitrogen-doped ruthenium electrode, are key intermediates that directly reduce aromatic compounds. This quick and cost-effective methodology for the preparation of highly deuterium-labelled saturated (hetero)cyclic compounds could be applied in drug development and metabolism studies.

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for P. aeruginosa in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant P. aeruginosa L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.IMPORTANCEPseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control the preference of P. aeruginosa for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.

TET2-STAT3-CXCL5 nexus promotes neutrophil lipid transfer to fuel lung adeno-to-squamous transition

Phenotypic plasticity is a rising cancer hallmark, and lung adeno-to-squamous transition (AST) triggered by LKB1 inactivation is significantly associated with drug resistance. Mechanistic insights into AST are urgently needed to identify therapeutic vulnerability in LKB1-deficient lung cancer. Here, we find that ten-eleven translocation (TET)-mediated DNA demethylation is elevated during AST in KrasLSL-G12D/+; Lkb1L/L (KL) mice, and knockout of individual Tet genes reveals that Tet2 is required for squamous transition. TET2 promotes neutrophil infiltration through STAT3-mediated CXCL5 expression. Targeting the STAT3-CXCL5 nexus effectively inhibits squamous transition through reducing neutrophil infiltration. Interestingly, tumor-infiltrating neutrophils are laden with triglycerides and can transfer the lipid to tumor cells to promote cell proliferation and squamous transition. Pharmacological inhibition of macropinocytosis dramatically inhibits neutrophil-to-cancer cell lipid transfer and blocks squamous transition. These data uncover an epigenetic mechanism orchestrating phenotypic plasticity through regulating immune microenvironment and metabolic communication, and identify therapeutic strategies to inhibit AST.

Imaging immunometabolism in situ in live animals

Immunometabolism is a rapidly developing field that holds great promise for diagnostic and therapeutic benefits to human diseases. The field has emerged based on seminal findings from in vitro and ex vivo studies that established the fundamental role of metabolism in immune cell effector functions. Currently, the field is acknowledging the necessity of investigating cellular metabolism within the natural context of biological processes. Examining cells in their native microenvironment is essential not only to reveal cell-intrinsic mechanisms but also to understand how cross-talk between neighboring cells regulates metabolism at the tissue level in a local niche. This necessity is driving innovation and advancement in multiple imaging-based technologies to enable analysis of dynamic intracellular metabolism at the single-cell level, with spatial and temporal resolution. In this review, we tally the currently available imaging-based technologies and explore the emerging methods of Raman and autofluorescence lifetime imaging microscopy, which hold significant potential and offer broad applications in the field of immunometabolism.

Microglial lipid droplet accumulation in tauopathy brain is regulated by neuronal AMPK

The accumulation of lipid droplets (LDs) in aging and Alzheimer's disease brains is considered a pathological phenomenon with unresolved cellular and molecular mechanisms. Utilizing stimulated Raman scattering (SRS) microscopy, we observed significant in situ LD accumulation in microglia of tauopathy mouse brains. SRS imaging, combined with deuterium oxide (D2O) labeling, revealed heightened lipogenesis and impaired lipid turnover within LDs in tauopathy fly brains and human neurons derived from induced pluripotent stem cells (iPSCs). Transfer of unsaturated lipids from tauopathy iPSC neurons to microglia induced LD accumulation, oxidative stress, inflammation, and impaired phagocytosis. Neuronal AMP-activated protein kinase (AMPK) inhibits lipogenesis and promotes lipophagy in neurons, thereby reducing lipid flux to microglia. AMPK depletion in prodromal tauopathy mice increased LD accumulation, exacerbated pro-inflammatory microgliosis, and promoted neuropathology. Our findings provide direct evidence of native, aberrant LD accumulation in tauopathy brains and underscore the critical role of AMPK in regulating brain lipid homeostasis.

Enhanced optical imaging and fluorescent labeling for visualizing drug molecules within living organisms

The visualization of drugs in living systems has become key techniques in modern therapeutics. Recent advancements in optical imaging technologies and molecular design strategies have revolutionized drug visualization. At the subcellular level, super-resolution microscopy has allowed exploration of the molecular landscape within individual cells and the cellular response to drugs. Moving beyond subcellular imaging, researchers have integrated multiple modes, like optical near-infrared II imaging, to study the complex spatiotemporal interactions between drugs and their surroundings. By combining these visualization approaches, researchers gain supplementary information on physiological parameters, metabolic activity, and tissue composition, leading to a comprehensive understanding of drug behavior. This review focuses on cutting-edge technologies in drug visualization, particularly fluorescence imaging, and the main types of fluorescent molecules used. Additionally, we discuss current challenges and prospects in targeted drug research, emphasizing the importance of multidisciplinary cooperation in advancing drug visualization. With the integration of advanced imaging technology and molecular design, drug visualization has the potential to redefine our understanding of pharmacology, enabling the analysis of drug micro-dynamics in subcellular environments from new perspectives and deepening pharmacological research to the levels of the cell and organelles.

Efficacy of Sailuotong on neurovascular unit in amyloid precursor protein/presenilin-1 transgenic mice with Alzheimer's disease

OBJECTIVE

To discuss the influence of Sailuotong (, SLT) on the Neurovascular Unit (NVUs) of amyloid precursor protein (APP)/presenilin-1(PS1) mice and evaluate the role of gas supplementation in activating blood circulation during the progression of Alzheimer's disease (AD).

METHODS

The mice were allocated into the following nine groups: (a) the C57 Black (C57BL) sham-operated group (control group), (b) ischaemic treatment in C57BL mice (the C57 ischaemic group), (c) the APP/PS1 sham surgery group (APP/PS1 model group), (d) ischaemic treatment in APP/PS1 mice (APP/PS1 ischaemic group), (e) C57BL mice treated with aspirin following ischaemic treatment (C57BL ischaemic + aspirin group), (f) C57BL mice treated with SLT following ischaemic treatment (C57BL ischaemic + SLT group), (g) APP/PS1 mice treated with SLT (APP/PS1 + SLT group), (h) APP/PS1 mice treated with donepezil hydrochloride following ischaemic treatment (APP/PS1 ischaemic + donepezil hydrochloride group) and (i) APP/PS1 mice treated with SLT following ischaemic treatment (APP/PS1 ischaemic + SLT group). The ischaemic model was established by operating on the bilateral common carotid arteries and creating a microembolism. The Morris water maze and step-down tests were used to detect the spatial behaviour and memory ability of mice. The hippocampus of each mouse was observed by haematoxylin and eosin (HE) and Congo red staining. The ultrastructure of NVUs in each group was observed by electron microscopy, and various biochemical indicators were detected by enzyme-linked immunosorbent assay (ELISA). The protein expression level was detected by Western blot. The mRNA expression was detected by quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

The results of the Morris water maze and step-down tests showed that ischemia reduced learning and memory in the mice, which were restored by SLT. The results of HE staining showed that SLT restored the pathological changes of the NVUs. The Congo red staining results revealed that SLT also improved the scattered orange-red sediments in the upper cortex and hippocampus of the APP/PS1 and APP/PS1 ischaemic mice. Furthermore, SLT significantly reduced the content of Aβ, improved the vascular endothelium and repaired the mitochondrial structures. The ELISA detection, western blot detection and qRT-PCR showed that SLT significantly increased the vascular endothelial growth factor (VEGF), angiopoietin and basic fibroblast growth factor, as well as the levels of gene and protein expression of low-density lipoprotein receptor-related protein-1 (LRP-1) and VEGF in brain tissue.

CONCLUSIONS

By increasing the expression of VEGF, SLT can promote vascular proliferation, up-regulate the expression of LRP-1, promote the clearance of Aβ and improve the cognitive impairment of APP/PS1 mice. These results confirm that SLT can improve AD by promoting vascular proliferation and Aβ clearance to protect the function of NVUs.

Advances in Bio-Optical Imaging Systems for Spatiotemporal Monitoring of Intestinal Bacteria

Vast and complex intestinal communities are regulated and balanced through interactions with their host organisms, and disruption of gut microbial balance can cause a variety of diseases. Studying the mechanisms of pathogenic intestinal flora in the host and early detection of bacterial translocation and colonization can guide clinical diagnosis, provide targeted treatments, and improve patient prognosis. The use of in vivo imaging techniques to track microorganisms in the intestine, and study structural and functional changes of both cells and proteins, may clarify the governing equilibrium between the flora and host. Despite the recent rapid development of in vivo imaging of intestinal microecology, determining the ideal methodology for clinical use remains a challenge. Advances in optics, computer technology, and molecular biology promise to expand the horizons of research and development, thereby providing exciting opportunities to study the spatio-temporal dynamics of gut microbiota and the origins of disease. Here, this study reviews the characteristics and problems associated with optical imaging techniques, including bioluminescence, conventional fluorescence, novel metabolic labeling methods, nanomaterials, intelligently activated imaging agents, and photoacoustic (PA) imaging. It hopes to provide a valuable theoretical basis for future bio-intelligent imaging of intestinal bacteria.

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosa's production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and - hydroxybutyrate, which, like lactate, are -hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.

Photoswitchable polyynes for multiplexed stimulated Raman scattering microscopy with reversible light control

Optical imaging with photo-controllable probes has greatly advanced biological research. With superb chemical specificity of vibrational spectroscopy, stimulated Raman scattering (SRS) microscopy is particularly promising for super-multiplexed optical imaging with rich chemical information. Functional SRS imaging in response to light has been recently demonstrated, but multiplexed SRS imaging with reversible photocontrol remains unaccomplished. Here, we create a multiplexing palette of photoswitchable polyynes with 16 Raman frequencies by coupling asymmetric diarylethene with super-multiplexed Carbow (Carbow-switch). Through optimization of both electronic and vibrational spectroscopy, Carbow-switch displays excellent photoswitching properties under visible light control and SRS response with large frequency change and signal enhancement. Reversible and spatial-selective multiplexed SRS imaging of different organelles are demonstrated in living cells. We further achieve photo-selective time-lapse imaging of organelle dynamics during oxidative stress and protein phase separation. The development of Carbow-switch for photoswitchable SRS microscopy will open up new avenues to study complex interactions and dynamics in living cells with high spatiotemporal precision and multiplexing capability.

Probing delivery of a lipid nanoparticle encapsulated self-amplifying mRNA vaccine using coherent Raman microscopy and multiphoton imaging

The COVID-19 pandemic triggered the resurgence of synthetic RNA vaccine platforms allowing rapid, scalable, low-cost manufacturing, and safe administration of therapeutic vaccines. Self-amplifying mRNA (SAM), which self-replicates upon delivery into the cellular cytoplasm, leads to a strong and sustained immune response. Such mRNAs are encapsulated within lipid nanoparticles (LNPs) that act as a vehicle for delivery to the cell cytoplasm. A better understanding of LNP-mediated SAM uptake and release mechanisms in different types of cells is critical for designing effective vaccines. Here, we investigated the cellular uptake of a SAM-LNP formulation and subsequent intracellular expression of SAM in baby hamster kidney (BHK-21) cells using hyperspectral coherent anti-Stokes Raman scattering (HS-CARS) microscopy and multiphoton-excited fluorescence lifetime imaging microscopy (FLIM). Cell classification pipelines based on HS-CARS and FLIM features were developed to obtain insights on spectral and metabolic changes associated with SAM-LNPs uptake. We observed elevated lipid intensities with the HS-CARS modality in cells treated with LNPs versus PBS-treated cells, and simultaneous fluorescence images revealed SAM expression inside BHK-21 cell nuclei and cytoplasm within 5 h of treatment. In a separate experiment, we observed a strong correlation between the SAM expression and mean fluorescence lifetime of the bound NAD(P)H population. This work demonstrates the ability and significance of multimodal optical imaging techniques to assess the cellular uptake of SAM-LNPs and the subsequent changes occurring in the cellular microenvironment following the vaccine expression.

Multi-molecular hyperspectral PRM-SRS microscopy

Lipids play crucial roles in many biological processes. Mapping spatial distributions and examining the metabolic dynamics of different lipid subtypes in cells and tissues are critical to better understanding their roles in aging and diseases. Commonly used imaging methods (such as mass spectrometry-based, fluorescence labeling, conventional optical imaging) can disrupt the native environment of cells/tissues, have limited spatial or spectral resolution, or cannot distinguish different lipid subtypes. Here we present a hyperspectral imaging platform that integrates a Penalized Reference Matching algorithm with Stimulated Raman Scattering (PRM-SRS) microscopy. Using this platform, we visualize and identify high density lipoprotein particles in human kidney, a high cholesterol to phosphatidylethanolamine ratio inside granule cells of mouse hippocampus, and subcellular distributions of sphingosine and cardiolipin in human brain. Our PRM-SRS displays unique advantages of enhanced chemical specificity, subcellular resolution, and fast data processing in distinguishing lipid subtypes in different organs and species.

Femtosecond optical Kerr effect in normal and grades of cancerous breast tissues as a new optical biopsy method

This study reports on the first use of the optical Kerr effect (OKE) in breast cancer tissue. This proposed optical biopsy method utilizes a Femtosecond Optical Kerr Gate to detect changes in dielectric relaxation and conductivity created by a cancerous infection. Here, the temporal behavior of the OKE is tracked in normal and cancerous samples of human and mouse breast. These tissues display a double peaked temporal structure and its decay rate changes depending on the tissue's infection status. The decay of the secondary peak, attributed to ultrafast plasma response, indicates that the tissue's conductivity has doubled once infected. A slower molecular contribution to the Kerr effect can also be observed in healthy tissues. These findings suggest two possible biomarkers for the use of OKE in optical biopsy. Both markers arise from alterations in the infected tissue's cellular structure, which changes the rate at which electronic and molecular processes occur.

Facilitated Transport of EGFR Inhibitors Plays an Important Role in Their Cellular Uptake

Epidermal growth factor receptor (EGFR) is a transmembrane protein commonly targeted by tyrosine kinase inhibitors (TKIs) as a front-line therapy for patients with many cancers including nonsmall cell lung cancer (NSCLC). Effective treatment requires efficient intracellular drug uptake and target binding. However, despite the recent success in the development of new TKI drugs, the mechanisms of uptake for many TKIs are still poorly understood due to the difficulty in imaging and measuring nonfluorescent drug molecules at a subcellular resolution. It has previously been shown that weakly basic TKI drugs are sequestered in lysosomes. Leveraging this property, we apply hyperspectral stimulated Raman scattering imaging to directly visualize and quantify two Food and Drug Administration-approved EGFR inhibitor drugs (lapatinib and afatinib) inside living cells and the changes in their cellular uptake upon the addition of organic cation transporter inhibitors. These single-cell quantitative measurements provide new insight into the role of membrane transporters in the uptake of TKI drugs in living cells.

Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems

Understanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.

Raman spectroscopy of yeast cells cultured on a deuterated substrate

Raman spectroscopy of cells cultured in a deuterated substrate is a promising approach to the characterization of mass transfer and enzymatic reactions in living cells. Here, we studied the potential of this approach using the example of yeast cells cultured under aerobic and anaerobic conditions. In our experiments, unadapted to D2O Saccharomyces cerevisiae were cultured in a medium with different concentrations of deuterium oxide and deuterated glucose. It has been shown that the addition of even 10% heavy water leads to a general decrease in the amount of lipids in cells. In the Raman spectra of cells cultured at high concentrations of D2O, additional peaks are found, which are associated with the deuteration of entire chemical groups. We observed a similar effect in the ethanol synthesized by yeast fermentation, the deuteration of which also depends on the concentration of D2O. The results on the characterization of cell deuteration turned out to be in qualitative agreement with the known estimate that aerobic metabolism is 15 times more active than ethanol fermentation. The results of our work determine new limitations and prospects for further application and development of the Raman method of spectroscopy of deuterium tags.

Click and Detect: Versatile Ampicillin Aptasensor Enabled by Click Chemistry on a Graphene-Alkyne Derivative

Tackling the current problem of antimicrobial resistance (AMR) requires fast, inexpensive, and effective methods for controlling and detecting antibiotics in diverse samples at the point of interest. Cost-effective, disposable, point-of-care electrochemical biosensors are a particularly attractive option. However, there is a need for conductive and versatile carbon-based materials and inks that enable effective bioconjugation under mild conditions for the development of robust, sensitive, and selective devices. This work describes a simple and fast methodology to construct an aptasensor based on a novel graphene derivative equipped with alkyne groups prepared via fluorographene chemistry. Using click chemistry, an aptamer is immobilized and used as a successful platform for the selective determination of ampicillin in real samples in the presence of interfering molecules. The electrochemical aptasensor displayed a detection limit of 1.36 nM, high selectivity among other antibiotics, the storage stability of 4 weeks, and is effective in real samples. Additionally, structural and docking simulations of the aptamer shed light on the ampicillin binding mechanism. The versatility of this platform opens up wide possibilities for constructing a new class of aptasensor based on disposable screen-printed carbon electrodes usable in point-of-care devices.

Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level

As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.

Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer

Triple negative breast cancer (TNBC) is a highly aggressive form of cancer. Detecting TNBC early is crucial for improving disease prognosis and optimizing treatment. Unfortunately, conventional imaging techniques fall short in providing a comprehensive differentiation of TNBC subtypes due to their limited sensitivity and inability to capture subcellular details. In this study, we present a multimodal imaging platform that integrates heavy water (D2O)-probed stimulated Raman scattering (DO-SRS), two-photon fluorescence (TPF), and second harmonic generation (SHG) imaging. This platform allows us to directly visualize and quantify the metabolic activities of TNBC subtypes at a subcellular level. By utilizing DO-SRS imaging, we were able to identify distinct levels of de novo lipogenesis, protein synthesis, cytochrome c metabolic heterogeneity, and lipid unsaturation rates in various TNBC subtype tissues. Simultaneously, TPF imaging provided spatial distribution mapping of NAD[P]H and flavin signals in TNBC tissues, revealing a high redox ratio and significant lipid turnover rate in TNBC BL2 (HCC1806) samples. Furthermore, SHG imaging enabled us to observe diverse orientations of collagen fibers in TNBC tissues, with higher anisotropy at the tissue boundary compared to the center. Our multimodal imaging platform offers a highly sensitive and subcellular approach to characterizing not only TNBC, but also other tissue subtypes and cancers.

Stimulated Raman photothermal microscopy toward ultrasensitive chemical imaging

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics, and couplings in complex systems. However, the sensitivity of SRS is fundamentally limited to the millimolar level due to shot noise and the small modulation depth. To overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrationally excited states. The subsequent relaxation heats up the surroundings and induces refractive index changes. By probing the refractive index changes with a laser beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved. The versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. SRP microscopy opens a way to perform vibrational spectroscopic imaging with ultrahigh sensitivity.

Rapid Antifungal Susceptibility Testing Based on Single-Cell Metabolism Analysis Using Stimulated Raman Scattering Imaging

Rapid antifungal susceptibility testing (AFST) is urgently needed in clinics to treat invasive fungal infections with the appropriate antifungal drugs and to slow the emergence of antifungal resistance. However, current AFST methods are time-consuming (24-48 h) due to the slow growth of fungal cells and the methods not being able to work directly for clinical samples. Here, we demonstrate rapid AFST by measuring the metabolism in single fungal cells using stimulated Raman scattering imaging and deuterium probing. Distinct metabolic responses were observed in Candida albicans to different classes of antifungal drugs: while the metabolism was inhibited by amphotericin B, it was stimulated by azoles (fluconazole and voriconazole) and micafungin. Accordingly, we propose metabolism change as a biomarker for rapid AFST. The results were obtained in 4 h with 100% categorical agreement with the gold standard broth microdilution test. In addition, a protocol was developed for direct AFST from positive blood cultures. This method overcomes the limitation of slow growth in conventional methods and has the potential for the rapid diagnosis of candidemia and other clinical fungal infections.

Stimulated Raman Photothermal Microscopy towards Ultrasensitive Chemical Imaging

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics and coupling in a complex system. However, the bond-detection sensitivity of SRS microscopy is fundamentally limited to milli-molar level due to the shot noise and the small modulation depth in either pump or Stokes beam4. Here, to overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrational excited states. The thereafter relaxation heats up the surrounding and induces a change in refractive index. By probing the refractive index change with a continuous wave beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved on dimethyl sulfide with conserved average power. Versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. With much improved signal to noise ratio compared to SRS, SRP microscopy opens a new way to perform vibrational spectroscopic imaging with ultrahigh sensitivity and minimal water absorption.

Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology

Single-molecule imaging technologies, especially those based on fluorescence, have been developed to probe both the equilibrium and dynamic properties of biomolecules at the single-molecular and quantitative levels. In this review, we provide an overview of the state-of-the-art advancements in single-molecule fluorescence imaging techniques. We systematically explore the advanced implementations of in vitro single-molecule imaging techniques using total internal reflection fluorescence (TIRF) microscopy, which is widely accessible. This includes discussions on sample preparation, passivation techniques, data collection and analysis, and biological applications. Furthermore, we delve into the compatibility of microfluidic technology for single-molecule fluorescence imaging, highlighting its potential benefits and challenges. Finally, we summarize the current challenges and prospects of fluorescence-based single-molecule imaging techniques, paving the way for further advancements in this rapidly evolving field.

Stimulated Raman scattering microscopy reveals a unique and steady nature of brain water dynamics

The biological activities of substances in the brain are shaped by their spatiotemporal dynamics in brain tissues, all of which are regulated by water dynamics. In contrast to solute dynamics, water dynamics have been poorly characterized, owing to the lack of appropriate analytical tools. To overcome this limitation, we apply stimulated Raman scattering multimodal multiphoton microscopy to live brain tissues. The microscopy system allows for the visualization of deuterated water, fluorescence-labeled solutes, and cellular structures at high spatiotemporal resolution, revealing that water moves faster than fluorescent molecules in brain tissues. Detailed analyses demonstrate that water, unlike solutes, diffuses homogeneously in brain tissues without differences between the intra- and the extracellular routes. Furthermore, we find that the water dynamics are steady during development and ischemia, when diffusions of solutes are severely affected. Thus, our approach reveals routes and uniquely robust properties of water diffusion in brain tissues.

Alkyne-tethered oligodeoxynucleotides that allow simultaneous detection of multiple DNA/RNA targets using Raman spectroscopy

Detection of multiple DNA/RNA targets is essential for understanding cellular function. Herein, we propose a general method for the simultaneous detection of plural nucleic acids based on surface-enhanced Raman scattering (SERS) using gold nanoparticles bearing functional oligodeoxynucleotides (ODNs) on their surface. Modified ODNs bearing an acetylene tag hybridized with their complementary ODNs on the surface of the gold nanoparticles, inducing a strong SERS signal of the acetylene tag. The addition of the target nucleic acid to the system resulted in a spontaneous displacement of the strand on the particle and dissociation of the alkyne-tagged ODN from the particle, resulting in a dramatic decrease in signal intensity. By using an alkyne tag for each of the multiple target nucleic acids, each target could be detected simultaneously. In addition, we successfully detected cellular microRNA. Different targets showed changes with different wavenumbers in the Raman spectra, allowing for the detection of multiple nucleic acids.

Alzheimer's-Associated Upregulation of Mitochondria-Associated ER Membranes After Traumatic Brain Injury

Traumatic brain injury (TBI) can lead to neurodegenerative diseases such as Alzheimer's disease (AD) through mechanisms that remain incompletely characterized. Similar to AD, TBI models present with cellular metabolic alterations and modulated cleavage of amyloid precursor protein (APP). Specifically, AD and TBI tissues display increases in amyloid-β as well as its precursor, the APP C-terminal fragment of 99 a.a. (C99). Our recent data in cell models of AD indicate that C99, due to its affinity for cholesterol, induces the formation of transient lipid raft domains in the ER known as mitochondria-associated endoplasmic reticulum (ER) membranes ("MAM" domains). The formation of these domains recruits and activates specific lipid metabolic enzymes that regulate cellular cholesterol trafficking and sphingolipid turnover. Increased C99 levels in AD cell models promote MAM formation and significantly modulate cellular lipid homeostasis. Here, these phenotypes were recapitulated in the controlled cortical impact (CCI) model of TBI in adult mice. Specifically, the injured cortex and hippocampus displayed significant increases in C99 and MAM activity, as measured by phospholipid synthesis, sphingomyelinase activity and cholesterol turnover. In addition, our cell type-specific lipidomics analyses revealed significant changes in microglial lipid composition that are consistent with the observed alterations in MAM-resident enzymes. Altogether, we propose that alterations in the regulation of MAM and relevant lipid metabolic pathways could contribute to the epidemiological connection between TBI and AD.

Toward Gene-Correlated Spatially Resolved Metabolomics with Fingerprint Coherent Raman Imaging

Raman spectroscopy has long been known to provide sufficient information to discriminate distinct cell phenotypes. Underlying this discriminating capability is that Raman spectra provide an overall readout of the metabolic profiles that change with transcriptomic activity. Robustly associating Raman spectral changes with the regulation of specific signaling pathways may be possible, but the spectral signals of interest may be weak and vary somewhat among individuals. Establishing a Raman-to-transcriptome mapping will thus require tightly controlled and easily manipulated biological systems and high-throughput spectral acquisition. We attempt to meet these requirements using broadband coherent anti-Stokes Raman scattering (BCARS) microscopy to spatio-spectrally map the C. elegans hermaphrodite gonad in vivo at subcellular resolution. The C. elegans hermaphrodite gonad is an ideal model system with a sequential, continuous process of highly regulated spatiotemporal cellular events. We demonstrate that the BCARS spatio-spectral signatures correlate with gene expression profiles in the gonad, evincing that BCARS has potential as a spatially resolved omics surrogate.

Bioorthogonal Stimulated Raman Scattering Imaging Uncovers Lipid Metabolic Dynamics in Drosophila Brain During Aging

Studies have shown that brain lipid metabolism is associated with biological aging and influenced by dietary and genetic manipulations; however, the underlying mechanisms are elusive. High-resolution imaging techniques propose a novel and potent approach to understanding lipid metabolic dynamics in situ. Applying deuterium water (D2O) probing with stimulated Raman scattering (DO-SRS) microscopy, we revealed that lipid metabolic activity in Drosophila brain decreased with aging in a sex-dependent manner. Female flies showed an earlier occurrence of lipid turnover decrease than males. Dietary restriction (DR) and downregulation of insulin/IGF-1 signaling (IIS) pathway, two scenarios for lifespan extension, led to significant enhancements of brain lipid turnover in old flies. Combining SRS imaging with deuterated bioorthogonal probes (deuterated glucose and deuterated acetate), we discovered that, under DR treatment and downregulation of IIS pathway, brain metabolism shifted to use acetate as a major carbon source for lipid synthesis. For the first time, our study directly visualizes and quantifies spatiotemporal alterations of lipid turnover in Drosophila brain at the single organelle (lipid droplet) level. Our study not only demonstrates a new approach for studying brain lipid metabolic activity in situ but also illuminates the interconnection of aging, dietary, and genetic manipulations on brain lipid metabolic regulation.

Toward next-generation endoscopes integrating biomimetic video systems, nonlinear optical microscopy, and deep learning

According to the World Health Organization, the proportion of the world's population over 60 years will approximately double by 2050. This progressive increase in the elderly population will lead to a dramatic growth of age-related diseases, resulting in tremendous pressure on the sustainability of healthcare systems globally. In this context, finding more efficient ways to address cancers, a set of diseases whose incidence is correlated with age, is of utmost importance. Prevention of cancers to decrease morbidity relies on the identification of precursor lesions before the onset of the disease, or at least diagnosis at an early stage. In this article, after briefly discussing some of the most prominent endoscopic approaches for gastric cancer diagnostics, we review relevant progress in three emerging technologies that have significant potential to play pivotal roles in next-generation endoscopy systems: biomimetic vision (with special focus on compound eye cameras), non-linear optical microscopies, and Deep Learning. Such systems are urgently needed to enhance the three major steps required for the successful diagnostics of gastrointestinal cancers: detection, characterization, and confirmation of suspicious lesions. In the final part, we discuss challenges that lie en route to translating these technologies to next-generation endoscopes that could enhance gastrointestinal imaging, and depict a possible configuration of a system capable of (i) biomimetic endoscopic vision enabling easier detection of lesions, (ii) label-free in vivo tissue characterization, and (iii) intelligently automated gastrointestinal cancer diagnostic.

Femtosecond Optical Kerr Gates in Cancerous Breast Tissue for a New Optical Biopsy Method

The Optical Kerr Effect was demonstrated for the first time as a new optical biopsy method to detect normal and grades of cancer of human breast tissues. The technique works by temporally tracking the various electronic and molecular processes that give rise to the nonlinear index of refraction (n2). The rate at which these processes populate and dissipate varies depending on the internal properties of the sample. It is shown here that in tissues, the variances in the ultrafast plasma Kerr responses that relates to the dielectric relaxation can be used as a biomarker for cancer. The relaxation of this response changes significantly between healthy and different grades of triple negative breast cancer tissues. This change can be attributed to a doubling or tripling of the tissue's conductivity depending on the cancer grade.

Label-Free Cytometric Evaluation of Mitosis via Stimulated Raman Scattering Microscopy and Spectral Phasor Analysis

Hyperspectral stimulated Raman scattering (SRS) microscopy is a robust imaging tool for the analysis of biological systems. Here, we present a unique perspective, a label-free spatiotemporal map of mitosis, by integrating hyperspectral SRS microscopy with advanced chemometrics to assess the intrinsic biomolecular properties of an essential process of mammalian life. The application of spectral phasor analysis to multiwavelength SRS images in the high-wavenumber (HWN) region of the Raman spectrum enabled the segmentation of subcellular organelles based on innate SRS spectra. Traditional imaging of DNA is primarily reliant on using fluorescent probes or stains which can affect the biophysical properties of the cell. Here, we demonstrate the label-free visualization of nuclear dynamics during mitosis coupled with an evaluation of its spectral profile in a rapid and reproducible manner. These results provide a snapshot of the cell division cycle and chemical variability between intracellular compartments in single-cell models, which is central to understanding the molecular foundations of these fundamental biological processes. The evaluation of HWN images by phasor analysis also facilitated the differentiation between cells in separate phases of the cell cycle based solely on their nuclear SRS spectral signal, which offers an interesting label-free approach in combination with flow cytometry. Therefore, this study demonstrates that SRS microscopy combined with spectral phasor analysis is a valuable method for detailed optical fingerprinting at the subcellular level.

Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling

Heavy water metabolic labeling followed by liquid chromatography coupled with mass spectrometry is a powerful high throughput technique for measuring the turnover rates of individual proteins in vivo. The turnover rate is obtained from the exponential decay modeling of the depletion of the monoisotopic relative isotope abundance. We provide theoretical formulas for the time course dynamics of six mass isotopomers and use the formulas to introduce a method that utilizes partial isotope profiles, only two mass isotopomers, to compute protein turnover rate. The use of partial isotope profiles alleviates the interferences from co-eluting contaminants in complex proteome mixtures and improves the accuracy of the estimation of label enrichment. In five different datasets, the technique consistently doubles the number of peptides with high goodness-of-fit characteristics of the turnover rate model. We also introduce a software tool, d2ome+, which automates the protein turnover estimation from partial isotope profiles.

Identifying lipid particle sub-types in live Caenorhabditis elegans with two-photon fluorescence lifetime imaging

Fat metabolism is an important modifier of aging and longevity in Caenorhabditis elegans. Given the anatomy and hermaphroditic nature of C. elegans, a major challenge is to distinguish fats that serve the energetic needs of the parent from those that are allocated to the progeny. Broadband coherent anti-Stokes Raman scattering (BCARS) microscopy has revealed that the composition and dynamics of lipid particles are heterogeneous both within and between different tissues of this organism. Using BCARS, we have previously succeeded in distinguishing lipid-rich particles that serve as energetic reservoirs of the parent from those that are destined for the progeny. While BCARS microscopy produces high-resolution images with very high information content, it is not yet a widely available platform. Here we report a new approach combining the lipophilic vital dye Nile Red and two-photon fluorescence lifetime imaging microscopy (2p-FLIM) for the in vivo discrimination of lipid particle sub-types. While it is widely accepted that Nile Red staining yields unreliable results for detecting lipid structures in live C. elegans due to strong interference of autofluorescence and non-specific staining signals, our results show that simple FLIM phasor analysis can effectively separate those signals and is capable of differentiating the non-polar lipid-dominant (lipid-storage), polar lipid-dominant (yolk lipoprotein) particles, and the intermediates that have been observed using BCARS microscopy. An advantage of this approach is that images can be acquired using common, commercially available 2p-FLIM systems within about 10% of the time required to generate a BCARS image. Our work provides a novel, broadly accessible approach for analyzing lipid-containing structures in a complex, live whole organism context.