In vivo biomolecular imaging of zebrafish embryos using confocal Raman spectroscopy

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Accurate categorization and rapid pathological diagnosis correction with Micro-Raman technique in human lung adenocarcinoma infiltration level

Background

In the context of surgical interventions for lung adenocarcinoma (LADC), precise determination of the extent of LADC infiltration plays a pivotal role in shaping the surgeon's strategic approach to the procedure. The prevailing diagnostic standard involves the expeditious intraoperative pathological diagnosis of areas infiltrated by LADC. Nevertheless, current methodologies rely on the visual interpretation of tissue images by proficient pathologists, introducing an error margin of up to 15.6%.

Methods

In this study, we investigated the utilization of Micro-Raman technique on isolated specimens of human LADC with the objective of formulating and validating a workflow for the pathological diagnosis of LADC featuring diverse degrees of infiltration. Our strategy encompasses a thorough pathological characterization of LADC, spanning different tissue types and levels of infiltration. Through the integration of Raman spectroscopy with advanced deep learning models for simultaneous diagnosis, this approach offers a swift, precise, and clinically relevant means of analysis.

Results

The diagnostic performance of the convolutional neural network (CNN) model, coupled with the microscopic Raman technique, was found to be exceptional and consistent, surpassing the traditional support vector machine (SVM) model. The CNN model exhibited an area under the curve (AUC) value of 96.1% for effectively distinguishing normal tissue from LADC and an impressive 99.0% for discerning varying degrees of infiltration in LADCs. To comprehensively assess its clinical utility, Raman datasets from patients with intraoperative rapid pathologic diagnostic errors were utilized as test subjects and input into the established CNN model. The results underscored the substantial corrective capacity of the Micro-Raman technique, revealing a misdiagnosis correction rate exceeding 96% in all cases.

Conclusions

Ultimately, our discoveries highlight the Micro-Raman technique's potential to augment the intraoperative diagnostic precision of LADC with varying levels of infiltration. And compared to the traditional SVM model, the CNN model has better generalization ability in diagnosing different infiltration levels. This method furnishes surgeons with an objective groundwork for making well-informed decisions concerning subsequent surgical plans.

The interaction between particles and vascular endothelium in blood flow

Particle-based drug delivery systems have shown promising application potential to treat human diseases; however, an incomplete understanding of their interactions with vascular endothelium in blood flow prevents their inclusion into mainstream clinical applications. The flow performance of nano/micro-sized particles in the blood are disturbed by many external/internal factors, including blood constituents, particle properties, and endothelium bioactivities, affecting the fate of particles in vivo and therapeutic effects for diseases. This review highlights how the blood constituents, hemodynamic environment and particle properties influence the interactions and particle activities in vivo. Moreover, we briefly summarized the structure and functions of endothelium and simulated devices for studying particle performance under blood flow conditions. Finally, based on particle-endothelium interactions, we propose future opportunities for novel therapeutic strategies and provide solutions to challenges in particle delivery systems for accelerating their clinical translation. This review helps provoke an increasing in-depth understanding of particle-endothelium interactions and inspires more strategies that may benefit the development of particle medicine.

Novel Development of Magnetic Resonance Imaging to Quantify the Structural Anatomic Growth of Diverse Organs in Adult and Mutant Zebrafish

Zebrafish (Danio rerio) is a widely used vertebrate animal for modeling genetic diseases by targeted editing strategies followed by gross phenotypic and biomarker characterization. While larval transparency permits microscopic detection of anatomical defects, histological adult screening for organ-level defects remains invasive, tedious, inefficient, and subject to technical artifact. Here, we describe a noninvasive magnetic resonance imaging (MRI) approach to systematically screen adult zebrafish for anatomical growth defects. An anatomical atlas of wild-type (WT) zebrafish at 5-31 months post-fertilization was created by ex vivo MRI with a 9.4 T magnet. Volumetric growth over time was measured of animals and major organs, including the brain, spinal cord, heart, eyes, optic nerve, ear, liver, kidneys, and swim bladder. Subsequently, surf1-/-, fbxl4-/-, and opa1+/- mitochondrial disease mutant adult zebrafish were quantitatively studied to compare organ volumes with age-matched WT zebrafish. Results demonstrated that MRI enabled noninvasive, high-resolution, rapid screening of mutant adult zebrafish for overall and organ-specific growth abnormalities. Detailed volumetric analyses of three mitochondrial disease mutants delineated specific organ differences, including significantly increased brain growth in surf1-/- and opa1+/-, and marginally significant decreased heart and spinal cord volumes in surf1-/- mutants. This is interesting as we know neurological involvement can be seen in SURF1-/- patients with ataxia, dystonia, and lesions in basal ganglia, as well as in OPA1+/- patients with spasticity, ataxia, and hyperreflexia indicative of neuropathology. Similarly, cardiomyopathy is a known sequelae of cardiac pathology in patients with SURF1-/--related disease. Future studies will define MRI signaling patterns of organ dysfunction to further delineate specific pathology.

The art of simplicity: Water-soluble porphyrin-like carbon dots self-assemble into mesmerizing red glow

In this new study, we present an intriguing development in the field of theranostics: the simplistic self-assembly of red-emissive amphiphilic porphyrin-like carbon dots (P-CDs). By harnessing their exceptional photophysical properties, we have revealed a strong candidate as the ideal photosensitizer (PS) for applications, particularly in the realm of imaging. Spanning a remarkable size average between 1-4 nm, these particles exhibit both highly stable and unparalleled emission characteristics between 650 and 715 nm in water in comparison to current carbon dots (CDs) available. Lastly, these CDs were fairly non-toxic when tested against normal human cell lines as well as were found to have favorable imaging capabilities in zebrafish embryo.

Noise learning of instruments for high-contrast, high-resolution and fast hyperspectral microscopy and nanoscopy

The low scattering efficiency of Raman scattering makes it challenging to simultaneously achieve good signal-to-noise ratio (SNR), high imaging speed, and adequate spatial and spectral resolutions. Here, we report a noise learning (NL) approach that estimates the intrinsic noise distribution of each instrument by statistically learning the noise in the pixel-spatial frequency domain. The estimated noise is then removed from the noisy spectra. This enhances the SNR by ca. 10 folds, and suppresses the mean-square error by almost 150 folds. NL allows us to improve the positioning accuracy and spatial resolution and largely eliminates the impact of thermal drift on tip-enhanced Raman spectroscopic nanoimaging. NL is also applicable to enhance SNR in fluorescence and photoluminescence imaging. Our method manages the ground truth spectra and the instrumental noise simultaneously within the training dataset, which bypasses the tedious labelling of huge dataset required in conventional deep learning, potentially shifting deep learning from sample-dependent to instrument-dependent.

High species homology potentiates quantitative inflammation profiling in zebrafish using immunofluorescence

Due to substantial homology between the human and zebrafish genome and a high level of conservation of the innate immune system across species, zebrafish larvae have become an invaluable research tool for studying inflammation and modelling inflammatory disease. However, further microscopy techniques need to be developed for better profiling of inflammation and in particular, integrated cytokine responses to different stimuli - approaches are currently largely limited to assessment of changes in cytokine gene transcription and in vivo visualisation using transgenics, which is limited in terms of the number of cytokines that may be assessed at once. In this study, after confirming substantial homology of human vs zebrafish cytokine amino acid sequences, immunofluorescence staining using antibodies directed at human cytokines was performed. Inflammatory cytokine signalling responses to experimental tailfin transection was assessed over 24 h (1 hpi (hours post injury), 2 hpi, 4 hpi, 24 hpi) in zebrafish larvae, with experimental end point at 120 h post fertilization (hpf). When immunofluorescence results were compared to responses observed in rodent and human literature, it is clear that the cytokines follow a similar response, albeit with a condensed total time course. Notably, tumor necrosis factor-α and monocyte chemoattractant protein-1 increased and remained elevated over the 24-h period. In contrast, interleukin-1β and interleukin-6 peaked at 4 hpi and 2 hpi respectively but had both returned to baseline levels by 24 hpi. Macrophage migration inhibitory factor was lowest at 1 hpi, potentially encouraging macrophage movement into the site of injury, followed by a sharp increase. This protocol provides valuable insight into inflammation over a time course and more so, provides an affordable and accessible method to comprehensively assess inflammation in zebrafish disease models.

Protein Tyrosine Phosphatase Studies in Zebrafish

The zebrafish is an ideal model for functional analysis of genes at the molecular, protein, cell, organ, and organism levels. We have used zebrafish to analyze the function of members of the protein tyrosine phosphatase (PTP) superfamily for more than two decades. The molecular genetic toolbox has significantly improved over the years. Currently, generating mutant lines that lack the function of a PTP gene is relatively straightforward by CRISPR/Cas9 technology-mediated generation of insertions or deletions in the target gene. In addition, generating point mutations using CRISPR/Cas9 technology and homology-directed repair (HDR) is feasible, albeit the success rate could be higher. Here, we describe the methods, including the tips and tricks, that we have used to generate knock-out and knock-in zebrafish lines in PTP genes successfully.

Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species

Detecting skeletal or bone-related deformities in model and aquaculture fish is vital for numerous biomedical studies. In biomedical research, model fish with bone-related disorders are potential indicators of various chemically induced toxins in their environment or poor dietary conditions. In aquaculture, skeletal deformities are affecting fish health, and economic losses are incurred by fish farmers. This survey paper focuses on showcasing the cutting-edge image analysis tools and techniques based on artificial intelligence that are currently applied in the analysis of bone-related deformities in aquaculture and model fish. These methods and tools play a significant role in improving research by automating various aspects of the analysis. This paper also sheds light on some of the hurdles faced when dealing with high-content bioimages and explores potential solutions to overcome these challenges.

A perspective on psychedelic teratogenicity: the utility of zebrafish models

Psychedelic drugs have experienced an unprecedented surge in recreational use within the past few years. Among recreational users, the risks of psychedelic use by pregnant and breastfeeding women are severely understudied and there is little information on the potential teratogenic effects of these drugs. We provide an overview of the previous data on psychedelic teratogenicity from rodent studies and human surveys, discuss their limitations, and propose the utility of the zebrafish as a potential effective model for investigating psychedelic teratogenicity. Recent years have validated the use of zebrafish in the study of fetal exposure and developmental biology; we highlight these properties of the zebrafish for its suitability in psychedelic toxicity research.

Viewing life without labels under optical microscopes

Optical microscopes today have pushed the limits of speed, quality, and observable space in biological specimens revolutionizing how we view life today. Further, specific labeling of samples for imaging has provided insight into how life functions. This enabled label-based microscopy to percolate and integrate into mainstream life science research. However, the use of labelfree microscopy has been mostly limited, resulting in testing for bio-application but not bio-integration. To enable bio-integration, such microscopes need to be evaluated for their timeliness to answer biological questions uniquely and establish a long-term growth prospect. The article presents key label-free optical microscopes and discusses their integrative potential in life science research for the unperturbed analysis of biological samples.

Development of a Triple-Negative Breast Cancer Leptomeningeal Disease Model in Zebrafish

Leptomeningeal disease occurs when cancer cells migrate into the ventricles of the brain and spinal cord and then colonize the meninges of the central nervous system. The triple-negative subtype of breast cancer often progresses toward leptomeningeal disease and has a poor prognosis because of limited treatment options. This is due, in part, to a lack of animal models with which to study leptomeningeal disease. Here, we developed a translucent zebrafish casper (roy-/-; nacre-/-) xenograft model of leptomeningeal disease in which fluorescent labeled MDA-MB-231 human triple-negative breast cancer cells are microinjected into the ventricles of zebrafish embryos and then tracked and measured using fluorescent microscopy and multimodal plate reader technology. We then used these techniques to measure tumor area, cell proliferation, and cell death in samples treated with the breast cancer drug doxorubicin and a vehicle control. We monitored MDA-MB-231 cell localization and tumor area, and showed that samples treated with doxorubicin exhibited decreased tumor area and proliferation and increased apoptosis compared to control samples.

Label-free structural and functional volumetric imaging by dual-modality optical-Raman projection tomography

Mesoscale volumetric imaging is of great importance for the study of bio-organisms. Among others, optical projection tomography provides unprecedented structural details of specimens, but it requires fluorescence label for chemical targeting. Raman spectroscopic imaging is able to identify chemical components in a label-free manner but lacks microstructure. Here, we present a dual-modality optical-Raman projection tomography (ORPT) technology, which enables label-free three-dimensional imaging of microstructures and components of millimeter-sized samples with a micron-level spatial resolution on the same device. We validate the feasibility of our ORPT system using images of polystyrene beads in a volume, followed by detecting biomolecules of zebrafish and Arabidopsis, demonstrating that fused three-dimensional images of the microstructure and molecular components of bio-samples could be achieved. Last, we observe the fat body of Drosophila melanogaster at different developmental stages. Our proposed technology enables bimodal label-free volumetric imaging of the structure and function of biomolecules in a large sample.

Zebrafish Models to Study Ectopic Calcification and Calcium-Associated Pathologies

Ectopic calcification refers to the pathological accumulation of calcium ions in soft tissues and is often the result of a dysregulated action or disrupted function of proteins involved in extracellular matrix mineralization. While the mouse has traditionally been the go-to model organism for the study of pathologies associated with abnormal calcium deposition, many mouse mutants often have exacerbated phenotypes and die prematurely, limiting the understanding of the disease and the development of effective therapies. Since the mechanisms underlying ectopic calcification share some analogy with those of bone formation, the zebrafish (Danio rerio)-a well-established model for studying osteogenesis and mineralogenesis-has recently gained momentum as a model to study ectopic calcification disorders. In this review, we outline the mechanisms of ectopic mineralization in zebrafish, provide insights into zebrafish mutants that share phenotypic similarities with human pathological mineralization disorders, list the compounds capable of rescuing mutant phenotypes, and describe current methods to induce and characterize ectopic calcification in zebrafish.

Direct imaging of intracellular RNA, DNA, and liquid-liquid phase separated membraneless organelles with Raman microspectroscopy

Methodologies for direct intracellular imaging of RNA and DNA are necessary for the advancement of bioimaging. Here we show direct label-free imaging of RNA and DNA in single cells by isolating their accurate Raman spectra. Raman images of DNA from interphase cells show intact nucleus, while those from mitotic cells reveal condensed chromosome. The condensed chromosome images are accurate enough to assign the stage of mitotic cell division (e.g., metaphase). Raman spectral features indicate B-DNA double helical conformational form in all the cell lines investigated here. The Raman images of RNAs, on the other hand, reveal liquid-liquid phase separated (LLPS) membraneless organelles in interphase cells, which disappears during mitosis. Further, the Raman spectrum of proteins from the intracellular LLPS organelles indicates slight enrichment of amyloid-like secondary structural features. Vibrational imaging of intracellular DNA and RNA simultaneously would open myriad of opportunities for examining functional biochemical aspects of cells and organelles.

Detection and analysis of microplastics in offshore sediment by microscopic differential Raman spectroscopy

In view of the problems of low pre-screening efficiency, a weak Raman signal, and strong fluorescence interference in the detection of microplastics by traditional Raman spectroscopy, a set of rapid detection system and research methods for microplastics, including fluorescence imaging technology, differential Raman spectroscopy technology, and confocal microscopic Raman technology, are constructed in this paper. A 784/785 nm dual-wavelength laser was used as the excitation light source in the rapid detection system for microplastics. The sediment in the coastal waters of Qingdao Shilaoren was taken as the research object. Polycarbonate and high-density polyethylene with a particle size of 40 µm in the samples were accurately detected and analyzed. The research method for microplastics proposed in this study breaks through relevant key technologies, which we believe will help promote the development of microplastic monitoring technology in the global marine environment and provide strong technical support for the healthy development of the global marine ecological environment.

Neither too little nor too much: Finding the ideal proportion of excipients using confocal Raman and chemometrics

The applications of Raman imaging in pharmaceutical field are ever-increasing due its ability to obtain spatial and spectral information simultaneously, once it allows determine the chemical distribution of compounds. In this sense, it is used to study homogeneity, of paramount importance during the development of pharmaceutical formulations due to its relation to stability, safety and efficacy. Commonly, just surface is analyzed, but confocal Raman spectroscopy can also characterize the inner part of samples, allowing to determine phase separation in the early stages. In this sense, confocal 3D Raman microscopy was crucial to obtain the optimal proportion of Apifil®, Capryol® 90 and Transcutol® to promote controlled release of the local anesthetic butamben (BTB). 3D chemical maps were obtained by classical least squares (CLS) using pure compound spectra as S matrix, showing that chemical distribution throughout the material was different. Knowing that the composition of samples affects the homogeneity parameter, standard deviation and distributional homogeneity index (DHI) were used in mixture experimental design (DoE). From this analysis, it was revealed that a correct amount of Capryol® 90 enhances both miscibility and solubility. Furthermore, suitable miscibility was observed in two ratio proportions of excipients with a desirability of 0.783 and 0.742. These results unequivocally demonstrated that confocal Raman microscopy combined to DoE can bring pharmaceutical development to a higher level.

Nutrient limitation regulates the properties of extracellular electron transfer and hydraulic shear resistance of electroactive biofilm

Understanding the roles of nutrient restriction in extracellular electron transfer (EET) and stability of mixed electroactive biofilm is essential in pollutant degradation and bioenergy production. However, the relevant studies are still limited so far. Herein, the effect of nutrient restriction on the EET pathways and stability of mixed electroactive biofilm was explored. It was found that the electroactive Pseudomonas and Geobacter genera were selectively enriched in the biofilms cultured under total nutrient and P-constrained conditions, and two EET pathways including direct and indirect were found, while Rhodopseudomonas genus was enriched in the N-constrained biofilm, which only had the direct EET pathway. Moreover, multiple analyses including 2D confocal Raman spectra revealed that P-constrained biofilm was rich in extracellular polymeric substances (EPS) especially for polysaccharide, presented a dense and uniform layered distribution, and had better stability than N-constrained biofilm with lower EPS and biofilm with heterostructures cultured under total nutrient conditions.

Screening of Mineralogenic and Osteogenic Compounds in Zebrafish—Tools to Improve Assay Throughput and Data Accuracy

Bone disorders affect millions of people worldwide and treatments currently available often produce undesirable secondary effects or have limited efficacy. It is therefore of the utmost interest for patients to develop more efficient drugs with reduced off-target activities. In the long process of drug development, screening and preclinical validation have recently gained momentum with the increased use of zebrafish as a model organism to study pathological processes related to human bone disorders, and the development of zebrafish high-throughput screening assays to identify bone anabolic compounds. In this review, we provided a comprehensive overview of the literature on zebrafish bone-related assays and evaluated their performance towards an integration into screening pipelines for the discovery of mineralogenic/osteogenic compounds. Tools available to standardize fish housing and feeding procedures, synchronize embryo production, and automatize specimen sorting and image acquisition/analysis toward faster and more accurate screening outputs were also presented.

Microscopic Visualization of Cell-Cell Adhesion Complexes at Micro and Nanoscale

Considerable progress has been made in our knowledge of the morphological and functional varieties of anchoring junctions. Cell-cell adhesion contacts consist of discrete junctional structures responsible for the mechanical coupling of cytoskeletons and allow the transmission of mechanical signals across the cell collective. The three main adhesion complexes are adherens junctions, tight junctions, and desmosomes. Microscopy has played a fundamental role in understanding these adhesion complexes on different levels in both physiological and pathological conditions. In this review, we discuss the main light and electron microscopy techniques used to unravel the structure and composition of the three cell-cell contacts in epithelial and endothelial cells. It functions as a guide to pick the appropriate imaging technique(s) for the adhesion complexes of interest. We also point out the latest techniques that have emerged. At the end, we discuss the problems investigators encounter during their cell-cell adhesion research using microscopic techniques.

Looking Inside Non-Destructively: Label-Free, Raman-Based Visualization of Intracellular Coxiella burnetii

The life cycle of intracellular pathogens is often complex and can include different morphoforms. Treatment of intracellular infections and unperturbed studying of the pathogen inside the host cell are frequently challenging. Here, we present a Raman-based, label-free, non-invasive, and non-destructive method to localize, visualize, and even quantify intracellular bacteria in 3D within intact host cells in a Coxiella burnetii infection model. C. burnetii is a zoonotic obligate intracellular pathogen that causes infections in ruminant livestock and humans with an acute disease known as Q fever. Using statistical data analysis, no isolation is necessary to gain detailed information on the intracellular pathogen's metabolic state. High-quality false color image stacks with diffraction-limited spatial resolution enable a 3D spatially resolved single host cell analysis that shows excellent agreement with results from transmission electron microscopy. Quantitative analysis at different time points post infection allows to follow the infection cycle with the transition from the large cell variant (LCV) to the small cell variant (SCV) at around day 6 and a gradual change in the lipid composition during vacuole maturation. Spectral characteristics of intracellular LCV and SCV reveal a higher lipid content of the metabolically active LCV.

Noble Metal Nanoparticle Biosensors: From Fundamental Studies toward Point-of-Care Diagnostics

Noble metal nanoparticles (NMNPs) have become firmly established as effective agents to detect various biomolecules with extremely high sensitivity. This ability stems from the collective oscillation of free electrons and extremely large electric field enhancement under exposure to light, leading to various light-matter interactions such as localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering. A remarkable feature of NMNPs is their customizability by mechanisms such as particle etching, growth, and aggregation/dispersion, yielding distinct color changes and excellent opportunities for colorimetric biosensing in user-friendly assays and devices. They are readily functionalized with a large variety of capping agents and biomolecules, with resultant bioconjugates often possessing excellent biocompatibility, which can be used to quantitatively detect analytes from physiological fluids. Furthermore, they can possess excellent catalytic properties that can achieve significant signal amplification through mechanisms such as the catalytic transformation of colorless substrates to colored reporters. The various excellent attributes of NMNP biosensors have put them in the spotlight for developing high-performance in vitro diagnostic (IVD) devices that are particularly well-suited to mitigate the societal threat that infectious diseases pose. This threat continues to dominate the global health care landscape, claiming millions of lives annually. NMNP IVDs possess the potential to sensitively detect infections even at very early stages with affordable and field-deployable devices, which will be key to strengthening infectious disease management. This has been the major focal point of current research, with a view to new avenues for early multiplexed detection of infectious diseases with portable devices such as smartphones, especially in resource-limited settings.In this Account, we provide an overview of our original inspiration and efforts in NMNP-based assay development, together with some more sophisticated IVD assays by ourselves and many others. Our work in the area has led to our recent efforts in developing IVDs for high-profile infectious diseases, including Ebola and HIV. We emphasize that integration with digital platforms represents an opportunity to establish and efficiently manage widespread testing, tracking, epidemiological intelligence, and data sharing backed by community participation. We highlight how digital technologies can address the limitations of conventional diagnostic technologies at the point of care (POC) and how they may be used to abate and contain the spread of infectious diseases. Finally, we focus on more recent integrations of noble metal nanoparticles with Raman spectroscopy for accurate, noninvasive POC diagnostics with improved sensitivity and specificity.

Surface-enhanced Raman probes based on gold nanomaterials for in vivo diagnosis and imaging

Surface-enhanced Raman scattering (SERS) has received considerable attention from researchers due to its high molecular specificity, high sensitivity, non-invasive and multiplexing. Recently, various metal substrates have been exploited for SERS analysis and imaging. Among them, gold nanomaterials are important SERS substrates with outstanding surface plasmon resonance effects, structural adjustability and good biocompatibility, making them widely used in biomedical diagnosis and clinical fields. In this minireview, we discuss the latest progress about the application of gold-based nanomaterials as SERS probes in biomedical research, primarily for in vivo disease diagnosis and imaging. This review mainly includes the basic shapes and morphologies of gold based SERS probes, such as gold nanoparticles (AuNPs), gold nanorods (AuNRs), gold nanostars (AuNSs), as well as other gold nanostructures. Finally, a brief outlook for the future development of SERS technique in the context of efficient diagnostics and therapy guidance is provided. We hope that this minireview will facilitate the design and future development of Surface-enhanced Raman probes based on gold nanomaterials.

Of form and function: Early cardiac morphogenesis across classical and emerging model systems

The heart is the earliest organ to develop during embryogenesis and is remarkable in its ability to function efficiently as it is being sculpted. Cardiac heart defects account for a high burden of childhood developmental disorders with many remaining poorly understood mechanistically. Decades of work across a multitude of model organisms has informed our understanding of early cardiac differentiation and morphogenesis and has simultaneously opened new and unanswered questions. Here we have synthesized current knowledge in the field and reviewed recent developments in the realm of imaging, bioengineering and genetic technology and ex vivo cardiac modeling that may be deployed to generate more holistic models of early cardiac morphogenesis, and by extension, new platforms to study congenital heart defects.

The Role of Macrophages During Zebrafish Injury and Tissue Regeneration Under Infectious and Non-Infectious Conditions

The future of regenerative medicine relies on our understanding of the mechanistic processes that underlie tissue regeneration, highlighting the need for suitable animal models. For many years, zebrafish has been exploited as an adequate model in the field due to their very high regenerative capabilities. In this organism, regeneration of several tissues, including the caudal fin, is dependent on a robust epimorphic regenerative process, typified by the formation of a blastema, consisting of highly proliferative cells that can regenerate and completely grow the lost limb within a few days. Recent studies have also emphasized the crucial role of distinct macrophage subpopulations in tissue regeneration, contributing to the early phases of inflammation and promoting tissue repair and regeneration in late stages once inflammation is resolved. However, while most studies were conducted under non-infectious conditions, this situation does not necessarily reflect all the complexities of the interactions associated with injury often involving entry of pathogenic microorganisms. There is emerging evidence that the presence of infectious pathogens can largely influence and modulate the host immune response and the regenerative processes, which is sometimes more representative of the true complexities underlying regenerative mechanics. Herein, we present the current knowledge regarding the paths involved in the repair of non-infected and infected wounds using the zebrafish model.

Time-encoded stimulated Raman scattering microscopy of tumorous human pharynx tissue in the fingerprint region from 1500-1800 cm-1

Stimulated Raman scattering (SRS) microscopy for biomedical analysis can provide a molecular localization map to infer pathological tissue changes. Compared to spontaneous Raman, SRS achieves much faster imaging speeds at reduced spectral coverage. By targeting spectral features in the information dense fingerprint region, SRS allows fast and reliable imaging. We present time-encoded (TICO) SRS microscopy of unstained head-and-neck biopsies in the fingerprint region with molecular contrast. We combine a Fourier-domain mode-locked (FDML) laser with a master oscillator power amplifier (MOPA) to cover Raman transitions from 1500-1800cm^-1. Both lasers are fiber-based and electronically programmable making this fingerprint TICO system robust and reliable. The results of our TICO approach were cross-checked with a spontaneous Raman micro-spectrometer and show good agreement, paving the way toward clinical applications.

An in vivo reporter for tracking lipid droplet dynamics in transparent zebrafish

Lipid droplets are lipid storage organelles found in nearly all cell types from adipocytes to cancer cells. Although increasingly implicated in disease, current methods to study lipid droplets in vertebrate models rely on static imaging or the use of fluorescent dyes, limiting investigation of their rapid in vivo dynamics. To address this, we created a lipid droplet transgenic reporter in whole animals and cell culture by fusing tdTOMATO to Perilipin-2 (PLIN2), a lipid droplet structural protein. Expression of this transgene in transparent casper zebrafish enabled in vivo imaging of adipose depots responsive to nutrient deprivation and high-fat diet. Simultaneously, we performed a large-scale in vitro chemical screen of 1280 compounds and identified several novel regulators of lipolysis in adipocytes. Using our Tg(-3.5ubb:plin2-tdTomato) zebrafish line, we validated several of these novel regulators and revealed an unexpected role for nitric oxide in modulating adipocyte lipid droplets. Similarly, we expressed the PLIN2-tdTOMATO transgene in melanoma cells and found that the nitric oxide pathway also regulated lipid droplets in cancer. This model offers a tractable imaging platform to study lipid droplets across cell types and disease contexts using chemical, dietary, or genetic perturbations.

Immunometabolism of Tissue-Resident Macrophages - An Appraisal of the Current Knowledge and Cutting-Edge Methods and Technologies

Tissue-resident macrophages exist in unique environments, or niches, that inform their identity and function. There is an emerging body of literature suggesting that the qualities of this environment, such as the types of cells and debris they eat, the intercellular interactions they form, and the length of time spent in residence, collectively what we call habitare, directly inform their metabolic state. In turn, a tissue-resident macrophage’s metabolic state can inform their function, including whether they resolve inflammation and protect the host from excessive perturbations of homeostasis. In this review, we summarize recent work that seeks to understand the metabolic requirements for tissue-resident macrophage identity and maintenance, for how they respond to inflammatory challenges, and for how they perform homeostatic functions or resolve inflammatory insults. We end with a discussion of the emerging technologies that are enabling, or will enable, in situ study of tissue-resident macrophage metabolism.

Applications of Vibrational Spectroscopy for Analysis of Connective Tissues

Advances in vibrational spectroscopy have propelled new insights into the molecular composition and structure of biological tissues. In this review, we discuss common modalities and techniques of vibrational spectroscopy, and present key examples to illustrate how they have been applied to enrich the assessment of connective tissues. In particular, we focus on applications of Fourier transform infrared (FTIR), near infrared (NIR) and Raman spectroscopy to assess cartilage and bone properties. We present strengths and limitations of each approach and discuss how the combination of spectrometers with microscopes (hyperspectral imaging) and fiber optic probes have greatly advanced their biomedical applications. We show how these modalities may be used to evaluate virtually any type of sample (ex vivo, in situ or in vivo) and how "spectral fingerprints" can be interpreted to quantify outcomes related to tissue composition and quality. We highlight the unparalleled advantage of vibrational spectroscopy as a label-free and often nondestructive approach to assess properties of the extracellular matrix (ECM) associated with normal, developing, aging, pathological and treated tissues. We believe this review will assist readers not only in better understanding applications of FTIR, NIR and Raman spectroscopy, but also in implementing these approaches for their own research projects.