Lipid conjugate dissociation analysis improves the in vivo understanding of lipid-based nanomedicine

Lipid conjugates have advanced the field of lipid-based nanomedicine by promoting active-targeting (ligand, peptide, antibody), stability (PEGylation), controlled release (lipoid prodrug), and probe-based tracking (fluorophore). Recent findings indicate lipid conjugates dissociating from nanomedicine upon encountering a biological environment. Yet, implications for (pre)clinical outcomes remain unclear. In this study, using the zebrafish model (Danio rerio), we investigated the fate of liposome-incorporated lipid fluorophore conjugates (LFCs) after intravenous (IV) administration. LFCs having a bilayer mismatch and relatively polar fluorophore revealed counter-predictive outcomes for Caelyx/Doxil (clearance vs. circulating) and AmBisome-like liposomes (scavenger endothelial cell vs. macrophage uptake). Findings on LFC (mis)match for Caelyx/Doxil-like liposomes were supported by translational intravital imaging studies in mice. Importantly, contradicting observations suggest to originate from LFC dissociation in vivo, which was investigated by Asymmetric Flow Field-Flow Fractionation (AF4) upon liposome-serum incubation in situ. Our data suggests that LFCs matching with the liposome bilayer composition - that did not dissociate upon serum incubation - revealed improved predictive outcomes for liposome biodistribution profiles. Altogether, this study highlights the critical importance of fatty acid tail length and headgroup moiety when selecting lipid conjugates for lipid-based nanomedicine.

Non-conservative behavior of organic matter and its interaction with metals in an equatorial estuary, Brazil

Droughts are becoming more intense and frequent in the Brazilian semiarid because of El Niño and global climate changes. The Jaguaribe River estuary is a semiarid ecosystem that experiences a reduction in freshwater discharges due to droughts and river damming. The decrease in freshwater fluxes has increased metal availability through the water residence time increase in the Jaguaribe River estuary. Then, this study aimed to evaluate the dissolved organic matter quality and its interaction with metals in the Jaguaribe River estuary after a severe drought period. It was performed through carbon analyses, fluorescence spectroscopy, ultrafiltration technique, and determinations of metals by ICP-MS. Optical analysis showed that the dissolved organic carbon (DOC) was preponderantly composed of terrestrial-derived humic compounds, while the low ratio between the particulate organic carbon (POC) and chlorophyll-a indicated that POC was predominantly phytoplankton-derived. DOC and POC presented non-conservative removal during the estuarine mixing. DOM and dissolved elements were mostly distributed within the LMW fraction and presented a low percentage in the colloidal fraction. Li, Rb, Sr, Mo, and U showed conservative behavior, while Cu, Fe, Cr, and V had non-conservative behavior with a significant positive correlation with DOM, suggesting DOM as a relevant driver of metal availability at the Jaguaribe River estuary even during the rainy season.

Water-Soluble Small Organic Fluorophores for Oncological Theragnostic Applications: Progress and Development

Cancer is one of the major noncommunicable diseases, responsible for millions of deaths every year worldwide. Though various cancer detection and treatment modalities are available today, many deaths occur owing to its late-stage detection and metastatic nature. Noninvasive detection using luminescence-based imaging tools is considered one of the promising techniques owing to its low cost, high sensitivity, and brightness. Moreover, these tools are unique and valuable as they can detect even the slightest changes in the cellular microenvironment. To achieve this, a fluorescent probe with strong tumor uptake and high spatial and temporal resolution, especially with high water solubility, is highly demanded. Recently, several water-soluble molecules with emission windows in the visible (400-700 nm), first near-infrared (NIR-I, 700-1000 nm), and second near-infrared (NIR-II, 1000-1700 nm) windows have been reported in literature. This review highlights recently reported water-soluble small organic fluorophores/dyes with applications in cancer diagnosis and therapeutics. We systematically highlight and describe the key concepts, structural classes of fluorophores, strategies for imparting water solubility, and applications in cancer therapy and diagnosis, i.e., theragnostics. We discuss examples of water-soluble fluorescent probes based on coumarin, xanthene, boron-dipyrromethene (BODIPY), and cyanine cores. Some other emerging classes of dyes based on carbocyclic and heterocyclic cores are also discussed. Besides, emerging molecular engineering methods to obtain such fluorophores are discussed. Finally, the opportunities and challenges in this research area are also delineated.

Detection of oral mucosal lesions by the fluorescence spectroscopy and classification of cancerous stages by support vector machine

Detection of oral mucosal lesions has been performed by an in-house developed fluorescence-based portable device in the present study. A laser diode of 405 nm wavelength and a UV-visible spectrometer are utilized in the portable device as excitation and detection sources. At the 405 nm excitation wavelength, the flavin adenine dinucleotide (FAD) band at 500 nm and three porphyrin bands at 634, 676, and 703 nm are observed in the fluorescence spectrum of the oral cavity tissue. We have conducted this clinical study on a total of 189 tissue sites of 36 oral squamous cell carcinoma (OSCC) patients, 18 dysplastic (precancerous) patients, and 34 volunteers. Analysis of the fluorescence data has been performed by using the principal component analysis (PCA) method and support vector machine (SVM) classifier. PCA is applied first in the spectral data to reduce the dimension, and then classification among the three groups has been executed by employing the SVM. The SVM classifier includes linear, radial basis function (RBF), polynomial, and sigmoid kernels, and their classification efficacies are computed. Linear and RBF kernels on the testing data sets differentiated OSCC and dysplasia to normal with an accuracy of 100% and OSCC to dysplasia with an accuracy of 95% and 97%, respectively. Polynomial and sigmoid kernels showed less accuracy values among the groups ranging from 48 to 88% and 51 to 100%, respectively. The result indicates that fluorescence spectroscopy and the SVM classifier can help to identify early oral mucosal lesions with significant high accuracy.

Utilization and transformation of Chrysotila dentata-derived dissolved organic matter by phycosphere bacteria Marinobacter hydrocarbonoclasticus and Bacillus firmus

The dissolved organic matter (DOM) released from the cocoolithophores (Chrysotila dentata) was studied in laboratory experiments after co-culturing C. dentata with bacteria. Marinobacter hydrocarbonoclasticus (CA6)-γ-Proteobacteria and Bacillus firmus (CF2) were used to investigate the utilization and processing of the DOM derived from C. dentata, utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC), while measuring algal abundance and photosynthetic parameters. The experimental groups consisted of axenic C. dentata groups, filter cultured with bacteria (CA6 or CF2) groups, C. dentata co-cultured with bacteria (CA6 or CF2) groups and axenic bacteria (CA6 or CF2) groups. We then evaluated the processing of DOM by determining four fluorescence indices. The number of C. dentata cells and the photosynthetic capacity of microalgae were enhanced by CA6 and CF2. The main known fluorophores, including humic-like components and protein-like components, were present in all sample. The protein-like component of algal-bacterial co-cultures was effectively utilized by CA6 and CF2. The humic-like components increased at the end of the culture time for all cultures. Meanwhile, the average fluorescence intensity of protein-like in CA6 co-culture with algae was lower than that in CF2 co-culture with algae over time. On the other hand, the average fluorescence intensity of humic-like in CA6 was higher than CF2. However, the total change in fluorescence in humic-like and protein-like of axenic CF2 cultures was lower than that of CA6. Hence, the ability of CA6 to transform microalgal-derived DOM was superior to that of CF2, and CF2's ability to consume bacterial-derived DOM was superior to that of CA6.

Single-Molecule FRET-Based Multiplexed Detection

Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.

Real-time Imaging of Nascent DNA in Live Cells by Monitoring the Fluorescence Lifetime of DNA-Incorporated Thiazole Orange-Modified Nucleotides

A modified 2'-deoxycytidine triphosphate derivative (dCTO TP) bearing a thiazole orange moiety tethered via an oligoethylene glycol linker was designed and synthesized. The nucleotide was incorporated into DNA by DNA polymerases in vitro as well as in live cells. Upon incorporation of dCTO TP into DNA, the thiazole orange moiety exhibited a fluorescence lifetime that differed significantly from the non-incorporated (i.e. free and non-covalently intercalated) forms of dCTO TP. When dCTO TP was delivered into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it allowed us to distinguish and monitor cells that were actively synthesizing DNA in real time, from the very first moments after the treatment. We anticipate that this probe could be used to study chromatin organization and dynamics.

Orderly Self-Assembly of Organic Fluorophores for Sensing and Imaging

Fluorescence imaging utilizing traditional organic fluorophores is extensively applied in both cellular and in vivo studies. However, it faces significant obstacles, such as low signal-to-background ratio (SBR) and spurious positive/negative signals, primarily due to the facile diffusion of these fluorophores. To cope with this challenge, orderly self-assembled functionalized organic fluorophores have gained significant attention in the past decades. These fluorophores can create nanoaggregates via a well-ordered self-assembly process, thus prolonging their residency time within cells and in vivo settings. The development of self-assembled-based fluorophores is an emerging field, and as such, in this review, we present a summary of the progress and challenges of self-assembly fluorophores, focusing on their development history, self-assembly mechanisms, and biomedical applications. We hope that the insights provided herein will assist scientists in further developing functionalized organic fluorophores for in situ imaging, sensing, and therapy.

Optical properties and molecular composition of wintertime atmospheric water-soluble organic carbon in different coastal cities of eastern China

To evaluate the optical properties and molecular composition of water-soluble organic carbon (WSOC) in the atmosphere of coastal cities, particle samples were collected in Tianjin, Qingdao and Shanghai, three coastal cities in eastern China. Subsequent analysis by ultraviolet visible and fluorescence spectrometer and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry were performed. The results showed that the concentration levels and light absorption of WSOC decreased from the north to south cities, ranking as Tianjin > Qingdao > Shanghai. Three major fluorescent components including less‑oxygenated humic-like substances (52-60 %), highly‑oxygenated humic-like substances (15-31 %) and protein-like substances (17-31 %) were identified in WSOC based on the fluorescence spectroscopy and parallel factor analysis, which might be closely related to anthropogenic emissions and continental sources as well as secondary formation processes. Five subgroups of molecular components were further identified in WSOC, including the predominant CHON compounds (35-43 %), sulfur-containing compounds (i.e., CHONS and CHOS compounds; 24-43 %), CHO compounds (20-26 %) and halogen-containing compounds (1-7 %). Compared to marine air masses influenced samples, WSOC affected by continental air masses exhibited higher light absorption coefficients and generally had a higher degree of aromaticity and unsaturation, as well as contained more molecular formulas of WSOC, especially enriched with sulfur-containing compounds. In contrast, relatively more abundant halogen-containing compounds were identified in the marine air masses influenced samples. Overall, this study provided new insights into the light-absorbing and chemical properties of WSOC in coastal cities, especially under the influences of continental and marine air masses.

Diaminobenzidine Photooxidation to Visualize Fluorescent Nanoparticles in Adhering Cultured Cells at Transmission Electron Microscopy

Visualizing nanoparticles made of organic material (e.g., polysaccharides, proteins, non-osmiophilic lipids) inside cells and tissues at transmission electron microscopy is a difficult task due to the intrinsic weak electron density of these nanoconstructs, which makes them hardly distinguishable in the biological environment. We describe here a simple protocol to apply photooxidation to fluorescently labeled nanoparticles administered to cultured cells in vitro. The conversion of the fluorescent signal into a granular electron-dense reaction product through light irradiation in the presence of diaminobenzidine makes the nanoparticles clearly visible at the ultrastructural level. Our procedure proved to be reliable with various fluorophores and may be applied to any cell type.

Leveraging Baird aromaticity for advancement of bioimaging applications

In this perspective, we highlight the recent progress in utilizing Baird aromatic species to improve fluorophore performance in microscopy and imaging applications. We specifically focus on the origins of the use of Baird aromaticity in fluorescence applications, the development of “self‐healing” fluorophores leveraging cyclooctatetraene’ Baird aromaticity, and where developments need to occur to optimize this technology.

Fluorescence fingerprinting characteristics of water-soluble organic carbon from size-resolved particles during pollution event

A typical haze pollution process in northern China has necessitated this study which focuses on the fluorescence characteristics of water-soluble organic carbon (WSOC) in size-resolved particles. High concentrations of WSOC were found in both fine (38 μg/m³) and coarse particles (36 μg/m³) during the pollution period, which may be related to the secondary formation of organic aerosols and stable meteorological conditions. Five fluorescent components in WSOC were extracted by parallel factor analysis. Our results showed that the fluorophores in fine and coarse particles were mainly humic-like substances (humic-like, terrestrial humic-like, and high oxidation humic-like substances) and protein-like substances (protein-like and tyrosine-like substances), respectively. Moreover, the aging degree analysis, pollution source tracing, and concentration prediction of WSOC were carried out by fluorescence index. An innovative technique called self-organizing map was proposed for an in-depth investigation of the contamination mechanism of the atmospheric organic aerosol. Furthermore, the difference in the fluorescence characteristics of WSOC in fine particles was higher than that in coarse particles. The atmospheric pollution process increased the degree of difference in fluorescence characteristics. Additionally, an effective method for predicting the size of atmospheric particles was established by combining excitation-emission matrix fluorescence spectroscopy with classification and regression tree analysis.

Triazole-derivatized near-infrared cyanine dyes enable local functional fluorescent imaging of ocular inflammation

Near-infrared (NIR) chemical fluorophores are promising tools for in-vivo imaging in real time but often succumb to rapid photodegradation. Indocyanine green (ICG) is the only NIR dye with regulatory approval for ocular imaging in humans; however, ICG, when employed for applications such as labelling immune cells, has limited sensitivity and does not allow precise detection of specific inflammatory events, for example leukocyte recruitment during uveitic flare-ups. We investigated the potential use of photostable novel triazole NIR cyanine (TNC) dyes for detecting and characterising activated T-cell activity within the eye. Three TNC dyes were evaluated for ocular cytotoxicity in-vitro using a MTT assay and optimised concentrations for intraocular detection within ex-vivo porcine eyes after topical application or intracameral injections of the dyes. TNC labelled T-cell tracking experiments and mechanistic studies were also performed in-vitro. TNC-1 and TNC-2 dyes exhibited greater fluorescence intensity than ICG at 10 μM, whereas TNC-3 was only detectable at 100 μM within the porcine eye. TNC dyes did not demonstrate any ocular cell toxicity at working concentrations of 10 μM. CD4⁺T-cells labelled with TNC-1 or TNC-2 were detected within the porcine eye, with TNC-1 being brighter than TNC-2. Detection of TNC-1 and TNC-2 into CD4⁺T-cells was prevented by prior incubation with dynole 34-2 (50 μM), suggesting active uptake of these dyes via dynamin-dependent processes. The present study provides evidence that TNC dyes are suitable to detect activated CD4⁺T-cells within the eye with potential as a diagnostic marker for ocular inflammatory diseases.

Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling

Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.

Pyridine-2-yl Quinoxaline (2-CPQ) Derivative As a Novel Pink Fluorophore: Synthesis, and Chemiluminescence Characteristics

Quinoxaline derivatives are well-known N-heterocycles with pharmacological and fluorescence activities. Almost all quinoxaline derivatives with extensive π-conjugation have been introduced as fluorophores which emit blue and green light. For the first time, we designed and synthesized 6-chloro-2,3 di(Pyridine-2yl) quinoxaline (2-CPQ) as a pink fluorophore in acetonitrile medium by simple route at room temperature whitin 30 min. The synthesized quinoxaline was identified using ¹H, ¹³C NMR, MS, and FT-IR spectroscopy. Our results showed that the iodine-catalyzed method for both oxidation and cyclization during the synthesis of quinoxaline from pyridine 2-carbaldehyde was straightforward, efficient, and clean. All of the mentioned characterization devices confirmed the synthesis of 2-CPQ.Moreover, we studied the photophysical properties of the synthesized fluorophore in which The UV-Vis absorption spectrum of 2-CPQ in DMF were three peaks at 451, 518 and 556 nm. Based on photophysical properties investigation, 2-CPQ shows good fluorescence with maximum peaks 607 and 653 nm in DMF as solvent (ф_F = 0.21). Hence, the fluorophore was applied in the peroxyoxalate chemiluminescence system. The reaction of imidazole, H₂O_2, and bis (2,4,6-trichlorophenyl) oxalate (TCPO) can transfer energy to a 6-chloro-2,3 di(pyridine-2yl) quinoxaline. In this process, dioxetane was synthesized, which chemically initiated the electron exchange luminescence (CIEEL) mechanism and led to pink light emission. We anticipate our synthesized fluorophores 2-CPQ will have great potential applications in imaging and medical markers.

Detection and Enumeration of Cytokine-Secreting Cells by FluoroSpot

The FluoroSpot assay is a development of the highly sensitive enzyme-linked immunospot (ELISpot) assay which enables functional measurement of immunity at the single-cell level. Both assays are performed in a 96-well format and measures the frequency of analyte-secreting cells, in ELISpot usually limited to one analyte per well due to the use of enzymes and precipitating substrates for detection. FluoroSpot, performed in a similar way as ELISpot, overcomes this limitation by detecting each analyte with an assigned fluorophore instead of an enzyme. By using readers equipped with fluorophore-specific filters, cells producing single or multiple cytokines can be identified simultaneously in the same well. This greatly facilitates the analysis of functionally distinct subpopulations in heterogenous cell samples, for example, the frequency of polyfunctional T cells, suggested to be of importance in various disease states. FluoroSpot maintains the simplicity and sensitivity of the ELISpot while taking the assay a step further towards a multiplex analysis and an in-depth understanding of the quality of an immune response. We describe here a 96-well plate method to analyze cells that have secreted up to four different cytokines simultaneously (Four-color Fluorospot).

Trends in small organic fluorescent scaffolds for detection of oxidoreductase

Oxidoreductases are diverse class of enzymes engaged in modulating the redox homeostasis and cellular signaling cascades. Abnormal expression of oxidoreductases including thioredoxin reductase, azoreductase, cytochrome oxidoreductase, tyrosinase and monoamine oxidase leads to the initiation of numerous disorders. Thus, enzymes are the promising biomarkers of the diseased cells and their accurate detection has utmost significance for clinical diagnosis. The detection method must be extremely selective, sensitive easy to use, long self-life, mass manufacturable and disposable. Fluorescence assay approach has been developed potential substitute to conventional techniques used in enzyme's quantification. The fluorescent probes possess excellent stability, high spatiotemporal ratio and reproducibility represent applications in real sample analysis. Therefore, the enzymatic transformations have been monitored by small activatable organic fluorescent probes. These probes are generally integrated with enzyme's substrate/inhibitors to improve their binding affinity toward the enzyme's catalytic site. As the recognition unit bio catalyzed, the signaling unit produces the readout signals and provides novel insights to understand the biochemical reactions for diagnosis and development of point of care devices. Several structural modifications are required in fluorogenic scaffolds to tune the selectivity for a particular enzyme. Hence, the fluorescent probes with their structural features and enzymatic reaction mechanism of oxidoreductase are the key points discussed in this review. The basic strategies to detect each enzyme are discussed. The selectivity, sensitivity and real-time applications are critically compared. The kinetic parameters and futuristic opportunities are present, which would be enormous benefits for chemists and biologists to understand the facts to design and develop unique fluorophore molecules for clinical applications.

Periphery Modification of Tetrathiafulvalenes: Recent Development and Applications

Tetrathiafulvalene (TTF) and its analogs are fascinating molecules in materials science based on their excellent electron-donating abilities. This personal account describes recent advances in the synthesis of TTF analogs for functional materials via the palladium-catalyzed modification of peripheries of TTF analogs. We first consider three types of molecules: fluorophore-TTF hybrid molecules, multi-redox systems, and an organic ligand for metal-organic frameworks. These molecules were successfully synthesized via Stille coupling or palladium-catalyzed direct C-H arylation and their structural, electrochemical, and optical properties were clarified. Subsequently, phosphorus-substituted TTF analogs were successfully synthesized for future applications of redox-active phosphine ligands for metal catalysts. The development of these molecules can significantly affect the advancement of chemical science.

Single molecule FRET methodology for investigating glutamate receptors

Single molecule Förster Resonance Energy Transfer (smFRET) allows us to measure variation in distances between donor and acceptor fluorophores attached to a protein, providing the conformational landscape of the protein with respect to this specific distance. smFRET can be performed on freely diffusing molecules or on tethered molecules. Here, we describe the tethered method used to study ionotropic glutamate receptors, which allows us to track the changes in FRET as a function of time, thus providing information on the conformations sampled and kinetics of conformational changes in the millisecond to second time scale. Strategies for attaching fluorophores to the proteins, methods for acquiring and analyzing the smFRET trajectories, and limitations are discussed.

Distinctive tunable photophysical properties of versatile environmentally-sensitive tribranched cyanopyridine fluorophores

In the present work, twenty-four environmentally-sensitive cyanopyridine fluorophores bearing pyrene and/ or fluorene with different para-substituted-phenyl moieties that have been previously designed and synthesized by us are studied in depth for their photophysical properties. Initially, the optical performances of the compounds were investigated by employing UV-visible and fluorescence spectroscopic tools in various aprotic and protic solvents. All the compounds exhibited absorption bands between 310 and 452 nm, and emission bands between 454 and 633 nm. High sensitivity emission spectra with solvents of different polarities were recorded and studied. The fluorescence quantum yield (ϕ_f) increased in solvents of low polarity and decreased on increasing the polarity of solvents. On the other hand, in case of strong electron donating (-NMe₂) and strong electron attracting (-CN) substitution, a pronounced increase in Stokes shifts (up to 252 nm, 14250 cm^-1) were recorded. Lippert-Mataga and Reichardts correlations, applied for estimating the variation in dipole moments (Δμ), suggested that the emissive state of designed fluorescence 3-cyanopyridine derivatives is of strong ICT character. The aprotic and protic solvents gave a linear plot for the Stokes shifts in a Lippert-Mataga plot, which appeared as two distinct domains in E_T(30) scales indicating the presence of hydrogen bondings. It was observed that for compounds 5b - 8b, with (-NMe₂) group on the skeleton of phenyl ring, the Lippert-Mataga and Reichardt-Dimroth's plots deviated from linearity signifying that 5b - 8b molecules were involved in specific interaction with protic solvents.

Not so innocent: Impact of fluorophore chemistry on the in vivo properties of bioconjugates

The combination of targeting ligands and fluorescent dyes is a powerful strategy to observe cell types and tissues of interest. Conjugates of peptides, proteins, and, in particular, monoclonal antibodies (mAbs) exhibit excellent tumor targeting in various contexts. This approach has been translated to a clinical setting to provide real-time molecular insights during the surgical resection of solid tumors. A critical element of this approach is the generation of highly fluorescent bioconjugates that maintain the properties of the parent targeting ligand. A number of studies have found that fluorophores can dramatically impact the pharmacokinetic and tumor-targeting properties of the bioconjugates they are meant to only innocently observe. In this review, we summarize several examples of these effects and highlight strategies that have been used to mitigate them. These include the application of site-specific labeling chemistries, modulating label density, and altering the structure of the fluorescent probe itself. In particular, we point out the significant potential of fluorophores with hydrophilic but net-neutral structures. Overall, this review highlights recent progress in refining the in vivo properties of fluorescent bioconjugates, and we hope, will inform future efforts in this area.

Principles of Protein Labeling Techniques

Protein labeling methods prior to separation and analysis have become indispensable approaches for proteomic profiling. Basically, three different types of tags are employed: stable isotopes, mass tags, and fluorophores. While proteins labeled with stable isotopes and mass tags are measured and differentiated by mass spectrometry, fluorescent labels are detected with fluorescence imagers. The major purposes for protein labeling are monitoring of biological processes, reliable quantification of compounds and specific detection of protein modifications and isoforms in multiplexed samples, enhancement of detection sensitivity, and simplification of detection workflows. Proteins can be labeled during cell growth by incorporation of amino acids containing different isotopes, or in biological fluids, cells or tissue samples by attaching specific groups to the ε-amino group of lysine, the N-terminus, or the cysteine residues. The principles and the modifications of the different labeling approaches on the protein level are described; benefits and shortcomings of the methods are discussed.

Flow Cytometry as an Important Tool in Proteomic Profiling

Flow cytometry enables the simultaneous detection of multiple surface and intracellular antigens for proteomic profiling of cells. This allows characterization and identification of specific cell subtypes within a heterogeneous population and is usually called immunophenotyping. Antigen-specific antibodies, conjugated to various fluorophores, are incubated with the sample to identify each marker. Fluorescent light of various wavelengths can be separated, detected, and converted into a digital signal in a flow cytometer. Here we describe an eight-color experiment to identify key peripheral blood cell types; however, this technique can be expanded to detect more than 30 parameters simultaneously.

Choosing Fluorescent Probes and Labeling Systems

Fluorescence microscopy is advantageous for investigating biological processes and mechanisms in living cells. One of the most important considerations when designing an experiment is the selection of an appropriate fluorescent probe. Equally important is deciding how the probe will be attached to the protein of interest. The advantages and disadvantages of different fluorescent probe types and their respective labeling methods are discussed to provide an overview on selecting appropriate fluorophores and labeling systems for fluorescence-based assays. Protocols are outlined when appropriate.

Use of Intraoperative Fluorophores

Fluorescence-guided surgery provides surgeons with improved visualization of tumor tissue in the operating room to allow for maximal safe resection of brain tumors. Multiple fluorescent agents have been studied for fluorescence-guided surgery. Both nontargeted and targeted fluorescent agents are currently being used for glioblastoma multiforme visualization and resection. Fluorescence detection in the visible light or near infrared spectrum is possible. Visualization device advancements have permitted greater detection of fluorescence down to the cellular level, which may provide even greater ability for the neurosurgeon to resect tumors.

Characterizing the Two-photon Absorption Properties of Fluorescent Molecules in the 680-1300 nm Spectral Range

Two-photon laser scanning microscopy (2PLSM) is a state-of-the-art technique used for non-invasive imaging deep inside the tissue, with high 3D resolution, minimal out-of-focus photodamage, and minimal autofluorescence background. For optimal application of fluorescent probes in 2PLSM, their two-photon absorption (2PA) spectra, expressed in absolute cross sections must be characterized. Excitation at optimum wavelength will make it possible to reduce the laser power and therefore minimize photodamage. Obtaining 2PA spectra and cross sections requires correcting the two-photon excited fluorescence signals for a combination of laser properties, including the beam spatial profile, pulse duration, and absolute power, at each wavelength of the tuning range. To avoid such tedious day-to-day laser characterization required in the absolute measurement method, a relative method based on independently characterized 2PA reference standards is often used. By carefully analyzing the available literature data, we selected the most reliable standards for both the 2PA spectral shape and cross section measurements. Here we describe a protocol for measuring the 2PA spectral shapes and cross sections of fluorescent proteins and other fluorophores with the relative fluorescence method using these reference standards. Our protocol first describes how to build an optical system and then how to perform the measurements. In our protocol, we use Coumarin 540A in dimethyl sulfoxide and LDS 798 in chloroform for the spectral shape measurements to cover the range from 680 to 1300 nm, and Rhodamine 590 in methanol and Fluorescein in alkaline water (pH 11) for the absolute two-photon cross section measurements.

Staining MIF in Cells for Confocal Microscopy

Confocal microscopy is a powerful technique for immunofluorescence imaging of cells and tissues. The technique allows for detailed analysis of intracellular localization of molecules, as well as three-dimensional representation and analysis of samples, and can be used as a gateway to more advanced techniques, including FLIM-FRET and super-resolution microscopy. Relatively few studies have used confocal microscopy to study intracellular localization of macrophage migration inhibitory factor (MIF) in detail. This chapter outlines basic protocols and tips for staining MIF in fixed cells for confocal analysis.

Applications of near infrared and surface enhanced Raman scattering techniques in tumor imaging: A short review

Imaging technologies play a vital role in clinical oncology and have undergone massive growth over the past few decades. Research in the field of tumor imaging and biomedical diagnostics requires early detection of physiological alterations so as to provide curative treatment in real time. The objective of this review is to provide an insight about near infrared fluorescence (NIRF) and surface enhanced Raman scattering (SERS) imaging techniques that can be used to expand their capabilities for the early detection and diagnosis of cancer cells. Basic setup, principle and working of the instruments has been provided and common NIRF imaging agents as well as SERS tags are also discussed besides the analytical advantages/disadvantages of these techniques. This review can help researchers working in the field of molecular imaging to design cost effective fluorophores and SERS tags to overcome the limitations of both NIRF as well as SERS imaging technologies.

Which are the main fluorophores in skin and oral mucosa? A review with emphasis on clinical applications of tissue autofluorescence

OBJECTIVES

The present review provides information about which molecules appear to be the main fluorophores in skin and oral mucosa, together with their clinical applications.

DESIGN

The MEDLINE database was searched, using "oral mucosa AND fluorophores", "skin AND fluorophores", "epidermal AND fluorophores", "dermal AND fluorophores" and "cutaneous AND fluorophores" as entry terms. We searched the literature following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The level of evidence in the studies was assessed using the Classification of the Oxford Centre for Evidence-based Medicine (CEBM) Levels for Diagnosis.

RESULTS

Five papers and 17 were primarily focused on description of fluorophores in oral mucosa and skin Evidence exists that fluorophores of oral mucosa and skin are mainly proteins such as collagen, elastin, keratin and tryptophan. Other possible fluorophores identified are: porphyrins, advanced glycation end products, flavins, lipopigment, nicotinamide adenine dinucleotide, flavin adenine dinucleotide, pheomelanin, eumelanin and components of lipofuscin. Clinical applications of oral mucosal autofluorescence (AF) are related to management of malignant and potentially malignant lesions. In the skin, AF has been used for acne assessment, diagnosis of sweat-gland pathologies, glycemic control and management of malignant lesions and as a marker for skin aging.

CONCLUSION

Fluorophores stimulated through AF devices are implied in different physiologic and pathologic processes. AF seems to be useful for several clinical applications, especially in skin department. Because most of the studies show a low level of evidence, further studies are necessary in such a promising and fascinating field.

Beyond the whole-mount phenotype: high-resolution imaging in fluorescence-based applications on zebrafish

Zebrafish is now widely used in biomedical research as a model for human diseases, but the relevance of the model depends on a rigorous analysis of the phenotypes obtained. Many zebrafish disease models, experimental techniques and manipulations take advantage of fluorescent reporter molecules. However, phenotypic analysis often does not go beyond establishing overall distribution patterns of the fluorophore in whole-mount embryos or using vibratome or paraffin sections with poor preservation of tissue architecture and limited resolution. Obtaining high-resolution data of fluorescent signals at the cellular level from internal structures mostly depends on the availability of expensive imaging technology. Here, we propose a new and easily applicable protocol for embedding and sectioning of zebrafish embryos using in-house prepared glycol methacrylate (GMA) plastic that is suited for preservation of fluorescent signals (including photoactivatable fluorophores) without the need for antibodies. Four main approaches are described, all involving imaging fluorescent signals on semithin (3 µm or less) sections. These include sectioning transgenic animals, whole-mount immunostained embryos, cell tracking, as well as on-section enzyme histochemistry.

Optimizing Parallel Factor (PARAFAC) Assisted Excitation-Emission Matrix Fluorescence (EEMF) Spectroscopic Analysis of Multifluorophoric Mixtures

Parallel factor (PARAFAC) analysis is the most commonly used mathematical technique to analyse the excitation-emission matrix fluorescence (EEMF) data sets of mutifluorophoric mixtures. PARAFAC essentially performs the mathematical chromatography on the EEMF data sets and helps in extracting pure excitation, pure emission and contribution profiles of each of the fluorophores without requiring any pre-separation step. The application of PARAFAC requires the initialisation of the spectral variables that is usually achieved by performing the singular value decomposition (SVD) analysis on EEMF data sets. One of the problem with SVD based initialisation is that it orthogonalises the data sets and makes the PARAFAC modelling of the EEMF data sets computationally challenging task that needs to be taken care. To address this issue, the present introduces an alternate approach for initialising the spectral variables for performing the PARAFAC analysis. The proposed approach essentially involve initialisation of the spectral variables with random numbers in a constraint manner. The proposed approach is found to provide the desired computational economy, robustness and analytical effectiveness to the PARAFAC analysis of EEMF data sets.

In Vivo Visualization of Microglia Using Tomato Lectin

Plant lectins bind to carbohydrates, which are found on the surface of different immune and endothelial cells including microglia. Using commercially available conjugates of lectins with different fluorophores allows one-step detection and visualization of microglia in vivo. Here, we describe a protocol enabling the use of a specific plant lectin isolated from Lycopersicon esculentum. Tomato lectin enables high-quality labeling of microglial cells in vivo and is applicable in any mouse strain at any age of the experimental animal without the need of genetic labeling, which is associated with time- and resource-consuming procedures.

Discrete Wavelet Transform (DWT) Assisted Partial Least Square (PLS) Analysis of Excitation-Emission Matrix Fluorescence (EEMF) Spectroscopic Data Sets: Improving the Quantification Accuracy of EEMF Technique

In the present work, it is shown that quantitative estimation efficiency of the partial least square (PLS) calibration model can be significantly improved by pre-processing the EEMF with discrete wavelet transform (DWT) analysis. The application of DWT essentially reduces the volume of data sets retaining all the analytically relevant information that subsequently helps in establishing a better correlation between the spectral and concentration data matrices. The utility of the proposed approach is successfully validated by analyzing the dilute aqueous mixtures of four fluorophores having significant spectral overlap with each other. The analytical procedure developed in the present study could be useful for analyzing the environmental, agricultural, and biological samples containing the fluorescent molecules at low concentration levels.

Immunohistochemistry of the Carotid Body

Immunohistochemistry (IHC) enables the detection and distribution of proteins in cells of tissues. IHC has become an indispensable approach for studying oxygen sensing by the carotid body (CB). This chapter provides a detailed description of IHC of CB tissue and isolated CB cells.

Immunofluorescence Technique to Detect Subcellular Structures Critical to Oocyte Maturation

Immunofluorescence is a useful technique for analysis of protein expression and localization, thereby providing information regarding protein function, regulation, and protein-protein interactions. It is a standard approach to determine the temporal and spatial location of gene products that function in oocyte meiotic maturation. Fixation is one of the critical steps in the immunofluorescence protocol. Here, we describe the use of antibodies that are widely utilized in oocytes studies: anti-centromeric antigen (ACA), anti-Aurora kinase A (AURKA) and anti-alpha and gamma-tubulin antibodies that require different technical approaches for successful visualization, and we provide protocols for these conditions that are amenable to mouse oocyte studies. Detection of these proteins provides phenotypic information about spindle morphology, chromosome alignment, and microtubule attachments to kinetochores critical to assessing oocyte quality.

Purification and Application of a Small Actin Probe for Single-Molecule Localization Microscopy

The cytoskeleton is involved in many cellular processes. Over the last decade, super-resolution microscopy has become widely available to image cytoskeletal structures, such as microtubules and actin, with great detail. For example, Single-Molecule Localization Microscopy (SMLM) achieves resolutions of 5-50 nm through repetitive sparse labeling of samples, followed by Point-Spread-Function analysis of individual fluorophores. Whereas initially this approach depended on the controlled photoswitching of fluorophores targeted to the structure of interest, alternative techniques now depend on the transient binding of fluorescently labeled probes, such as the small polypeptide lifeAct that can transiently interact with polymerized actin. These techniques allow for simple multicolor imaging and are no longer limited by a fluorophore's blinking properties. Here we describe a detailed step-by-step protocol to purify, label, and utilize the lifeAct fragment for SMLM. This purification and labeling strategy can potentially be extended to a variety of protein fragments compatible with SMLM.

Fluorescence (Multiwave) Confocal Microscopy

In addition to reflectance confocal microscopy, multiwave confocal microscopes with different laser wavelengths in combination with exogenous fluorophores allow fluorescence mode confocal microscopy in vivo and ex vivo. Fluorescence mode confocal microscopy improves the contrast between the epithelium and the surrounding soft tissue and allows the depiction of certain structures, like epithelial tumors, nerves, and glands.

Experimental Investigations on Fluorescence Excitation and Depletion of Carbon Dots

Carbon dots (CDs) can be readily synthesized and utilized as attractive fluorescent probes for a variety of applications. In this study, we have synthesized CDs using a previously published method and characterized their photo-physical properties. The resultant CDs possess prominent photo-stability and short emission wavelength in the violet region. Our study reveals that CDs, with weak photo-bleaching, enable them to be employed to achieve high spatial resolution in stimulated emission depletion (STED) microscopy. The depletion efficiency can reach 60%. More importantly, the shorter excitation wavelength of CDs contributes to further improvement of resolution for STED microscopy. An excellent candidate for fluorophores, these CDs have potential to be used in super-resolution imaging for STED microscopy.

Photostable and photoswitching fluorescent dyes for super-resolution imaging

Super-resolution fluorescence microscopy is a recently developed imaging tool for biological researches. Several methods have been developed for detection of fluorescence signals from molecules in a subdiffraction-limited area, breaking the diffraction limit of the conventional optical microscopies and allowing visualization of detailed macromolecular structures in cells. As objectives are exposed to intense laser in the optical systems, fluorophores for super-resolution microscopy must be tolerated even under severe light irradiation conditions. The fluorophores must also be photoactivatable and photoswitchable for single-molecule localization-based super-resolution microscopy, because the number of active fluorophores must be controlled by light irradiation. This has led to growing interest in these properties in the development of fluorophores. In this mini-review, we focus on the development of photostable and photoswitching fluorescent dyes for super-resolution microscopy. We introduce recent efforts, including improvement of fluorophore photostability and control of photoswitching behaviors of fluorophores based on photochemical and photophysical processes. Understanding and manipulation of chemical reactions in excited fluorophores can develop highly photostable and efficiently photoswitchable fluorophores that are suitable for super-resolution imaging applications.

STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells

Long time-lapse super-resolution imaging in live cells requires a labeling strategy that combines a bright, photostable fluorophore with a high-density localization probe. Lipids are ideal high-density localization probes, as they are >100 times more abundant than most membrane-bound proteins and simultaneously demark the boundaries of cellular organelles. Here, we describe Cer-SiR, a two-component, high-density lipid probe that is exceptionally photostable. Cer-SiR is generated in cells via a bioorthogonal reaction of two components: a ceramide lipid tagged with trans-cyclooctene (Cer-TCO) and a reactive, photostable Si-rhodamine dye (SiR-Tz). These components assemble within the Golgi apparatus of live cells to form Cer-SiR. Cer-SiR is benign to cellular function, localizes within the Golgi at a high density, and is sufficiently photostable to enable visualization of Golgi structure and dynamics by 3D confocal or long time-lapse STED microscopy.

Immunohisto- and Cytochemistry Analysis of Connexins

Immunohistochemistry (IHC) is a ubiquitous used technique to identify and analyze protein expression in the context of tissue and cell morphology. In the connexin research field, IHC is applied to identify the subcellular location of connexin proteins, as this can be directly linked to their functionality. The present chapter describes a protocol for fluorescent IHC to detect connexin proteins in tissues slices and cells, with slight modifications depending on the nature of biological sample, histological processing, and/or protein expression level. Basically, fluorescent IHC is a short, simple, and cost-effective technique, which allows the visualization of proteins based on fluorescent-labeled antibody-antigen recognition.

Cubosome formulations stabilized by a dansyl-conjugated block copolymer for possible nanomedicine applications

We present here an innovative, fluorescent, monoolein-based cubosome dispersion. Rather than embedded within the monoolein palisade, the fluorescent imaging agent, namely dansyl, was conjugated to the terminal ethylene oxide moieties of the block copolymer Pluronic F108. We discuss the physicochemical and photophysical properties of this fluorescent Pluronic and of a cubosome formulation stabilized by a mixture of dansyl-conjugated and non-conjugated Pluronic, also including an anticancer drug (quercetin). Furthermore, we performed biocompatibility tests against HeLa cells to assess internalization and cytotoxicity features of this nanoparticles aqueous dispersion. Cryo-TEM, SAXS, and DLS analysis, proved the bicontinuous cubic inner nanostructure and the morphology of this fluorescent cubosome dispersion, while photophysical measurements and biocompatibility results basically validate their potential use for theranostic nanomedicine applications.

Labeling of a protein with fluorophores using maleimide derivitization

Maleimide derivitization of a protein is an essential tool for putting probes such as fluorescent labels at different sites within a polypeptide chain. This allows one to better understand protein-protein or protein-nucleic acid interactions using various biophysical approaches such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).

Labeling a protein with fluorophores using NHS ester derivitization

N-hydroxysuccinimde (NHS) ester-mediated derivitization involves the reaction of this amine-reactive group with the primary amines of a protein or a biomolecule. Using NHS chemistry allows one to conjugate various fluorescent probes, biotin, and cross-linkers to primary amines. For example, we use NHS ester chemistry to fluorescently label the amino terminus of a protein with the dye, 5-(and-6)-carboxyfluorescein, succinimidyl ester (5(6)-FAM, SE).

A multispectral LED array for the reduction of background autofluorescence in brain tissue

The presence of fixative-induced and cellular-derived artifactual autofluorescences (AAFs) presents a challenge in histological analysis involving immunofluorescence. We have established a simple and highly effective method for the reduction of AAFs that are ubiquitous in fixed mammalian brain and other tissues. A compact AAF-quenching photo-irradiation device was constructed using a commercially available light emitting diode (LED) array, cooling unit, and supporting components. The LED panel is comprised of an array of multispectral high intensity LEDs which serve as the illumination source for the photo-irradiation process. Rabbit and cat brain specimens of 5 μm- and 40 μm-thicknesses, respectively, were photo-irradiated for various durations. The AAFs were reduced to near tissue background levels after 24h of treatment for both deparaffinized and paraffinized rabbit brain specimens, and for the free-floating cat brain specimens. Subsequent immunofluorescence staining using primary antibodies against GFAP, NeuN, Iba-1, and MAP-2, and the corresponding Qdot(®) and Alexafluor(®) fluoroconjugates confirmed that the LED photo-irradiation treatment did not compromise the efficiency of the immunofluorescence labeling. The use of the device is not labor intensive, and only requires minimal tissue processing and experimental set-up time, with very low maintenance and operating costs. Finally, multiple specimens, in both slide and well-plate format, can be simultaneously photo-irradiated, thus, allowing for scalable batch processing.

Synthesis and Spectroscopic Studies of N,N'-dialkyl Derivatives of Antisymmetrical 2H,5H-Dihydropyrrolo[3,4-c]pyrrole-1,4-diones

2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione derivatives (DPP) are chemically stable, fluorescent molecules, known as High Performance Pigments. Preparation of the soluble derivatives of DPPs provides great advantage in designing the optic sensor for new and existing applications and overcoming aggregation problems in solid matrices. For this purpose, the synthesis of antisymmetric DPPs and the formation of new organic dyes through N,N'-dialkylation and their spectroscopic studies have been carried out both in solutions and in solid phase.

Fluorescent labeling and modification of proteins

This review provides an outline for fluorescent labeling of proteins. Fluorescent assays are very diverse providing the most sensitive and robust methods for observing biological processes. Here, different types of labels and methods of attachment are discussed in combination with their fluorescent properties. The advantages and disadvantages of these different methods are highlighted, allowing the careful selection for different applications, ranging from ensemble spectroscopy assays through to single-molecule measurements.