The fluorescent toolbox for assessing protein location and function

Lanthanide-Doped Near-Infrared Nanoparticles for Biophotonics

Light in the near-infrared (NIR) spectral region is increasingly utilized in bioapplications, providing deeper penetration in biological tissues owing to the lower absorption and scattering in comparison with light in the visible range. Lanthanide-doped luminescent nanoparticles with excitation and/or emission in the NIR range have recently attracted tremendous attention as one of the prime candidates for noninvasive biological applications due to their unique optical properties, such as large Stokes shift, spectrally sharp luminescence emissions, long luminescence lifetimes, and excellent photostability. Herein, recent advances of lanthanide-doped nanoparticles with NIR upconversion or downshifting luminescence and their uses in cutting-edge biophotonic applications are presented. A set of efficient strategies for overcoming the fundamental limit of low luminescence brightness of lanthanide-doped nanoparticles is introduced. An in-depth literature review of their state-of-art biophotonics applications is also included, showing their superiority for high-resolution imaging, single-nanoparticle-level detection, and efficacy for tissue-penetrating diagnostics and therapeutics.

BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms

Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.

A Simple Preparation Method for CLEM Using Pre-Embedding Immunohistochemistry with a Novel Fluorescent Probe and Stable Embedding Resin

Correlative light and electron microscopy (CLEM) is an excellent approach for examining the cellular localization of biomolecules. Here, we developed a simple method for CLEM by combining pre-embedding immunohistochemistry with a novel fluorescent probe, namely Fluolid NS Orange, and an embedding resin called 'Durcupan™'. Specimens were embedded in Durcupan™ or LR White after immunolabeling and post-fixation using glutaraldehyde and osmium tetroxide. Next, ultrathin sections were prepared on a finder grid with navigation markers. The section of the specimen embedded in Durcupan™ was found to be more stable against electron beam irradiation than specimens embedded in LR White. A fluorescence light microscopy (FLM) image and a transmission electron microscopy (TEM) image, at wide-field, and low magnification, were independently obtained with the same ultrathin section. Using the three corners between finder grid bars as landmarks, FLM images were superimposed with wide-field, low magnification TEM images to identify the region of interest (ROI), which was subsequently enlarged to ascertain cellular structures localized beneath fluorescent signals. However, the enlarged TEM images appeared blurred and fluorescence signals had a hazy appearance. To resolve this, the enlarged TEM images were replaced by high-resolution TEM images focused directly on the ROI, thereby facilitating the collection of high-resolution CLEM images. The simple sample processing method for CLEM using osmium-resistant Fluolid NS Orange and electron beam damage-resistant Durcupan™ allowed the determination of the precise localization of fluorescence signals at subcellular levels.

Non-invasive multimodal imaging of Diabetic Retinopathy: A survey on treatment methods and Nanotheranostics

Diabetes Retinopathy (DR) is one of the most prominent microvascular complications of diabetes. It is one of the pre-eminent causes for vision impairment followed by blindness among the working-age population worldwide. The de facto cause for DR remains challenging, despite several efforts made to unveil the mechanism underlying the pathology of DR. There is quite less availability of the low cost pre-emptive theranostic imaging tools in terms of in-depth resolution, due to the multiple factors involved in the etiology of DR. This review work comprehensively explores the various reports and research works on all perspectives of diabetic retinopathy (DR), and its mechanism. It also discusses various advanced non-destructive imaging modalities, current, and future treatment approaches. Further, the application of various nanoparticle-based drug delivery strategies used for the treatment of DR are also discussed. In a nutshell, the present review work bolsters the pursuit of the development of an advanced non-invasive optical imaging modal with a nano-theranostic approach for the future diagnosis and treatment of DR and its associated ocular complications.

TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells

A wealth of single-cell imaging studies have contributed novel insights into chromatin organization and gene regulation. However, a comprehensive understanding of spatiotemporal gene regulation requires developing tools to combine multiple monitoring systems in a single study. Here, we report a versatile tag, termed TriTag, which integrates the functional capabilities of CRISPR-Tag (DNA labeling), MS2 aptamer (RNA imaging) and fluorescent protein (protein tracking). Using this tag, we correlate changes in chromatin dynamics with the progression of endogenous gene expression, by recording both transcriptional bursting and protein production. This strategy allows precise measurements of gene expression at single-allele resolution across the cell cycle or in response to stress. TriTag enables capturing an integrated picture of gene expression, thus providing a powerful tool to study transcriptional heterogeneity and regulation.

Synthesis of fluorescent nanoprobe with simultaneous response to intracellular pH and Zn2+ for tumor cell distinguishment

A novel dual-functional nanoprobe was designed and synthesized by facile assembly of quinoline derivative (PEIQ) and meso-tetra (4-carboxyphenyl) porphine (TCPP) via electrostatic interaction for simultaneous sensing of fluorescence of Zn²⁺ and pH. Under the single-wavelength excitation at 400 nm, this nanoprobe not only exhibits "OFF-ON" green fluorescence at 512 nm by specific PEIQ-Zn²⁺ chelation, but also presents red fluorescence enhancement at 654 nm by H⁺-triggered TCPP release. The nanoprobe demonstrated excellent sensing performance with a good linear range (Zn²⁺, 1-40 μM; pH, 5.0-8.0), low detection limit (Zn²⁺, 0.88 μM), and simultaneous response towards Zn²⁺ and pH in pure aqueous solution within 2 min. More importantly, this dual-functional nanoprobe demonstrates the capability of discerning cancerous cells from normal cells, as evidenced by the fact that cancerous HepG2 cells in tumor microenvironment exhibit substantially higher red fluorescence and significantly lower green fluorescence than normal HL-7702 cells. The simultaneous, real-time fluorescence imaging of multiple analytes in a living system could be significant for cell analysis and tracking, cancer diagnosis, and even fluorescence-guided surgery of tumors.

The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis

For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.

Method for fast staining and obtaining high-magnification and high-resolution cell images of Nicotiana benthamiana

As tools of plant molecular biology, fluorescence microscopy and Nicotiana benthamiana have been used frequently to study the structure and function of plant cells. However, it is difficult to obtain ideal micrographs; for example, the images are typically unclear, the inner cell structure cannot be observed under a high-power lens by fluorescence microscopy, etc. Here, we describe a method for observing the cell structure of N. benthamiana. This method significantly improves imaging by fluorescence microscopy and allows clear images to be obtained under a high-power lens. This method is easy to perform with good stability, and the stomatal structure, nucleus, nucleolus, chloroplast and other organelles in N. benthamiana cells as well as protein localizations and the locations of protein-protein interactions have been observed clearly. Furthermore, compared with traditional methods, fluorescent dye more efficiently dyes cells with this method. The applicability of this method was verified by performing confocal scanning laser microscopy (CSLM), and CSLM imaging was greatly improved. Thus, our results provided a method to visualize the subcellular structures of live cells in the leaves of N. benthamiana by greatly improving imaging under a fluorescence microscope and provided new insights and references for the study of cell structures and functions in other plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00931-5.

Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine

Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.

Single-Nanoparticle Orientation Sensing by Deep Learning

This paper describes a computational imaging platform to determine the orientation of anisotropic optical probes under differential interference contrast (DIC) microscopy. We established a deep-learning model based on data sets of DIC images collected from metal nanoparticle optical probes at different orientations. This model predicted the in-plane angle of gold nanorods with an error below 20°, the inherent limit of the DIC method. Using low-symmetry gold nanostars as optical probes, we demonstrated the detection of in-plane particle orientation in the full 0-360° range. We also showed that orientation predictions of the same particle were consistent even with variations in the imaging background. Finally, the deep-learning model was extended to enable simultaneous prediction of in-plane and out-of-plane rotation angles for a multibranched nanostar by concurrent analysis of DIC images measured at multiple wavelengths.

Imaging the future: the emerging era of single-cell spatial proteomics

The proteome of a human cell is partitioned within organelles, such as the nucleus, and other subcellular compartments, such as the cytoplasm, forming a myriad of membrane-bound and membrane-free ultrastructures. This compartmentalization allows discrete biochemical processes to occur efficiently in isolation, with relevant proteins localized to appropriate niches to fulfill their biological function(s). Proper delivery and dynamic exchange of proteins between compartments underlie the regulation of many cellular processes, such as cell signaling, division, and programmed cell death. To this end, cells deploy dedicated trafficking mechanisms to ensure correct protein localization, as mis-localization can result in pathology. In addition to trafficking, variation in the expression, modification, and physical associations of proteins within and between cells can result in biological heterogeneity, motivating the need for single-cell measurements. In this review, we introduce diverse platform technologies developed for subcellular proteomics and high-throughput systems biology, with the aim of providing mechanistic insights into fundamental cell biological processes underlying healthy and diseased states, and valuable public data resources. In contrast to the rapidly advancing field of single-cell genomics, the single-cell spatial proteomics toolbox remains in its infancy, but is poised to make considerable advances in the coming years.

Fluorine-18-Labeled Fluorescent Dyes for Dual-Mode Molecular Imaging

Recent progress realized in the development of optical imaging (OPI) probes and devices has made this technique more and more affordable for imaging studies and fluorescence-guided surgery procedures. However, this imaging modality still suffers from a low depth of penetration, thus limiting its use to shallow tissues or endoscopy-based procedures. In contrast, positron emission tomography (PET) presents a high depth of penetration and the resulting signal is less attenuated, allowing for imaging in-depth tissues. Thus, association of these imaging techniques has the potential to push back the limits of each single modality. Recently, several research groups have been involved in the development of radiolabeled fluorophores with the aim of affording dual-mode PET/OPI probes used in preclinical imaging studies of diverse pathological conditions such as cancer, Alzheimer's disease, or cardiovascular diseases. Among all the available PET-active radionuclides, 18F stands out as the most widely used for clinical imaging thanks to its advantageous characteristics (t1/2 = 109.77 min; 97% β+ emitter). This review focuses on the recent efforts in the synthesis and radiofluorination of fluorescent scaffolds such as 4,4-difluoro-4-bora-diazaindacenes (BODIPYs), cyanines, and xanthene derivatives and their use in preclinical imaging studies using both PET and OPI technologies.

Plasmon-Enhanced Fluorescence of EGFP on Short-Range Ordered Ag Nanohole Arrays

Fluorescence of organic molecules can be enhanced by plasmonic nanostructures through coupling to their locally amplified electromagnetic field, resulting in higher brightness and better photostability of fluorophores, which is particularly important for bioimaging applications involving fluorescent proteins as genetically encoded biomarkers. Here, we show that a hybrid bionanosystem comprised of a monolayer of Enhanced Green Fluorescent Protein (EGFP) covalently linked to optically thin Ag films with short-range ordered nanohole arrays can exhibit up to 6-fold increased brightness. The largest enhancement factor is observed for nanohole arrays with a propagating surface plasmon mode, tuned to overlap with both excitation and emission of EGFP. The fluorescence lifetime measurements in combination with FDTD simulations provide in-depth insight into the origin of the fluorescence enhancement, showing that the effect is due to the local amplification of the optical field near the edges of the nanoholes. Our results pave the way to improving the photophysical properties of hybrid bionanosystems based on fluorescent proteins at the interface with easily fabricated and tunable plasmonic nanostructures.

Fluorescent proteins for in vivo imaging, where's the biliverdin?

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10-18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

Metal Ions Doping for Boosting Luminescence of Lanthanide-Doped Nanocrystals

With the developing need for luminous materials with better performance, lanthanide-doped nanocrystals have been widely studied for their unique luminescence properties such as their narrow bandwidth emission, excellent chemical stability, and photostability, adjustable emission color, high signal-to-background ratio, deeper tissue penetration with less photo-damage, and low toxicity, etc., which triggered enthusiasm for research on the broad applications of lanthanide-doped nanocrystals in bioimaging, anti-counterfeiting, biosensing, and cancer diagnosis and treatment. Considerable progress has been made in the past few decades, but low upconversion luminescence efficiency has been a hindrance in achieving further progress. It is necessary to summarize the recently relevant literature and find solutions to improve the efficiency. The latest experimental and theoretical studies related to the deliberate design of rare earth luminescent nanocrystals have, however, shown the development of metal ion-doped approaches to enhance the luminescent intensity. Host lattice manipulation can enhance the luminescence through increasing the asymmetry, which improves the probability of electric dipole transition; and the energy transfer modulation offers a reduced cross-relaxation pathway to improve the efficiency of the energy transfer. Based on the mechanisms of host lattice manipulation and energy transfer modulation, a wide range of enhancements at all wavelengths or even within a particular wavelength have been accomplished with an enhancement of up to a hundred times. In this mini review, we present the strategy of metal ion-doped lanthanide nanocrystals to cope with the issue of enhancing luminescence, overview the advantages and tricky challenges in boosting the luminescence, and provide a potential trend of future study in this field.

Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives

In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.

Lipid-oligonucleotide conjugates for bioapplications

Lipid-oligonucleotide conjugates (LONs) are powerful molecular-engineering materials for various applications ranging from biosensors to biomedicine. Their unique amphiphilic structures enable the self-assembly and the conveyance of information with high fidelity. In particular, LONs present remarkable potential in measuring cellular mechanical forces and monitoring cell behaviors. LONs are also essential sensing tools for intracellular imaging and have been employed in developing cell-surface-anchored DNA nanostructures for biomimetic-engineering studies. When incorporating therapeutic oligonucleotides or small-molecule drugs, LONs hold promise for targeted therapy. Moreover, LONs mediate the controllable assembly and fusion of vesicles based on DNA-strand displacements, contributing to nanoreactor construction and macromolecule delivery. In this review, we will summarize the general synthesis strategies of LONs, provide some characterization analysis and emphasize recent advances in bioanalytical and biomedical applications. We will also consider the relevant challenges and suggest future directions for building better functional LONs in nanotechnology and materials-science applications.

A Fluorescence Resonance Energy Transfer-Based Analytical Tool for Nitrate Quantification in Living Cells

Nitrate (NO₃ ^-) is a critical source of nitrogen (N) available to microorganisms and plants. Nitrate sensing activates signaling pathways in the plant system that impinges upon, developmental, molecular, metabolic, and physiological responses locally, and globally. To sustain, the high crop productivity and high nutritional value along with the sustainable environment, the study of rate-controlling steps of a metabolic network of N assimilation through fluxomics becomes an attractive strategy. To monitor the flux of nitrate, we developed a non-invasive genetically encoded fluorescence resonance energy transfer (FRET)-based tool named "FLIP-NT" that monitors the real-time uptake of nitrate in the living cells. The developed nanosensor is suitable for real-time monitoring of nitrate flux in living cells at subcellular compartments with high spatio-temporal resolution. The developed FLIP-NT nanosensor was not affected by the pH change and have specificity for nitrate with an affinity constant (K _d) of ∼5 μM. A series of affinity mutants have also been generated to expand the physiological detection range of the sensor protein with varying K _d values. It has been found that this sensor successfully detects the dynamics of nitrate fluctuations in bacteria and yeast, without the disruption of cellular organization. This FLIP-NT nanosensor could be a very important tool that will help us to advance the understanding of nitrate signaling.

Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales

Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates as a highly dynamic feedback control system. Recent experimental techniques have provided increasingly detailed data that revise and augment the relatively static, hierarchical view of genomic architecture with an understanding of how dynamic processes drive organization. Here, we review how novel technologies from sequencing, imaging, and synthetic biology refine our understanding of chromatin structure and function and enable chromatin engineering. Finally, we discuss opportunities to use these tools to enhance understanding of the dynamic interrelationship of chromatin structure and function.

Autonomous adaptive data acquisition for scanning hyperspectral imaging

Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.

Holman et al. develop a grid-less autonomous adaptive sampling method to explore high-dimensional spatiochemical experimental systems. Their method greatly decreases image acquisition time while improving spatial resolution, and when implemented with FTIR, it outperforms existing standard grid sampling approaches. They further show its utility for a complex biological sample, C. elegans.

Subcellular Singlet Oxygen and Cell Death: Location Matters

We developed a tool for targeted generation of singlet oxygen using light activation of a genetically encoded fluorogen-activating protein complexed with a unique dye molecule that becomes a potent photosensitizer upon interaction with the protein. By targeting the protein receptor to activate this dye in distinct subcellular locations at consistent per-cell concentrations, we investigated the impact of localized production of singlet oxygen on induction of cell death. We analyzed light dose-dependent cytotoxic response and characterized the apoptotic vs. necrotic cell death as a function of subcellular location, including the nucleus, the cytosol, the endoplasmic reticulum, the mitochondria, and the membrane. We find that different subcellular origins of singlet oxygen have different potencies in cytotoxic response and the pathways of cell death, and we observed that CT26 and HEK293 cell lines are differentially sensitive to mitochondrially localized singlet oxygen stresses. This work provides new insight into the function of type II reactive oxygen generating photosensitizing processes in inducing targeted cell death and raises interesting mechanistic questions about tolerance and survival mechanisms in studies of oxidative stress in clonal cell populations.

Luminescent Conductive Columnar π-Gelators for Fe(II) Sensing and Bio-Imaging Applications

The high demand and scarcity of luminescent, photoconductive, and transparent gels necessitate its finding as they are potential components in photonic devices such as solar cell concentrators where optical losses via scattering and reabsorption require to be minimized. In this direction, we have reported highly transparent, blue luminescent as well as photoconductive gels exhibiting the hole mobility of 10^-3 cm²/V s at ambient temperature as investigated by the time-of-flight technique. The π-driven self-standing supergels were formed using triazole-modified phenylene-vinylene derivatives as gelators in a nonpolar solvent. Different microscopic studies revealed its entangled network of interwoven fibrilar self-assembly and anisotropic order in the gel state. Supramolecular assembly of xerogels, studied by small- and wide-angle X-ray scattering (SAXS/WAXS) suggesting their local columnar hexagonal (Col_h) superstructure, is beneficial for conducting gels. Rheological measurements direct the stiffness and robustness of the organogels. In addition, the gelators were developed as a sensing platform for the ultrasensitive detection of Fe(II) ions at ppb level. ¹H nuclear magnetic resonance (NMR) titrimetric studies revealed that the interaction of the H-atom of triazole units with Fe(II) is responsible for quenching of blue fluorescence. Also, one of the gelators was successfully applied in bio-imaging using the pollen grains of the Hibiscus rosa-sinensis plant.

Fluorogenic Protein Probes with Red and Near-Infrared Emission for Genetically Targeted Imaging*

Fluorogenic probes are important tools to image proteins with high contrast and no wash protocols. In this work, we rationally designed and synthesized a small set of four protein fluorogens with red or near-infrared emission. The fluorophores were characterized in the presence of albumin as a model protein environment and exhibited good fluorogenicity and brightness (fluorescence quantum yield up to 36 %). Once conjugated to a haloalkane ligand, the probes reacted with the protein self-labeling tag HaloTag with a high fluorescence enhancement (up to 156-fold). The spectroscopic properties of the fluorogens and their reaction with HaloTag were investigated experimentally in vitro and with the help of molecular dynamics. The two most promising probes, one in the red and one in the near-infrared range, were finally applied to image the nucleus or actin in live-cell and in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.

Development of small molecule inhibitor-based fluorescent probes for highly specific super-resolution imaging

To ensure the ultimate high-quality imaging of super-resolution fluorescence microscopy with increasingly high resolution, it is significant to use small specific fluorescent probes. Compared with the common biological fluorescent labeling technology, because of small size, strong specificity, abundance and special binding sites, single-targeted small-molecule inhibitors (SMIs) can link with organic dyes to form small fluorescent probes for various biomolecules. Herein, to confirm the feasibility of the SMI-probes, epidermal growth factor (EGF) receptor (EGFR)-targeted tyrosine kinase inhibitor Gefitinib was selected for modification with the fluorescent dye to form Gefitinib-probe. Then, the labeling superiority of Gefitinib-probe was revealed by comparing the direct stochastic optical reconstruction microscopy (dSTORM) images of EGFR labeled with different probes. Additionally, a high co-localization of fluorescent points from Gefitinib-probe and EGF-probe labeling indicated a high specificity of Gefitinib-probe to EGFR. Finally, higher co-localization of EGFR and HER3 labeled with the probe pair containing Gefitinib-probe than with the antibody-probe pair suggested that Gefitinib-probe with a cytoplasmic binding site benefited dual-color imaging. These results indicate that the SMI-probes are able to serve as versatile labeling tools for high-quality super-resolution imaging.

Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm

Rapidly changing features in an intact biological sample are challenging to efficiently trap and image by conventional electron microscopy (EM). For example, the model organism C. elegans is widely used to study embryonic development and differentiation, yet the fast kinetics of cell division makes the targeting of specific developmental stages for ultrastructural study difficult. We set out to image the condensed metaphase chromosomes of an early embryo in the intact worm in 3-D. To achieve this, one must capture this transient structure, then locate and subsequently image the corresponding volume by EM in the appropriate context of the organism, all while minimizing a variety of artifacts. In this methodological advance, we report on the high-pressure freezing of spatially constrained whole C. elegans hermaphrodites in a combination of cryoprotectants to identify embryonic cells in metaphase by in situ cryo-fluorescence microscopy. The screened worms were then freeze substituted, resin embedded and further prepared such that the targeted cells were successfully located and imaged by focused ion beam scanning electron microscopy (FIB-SEM). We reconstructed the targeted metaphase structure and also correlated an intriguing punctate fluorescence signal to a H2B-enriched putative polar body autophagosome in an adjacent cell undergoing telophase. By enabling cryo-fluorescence microscopy of thick samples, our workflow can thus be used to trap and image transient structures in C. elegans or similar organisms in a near-native state, and then reconstruct their corresponding cellular architectures at high resolution and in 3-D by correlative volume EM.

Nanobody-Based Probes for Subcellular Protein Identification and Visualization

Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.

Measurement of 3-Dimensional cAMP Distributions in Living Cells using 4-Dimensional (x, y, z, and λ) Hyperspectral FRET Imaging and Analysis

Cyclic AMP is a second messenger that is involved in a wide range of cellular and physiological activities. Several studies suggest that cAMP signals are compartmentalized, and that compartmentalization contributes to signaling specificity within the cAMP signaling pathway. The development of Fӧrster resonance energy transfer (FRET) based biosensors has furthered the ability to measure and visualize cAMP signals in cells. However, these measurements are often confined to two spatial dimensions, which may result in misinterpretation of data. To date, there have been only very limited measurements of cAMP signals in three spatial dimensions (x, y, and z), due to the technical limitations in using FRET sensors that inherently exhibit low signal to noise ratio (SNR). In addition, traditional filter-based imaging approaches are often ineffective for accurate measurement of cAMP signals in localized subcellular regions due to a range of factors, including spectral crosstalk, limited signal strength, and autofluorescence. To overcome these limitations and allow FRET-based biosensors to be used with multiple fluorophores, we have developed hyperspectral FRET imaging and analysis approaches that provide spectral specificity for calculating FRET efficiencies and the ability to spectrally separate FRET signals from confounding autofluorescence and/or signals from additional fluorescent labels. Here, we present the methodology for implementing hyperspectral FRET imaging as well as the need to construct an appropriate spectral library that is neither undersampled nor oversampled to perform spectral unmixing. While we present this methodology for measurement of three-dimensional cAMP distributions in pulmonary microvascular endothelial cells (PMVECs), this methodology could be used to study spatial distributions of cAMP in a range of cell types.

AIE-Based Dynamic in Situ Nanoscale Visualization of Amyloid Fibrillation from Hen Egg White Lysozyme

Protein misfolding and denaturation, represented by amyloid fibrillation, are associated with many diseases. However, as a general chemical biological process, the dynamic structure information on amyloid fibrillation has not been demonstrated categorically. Herein, hen egg white lysozyme (HEWL) was used as the model protein of interest to realize in situ nanoscale imaging of protein fibrillation process using the fluorophores with aggregation-induced emission (AIE) activity. The AIE-active fluorophores exhibit the reversible capability of association and dissociation with β-sheet structure and thus dynamic binding-induced emission, which causes the spontaneous switching of fluorescence. The entire HEWL denaturation process induced by sodium dodecyl sulfate (SDS) at ambient conditions was demonstrated in detail by using two AIE-active fluorophores (TPE-NaSO₃ and PD-BZ-OH) through reversible electrostatic interaction and specific labeling between AIE probes and β-sheet structures of amyloid fibrils, respectively. The results indicate that PD-BZ-OH is more specific AIE probe for amyloid fibrils than TPE-NaSO₃. In comparison, the SEM and TEM results show the same denaturation process of protein fibrillation induced by SDS at different concentrations. The static super-resolution imaging of amyloid fibrils is performed with a resolution of 35 nm using PD-BZ-OH aqueous solution without additional auxiliary conditions. The dynamic evolution process of HEWL amyloid fibrillation is in situ visualized through super-resolution fluorescent microscopy with nanoscale resolution. Both static and dynamic super-resolution imaging of amyloid fibrillation provides detailed nanoscale structure information exceeding 50 nm resolution, which is of great significance in the exploration of amyloid fibrillation and related diseases.

Photophysics of Isolated Rose Bengal Anions

Dye molecules based on the xanthene moiety are widely used as fluorescent probes in bioimaging and technological applications due to their large absorption cross-section for visible light and high fluorescence quantum yield. These applications require a clear understanding of the dye's inherent photophysics and the effect of a condensed-phase environment. Here, the gas-phase photophysics of the rose bengal doubly deprotonated dianion [RB - 2H]^2-, deprotonated monoanion [RB - H]^-, and doubly deprotonated radical anion [RB - 2H]^•- is investigated using photodetachment, photoelectron, and dispersed fluorescence action spectroscopies, and tandem ion mobility spectrometry (IMS) coupled with laser excitation. For [RB - 2H]^2-, photodetachment action spectroscopy reveals a clear band in the visible (450-580 nm) with vibronic structure. Electron affinity and repulsive Coulomb barrier (RCB) properties of the dianion are characterized using frequency-resolved photoelectron spectroscopy, revealing a decreased RCB compared with that of fluorescein dianions due to electron delocalization over halogen atoms. Monoanions [RB - H]^- and [RB - 2H]^•- differ in nominal mass by 1 Da but are difficult to study individually using action spectroscopies that isolate target ions using low-resolution mass spectrometry. This work shows that the two monoanions are readily distinguished and probed using the IMS-photo-IMS and photo-IMS-photo-IMS strategies, providing distinct but overlapping photodissociation action spectra in the visible spectral range. Gas-phase fluorescence was not detected from photoexcited [RB - 2H]^2- due to rapid electron ejection. However, both [RB - H]^- and [RB - 2H]^•- show a weak fluorescence signal. The [RB - H]^- action spectra show a large Stokes shift of ∼1700 cm^-1, while the [RB - 2H]^•- action spectra show no appreciable Stokes shift. This difference is explained by considering geometries of the ground and fluorescing states.

Full Color Tunable Aggregation-Induced Emission Luminogen for Bioimaging Based on an Indolizine Molecular Framework

By taking advantage of a unique mechanism of aggregation-induced emission (AIE) phenomena, AIE luminogens (AIEgens) have been provided as a solution to overcome the limitations of conventional fluorophores bearing the feature of aggregation-caused quenching (ACQ) phenomena. Especially, AIEgens paved the way to develop fluorogenic probes ideal for fluorescent imaging in live cell conditions. Despite the high demand for discovery of new AIEgens, it is still challenging to find a versatile molecular platform to generate diverse AIEgens. Herein, we report a new colorful molecular framework, Kaleidolizine (KIz), as a molecular platform for AIEgen generation. The KIz system allows systematic tuning of the emission wavelength from 455 to 564 nm via perturbation of the electron density of substituents on the indolizine core. Increasing the water fraction of the KIz solution in the THF/water mixture induces the fluorescence intensity increase up to 120-fold. Crystal structure analysis, computational calculations, and solvatochromism studies suggest that a synergistic effect between the intramolecular charge transfer and restriction of intramolecular rotation acts as the AIE mechanism in the KIz system. Conjugation of the triphenylphosphonium moiety to KIz allows successful development of triphenylphosphonium (TPP)-KIz for real-time bioimaging of innate mitochondria in live cells, thereby revealing the potential of KIz as a versatile molecular platform to generate fluorogenic probes based on AIE phenomena. We do believe the KIz system could serve as a new, reliable, and generally applicable molecular platform to develop various AIEgens having desired photophysical properties along with an excellent signal-to-noise ratio and with experimental convenience especially for fluorogenic live cell imaging.

A rationally designed orthogonal synthetase for genetically encoded fluorescent amino acids

The incorporation of non-canonical amino acids into proteins has emerged as a promising strategy to manipulate and study protein structure-function relationships with superior precision in vitro and in vivo. To date, fluorescent non-canonical amino acids (f-ncAA) have been successfully incorporated in proteins expressed in bacterial systems, Xenopus oocytes, and HEK-293T cells. Here, we describe the rational generation of a novel orthogonal aminoacyl-tRNA synthetase based on the E. coli tyrosine synthetase that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells.

Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack

A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems.IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.

Nanomedicine and Early Cancer Diagnosis: Molecular Imaging using Fluorescence Nanoparticles

Incorporating nanotechnology into fluorescent imaging and magnetic resonance imaging (MRI) has shown promising potential for accurate diagnosis of cancer at an earlier stage than the conventional imaging modalities. Molecular imaging (MI) aims to quantitatively characterize, visualize, and measure the biological processes or living cells at molecular and genetic levels. MI modalities have been exploited in different applications including noninvasive determination and visualization of diseased tissues, cell trafficking visualization, early detection, treatment response monitoring, and in vivo visualization of living cells. High-affinity molecular probe and imaging modality to detect the probe are the two main requirements of MI. Recent advances in nanotechnology and allied modalities have facilitated the use of nanoparticles (NPs) as MI probes. Within the extensive group of NPs, fluorescent NPs play a prominent role in optical molecular imaging. The fluorescent NPs used in molecular and cellular imaging can be categorized into three main groups including quantum dots (QDs), upconversion, and dyedoped NPs. Fluorescent NPs have great potential in targeted theranostics including cancer imaging, immunoassay- based cells, proteins and bacteria detections, imaging-guided surgery, and therapy. Fluorescent NPs have shown promising potentials for drug and gene delivery, detection of the chromosomal abnormalities, labeling of DNA, and visualizing DNA replication dynamics. Multifunctional NPs have been successfully used in a single theranostic modality integrating diagnosis and therapy. The unique characteristics of multifunctional NPs make them potential theranostic agents that can be utilized concurrently for diagnosis and therapy. This review provides the state of the art of the applications of nanotechnologies in early cancer diagnosis focusing on fluorescent NPs, their synthesis methods, and perspectives in clinical theranostics.

Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore

Genetically encoded fluorescent noncanonical amino acids (fNCAAs) could be used to develop novel fluorescent sensors of protein function. Previous efforts toward this goal have been limited by the lack of extensive physicochemical and structural characterizations of protein-based sensors containing fNCAAs. Here, we report the steady-state spectroscopic properties and first structural analyses of an fNCAA-containing Fab fragment of the 5c8 antibody, which binds human CD40L. A previously reported 5c8 variant in which the light chain residue Ile^L98 is replaced with the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) exhibits a 1.7-fold increase in fluorescence upon antigen binding. Determination and comparison of the apparent pK_as of 7-HCAA in the unbound and bound forms indicate that the observed increase in fluorescence is not the result of perturbations in pK_a. Crystal structures of the fNCAA-containing Fab in the apo and bound forms reveal interactions between the 7-HCAA side chain and surrounding residues that are disrupted upon antigen binding. This structural characterization not only provides insight into the manner in which protein environments can modulate the fluorescence properties of 7-HCAA but also could serve as a starting point for the rational design of new fluorescent protein-based reporters of protein function.

Imaging the Replication of Single Viruses: Lessons Learned from HIV and Future Challenges To Overcome

The molecular composition of viral particles indicates that a single virion is capable of initiating an infection. However, the majority of viruses that come into contact with cells fails to infect them. Understanding what makes one viral particle more successful than others requires visualizing the infection process directly in living cells, one virion at a time. In this Perspective, we explain how single-virus imaging using fluorescence microscopy can provide answers to unsolved questions in virology. We discuss fluorescent labeling of virus particles, resolution at the subviral and molecular levels, tracking in living cells, and imaging of interactions between viral and host proteins. We end this Perspective with a set of remaining questions in understanding the life cycle of retroviruses and how imaging a single virus can help researchers address these questions. Although we use examples from the HIV field, these methods are of value for the study of other viruses as well.

Rational programming of history-dependent logic in cellular populations

Genetic programs operating in a history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on standardized recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular, do not require cell-cell communication channels, and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed automated workflows that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare.

Recent advances in probe design to detect reactive sulfur species and in the chemical reactions employed for fluorescence switching

Reactive sulfur species, including hydrogen sulfide, hydropersulfide, and polysulfide, have many roles in biological systems. For example, hydrogen sulfide is involved in the relaxation of vascular smooth muscles and mediation of neurotransmission, while sulfane sulfur, which exists in cysteine persulfide/polysulfide, and glutathione persulfide/polysulfide, is involved in physiological antioxidation and cytoprotection mechanisms. Fluorescence imaging is well suited for real-time monitoring of reactive sulfur species in living cells, and many fluorescent probes for reactive sulfur species have been reported. In such probes, the choice of detection chemistry is extremely important, not only to achieve effective fluorescence switching and high selectivity, but also because the reactions may be applicable to develop other chemical tools, such as reactive sulfur species donors/scavengers. Here, we present an overview of both widely used and recently developed fluorescent probes for reactive sulfur species, focusing especially on the chemical reactions employed in them for fluorescence switching. We also briefly introduce some applications of fluorescent probes for hydrogen sulfide and sulfane sulfur.

Stoichiometric analysis of protein complexes by cell fusion and single molecule imaging

The composition, stoichiometry and interactions of supramolecular protein complexes are a critical determinant of biological function. Several techniques have been developed to study molecular interactions and quantify subunit stoichiometry at the single molecule level. However, these typically require artificially low expression levels or detergent isolation to achieve the low fluorophore concentrations required for single molecule imaging, both of which may bias native subunit interactions. Here we present an alternative approach where protein complexes are assembled at physiological concentrations and subsequently diluted in situ for single-molecule level observations while preserving them in a near-native cellular environment. We show that coupling this dilution strategy with fluorescence correlation spectroscopy permits quantitative assessment of cytoplasmic oligomerization, while stepwise photobleaching and single molecule colocalization may be used to study the subunit stoichiometry of membrane receptors. Single protein recovery after dilution (SPReAD) is a simple and versatile means of extending the concentration range of single molecule measurements into the cellular regime while minimizing potential artifacts and perturbations of protein complex stoichiometry.

A molecular sensor to quantify the localization of proteins, DNA and nanoparticles in cells

Intracellular trafficking governs receptor signaling, pathogenesis, immune responses and fate of nanomedicines. These processes are typically tracked by observing colocalization of fluorescent markers using confocal microscopy. However, this method is low throughput, limited by the resolution of microscopy, and can miss fleeting interactions. To address this, we developed a localization sensor composed of a quenched SNAP-tag substrate (SNAP_Switch) that can be conjugated to biomolecules using click chemistry. SNAP_Switch enables quantitative detection of trafficking to locations of interest within live cells using flow cytometry. Using SNAP_Switch, we followed the trafficking of DNA complexes from endosomes into the cytosol and nucleus. We show that antibodies against the transferrin or hyaluronan receptor are initially sorted into different compartments following endocytosis. In addition, we can resolve which side of the cellular membrane material was located. These results demonstrate SNAP_Switch is a high-throughput and broadly applicable tool to quantitatively track localization of materials in cells.

Determining the trafficking of intracellular material is commonly done by colocalisation analysis using microscopy. Here the authors monitor trafficking of select cargo by measuring the conversion of quenched SNAP-tag substrates by subcellularly-localised SNAP-tag and detection by flow cytometry.

Aggregation-Induced Emission Luminogens Married to 2D Black Phosphorus Nanosheets for Highly Efficient Multimodal Theranostics

Inspired by the respective advantages of aggregation-induced emission (AIE)-active photosensitizers and black phosphorus nanomaterials in cancer treatment, the facile construction of novel AIE photosensitizers married to 2D black phosphorus nanosheets and their application for multimodal theranostics are demonstrated. The developed nanomaterial simultaneously possesses distinctive properties and multiple functions including excellent stability, good biocompatibility, intensive fluorescence emission in the NIR region, high-performance reactive oxygen species generation, good photothermal conversion efficiency, outstanding cellular uptake, and effective accumulation at the tumor site. Both in vitro and in vivo evaluation show that the presented nanotheranostic system is an excellent candidate for NIR fluorescence-photothermal dual imaging-guided synergistic photodynamic-photothermal therapies. This study thus not only extends the applications scope of AIE and black phosphorus materials, but also offers useful insights into designing a new generation of cancer theranostic protocol for potential clinical applications.

In Situ Generated Silver Nanodot Förster Resonance Energy Transfer Pair Reveals Nanocage Sizes

Characterizing nanocages in macromolecules is one of the keys to understanding various biological activities and further utilizing nanocages for novel materials synthesis. However, fast and straightforward detection of the nanocage size remains challenging. Here, we present a new approach to detect the diameter of a nanocage by Förster resonance energy transfer (FRET) of luminescent silver nanodot pairs with reverse micelles as a model. Silver nanodot FRET pairs can be generated in situ from a single silver nanodot species with critical energy transfer distances, R₀, of 4.8-6.5 nm. We have applied this approach to clarify the size variation of the water nanocage in nonionic surfactant Triton X-100-based reverse micelles. FRET efficiency decreases as more water is added, indicating that the size of the reverse micelles continuously expands with water content. The silver element in the nanocage also enhances the visualization of the nanocage under cryo-TEM imaging. The diameter of the water nanocage measured with the above approach is consistent with that obtained by cryo-TEM, demonstrating that the FRET measurement of silver nanodots can be a fast and accurate tool to detect nanocage dimensions. The above demonstration allows us to apply our strategy to other protein-based nanocages.

MiniVIPER Is a Peptide Tag for Imaging and Translocating Proteins in Cells

Microscopy allows researchers to interrogate proteins within a cellular context. To deliver protein-specific contrast, we developed a new class of genetically encoded peptide tags called versatile interacting peptide (VIP) tags. VIP tags deliver a reporter to a target protein via the formation of a heterodimer between the peptide tag and an exogenously added probe peptide. We report herein a new VIP tag named MiniVIPER, which is comprised of a MiniE-MiniR heterodimer. We first demonstrated the selectivity of MiniVIPER by labeling three cellular targets: transferrin receptor 1 (TfR1), histone protein H2B, and the mitochondrial protein TOMM20. We showed that either MiniE or MiniR could serve as the genetically encoded tag. Next, we demonstrated MiniVIPER's versatility by generating five spectrally distinct probe peptides to label tagged TfR1 on live cells. Lastly, we demonstrated two new applications for VIP tags. First, we used MiniVIPER in combination with another VIP tag, VIPER, to selectively label two different proteins in a single cell (e.g., TfR1 with H2B or TOMM20). Second, we used MiniVIPER to translocate a fluorescent protein to the nucleus through in situ dimerization of mCherry with H2B-mEmerald. In summary, MiniVIPER is a new peptide tag that enables multitarget imaging and artificial dimerization of proteins in cells.

Self-Assembled Organic Nanomaterials for Drug Delivery, Bioimaging, and Cancer Therapy

Over the past few decades, tremendous progress has been made in the development of engineering nanomaterials, which opened new horizons in the field of diagnosis and treatment of various diseases. In particular, self-assembled organic nanomaterials with intriguing features including delicate structure tailoring, facile processability, low cost, and excellent biocompatibility have shown outstanding potential in biomedical applications because of the enhanced permeability and retention (EPR) effect and multifunctional properties. In this review, we briefly introduce distinctive merits of self-assembled organic nanomaterials for biomedical applications. The main focus will be placed on summarizing recent advances in self-assembled organic nanomedicine for drug delivery, bioimaging, and cancer phototherapy, followed by highlighting a critical perspective on further development of self-assembled organic nanomaterials for future clinical translation. We believe that the above themes will appeal to researchers from different fields, including material, chemical, and biological sciences, as well as pharmaceutics.

Interrogating Cellular Communication in Cancer with Genetically Encoded Imaging Reporters

Cells continuously communicate changes in their microenvironment, both locally and globally, with other cells in the organism. Integration of information arising from signaling networks impart continuous, time-dependent changes of cell function and phenotype. Use of genetically encoded reporters enable researchers to noninvasively monitor time-dependent changes in intercellular and intracellular signaling, which can be interrogated by macroscopic and microscopic optical imaging, nuclear medicine imaging, MRI, and even photoacoustic imaging techniques. Reporters enable noninvasive monitoring of changes in cell-to-cell proximity, transcription, translation, protein folding, protein association, protein degradation, drug action, and second messengers in real time. Because of their positive impact on preclinical research, attempts to improve the sensitivity and specificity of these reporters, and to develop new types and classes of reporters, remain an active area of investigation. A few reporters have migrated to proof-of-principle clinical demonstrations, and recent advances in genome editing technologies may enable the use of reporters in the context of genome-wide analysis and the imaging of complex genomic regulation in vivo that cannot be readily investigated through standard methodologies. The combination of genetically encoded imaging reporters with continuous improvements in other molecular biology techniques may enhance and expedite target discovery and drug development for cancer interventions and treatment. © RSNA, 2020.

Peptide-Based Nanoassemblies in Gene Therapy and Diagnosis: Paving the Way for Clinical Application

Nanotechnology approaches play an important role in developing novel and efficient carriers for biomedical applications. Peptides are particularly appealing to generate such nanocarriers because they can be rationally designed to serve as building blocks for self-assembling nanoscale structures with great potential as therapeutic or diagnostic delivery vehicles. In this review, we describe peptide-based nanoassemblies and highlight features that make them particularly attractive for the delivery of nucleic acids to host cells or improve the specificity and sensitivity of probes in diagnostic imaging. We outline the current state in the design of peptides and peptide-conjugates and the paradigms of their self-assembly into well-defined nanostructures, as well as the co-assembly of nucleic acids to form less structured nanoparticles. Various recent examples of engineered peptides and peptide-conjugates promoting self-assembly and providing the structures with wanted functionalities are presented. The advantages of peptides are not only their biocompatibility and biodegradability, but the possibility of sheer limitless combinations and modifications of amino acid residues to induce the assembly of modular, multiplexed delivery systems. Moreover, functions that nature encoded in peptides, such as their ability to target molecular recognition sites, can be emulated repeatedly in nanoassemblies. Finally, we present recent examples where self-assembled peptide-based assemblies with "smart" activity are used in vivo. Gene delivery and diagnostic imaging in mouse tumor models exemplify the great potential of peptide nanoassemblies for future clinical applications.