Fluorescent Labeling Research Articles

Liposomal Drug Delivery against Helicobacter pylori Using Furazolidone and N-Acetyl Cysteine in Augmented Therapy.

Helicobacter pylori (H. pylori) infection is a significant global health concern, affecting approximately 50% of the world's population and leading to gastric ulcers, gastritis, and gastric cancer. The increase in antibiotic resistance has compromised the efficacy of existing therapeutic regimens, necessitating novel approaches for effective eradication. This study aimed to develop a targeted liposomal drug delivery system incorporating furazolidone and N-acetylcysteine (NAC) to enhance mucopenetration and improve Helicobacter pylori eradication. Liposomes were formulated with furazolidone, NAC, and Pluronic F-127 using a modified reverse-phase evaporation technique. The formulations were categorized based on charge as neutral, negative, and positive and tested for mucopenetration using a modified silicon tube method with coumarin-6 as a fluorescent marker. The encapsulation efficiency and particle size were analyzed using HPLC and an Izon q-nano particle size analyzer. The results indicated that charged liposomes showed a higher encapsulation efficiency than neutral liposomes with Pluronic F-127. Notably, combining furazolidone with 1% NAC achieved complete eradication of H. pylori in 2.5 h, compared to six hours without NAC. The findings of this study suggest that incorporating NAC and Pluronic F-127 into liposomal formulations significantly enhances mucopenetration and antimicrobial efficacy.

CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota

The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.

Star-shaped flexible arm multivalent aptamers for largely improved virus binding affinity

Here we explore the click chemistry-based synthesis of high affinity multivalent aptamers and their application for virus detection. In contrast to attempts based on rigid constructs, such as aptamer-modified nanoparticles or hybridization-connected constructs, we propose highly flexible “star-shaped” multivalent aptamers to facilitate the cooperative binding to randomly distributed viral proteins on the surface of pleomorphic viruses such as the respiratory syncytial virus (RSV). Polyethylene glycols (PEGs) with 4 azide terminated flexible arms spanning from a pentaerythritol core were conjugated to aptamer strands with dibenzocyclooctyne and a fluorescent label at their, 3’ and 5’ terminus, respectively. By controlling the aptamer - PEG ratio and following electrophoretic separation all the different valency aptamer conjugates could be prepared. For proof of concept, we used an aptamer selected for the G protein of RSV. We show that significantly higher apparent affinities can be obtained by using multivalent aptamers for both the G protein and RSV virus than with the single stranded aptamer, i.e. with up to ca. 2 orders of magnitude. The inherent convenience of synthesizing fluorescently labelled multivalent aptamers leads to a versatile class of affinity ligands for sensing as demonstrated through the improved detection sensitivity of tetravalent aptamer tagged RSV by fluorescence nanoparticle tracking analysis.

Investigating the physicochemical, optical and microstructural properties of sodium doped CdO nano powders fabricated by co-precipitation technique for blue emission and antimicrobial applications

A series of cubic structured pristine and sodium doped CdO nanoparticles (Cd1-xNaxO NPs) with varying dopant concentrations have been synthesized using simple Co-precipitation process. Crystal structure and the connection between various structural parameters are evidenced using powder XRD diffractograms. The crystallite size is evaluated with different models and the mean crystallite size was reduced with Na ions doping concentration due to severe lattice distortion. The existence of various vibrational modes and functional groups were demonstrated through FTIR characterization. The signature of Cd–O and Na–O stretching modes were confirmed with FTIR. Raman spectra also confirmed the formation of metal–oxygen bond and the second order vibration features. The direct bandgap of the CdO material increased from 2.132 to 2.40 eV with an increase in the Na dopant content which presents the appearance of a blue shift as probed through UV–Vis spectroscopy. The surface morphology and microstructure of the samples were studied using FESEM and HRTEM images, respectively. EDAX measurements revealed the presence of Cd, and O in the host lattice and Cd, O and Na in the doped CdO constructions. The SAED concentric ring pattern of Cd1-xNaxO nanoparticles demonstrated the polycrystalline nature of the samples. PL study revealed the impression of intrinsic defects and the photoluminescence colour emission of the Cd1-xNaxO materials shifted more towards bright blue region as the Na doping concentration increased. CIE color coordinates of Na-doped CdO NPs shows intense bluish color and extending its applications in commercial UV lighting, blue LEDs and Fluorescent biological labelling and tagging. Cd1-xNaxO nanoparticles exhibited enhanced antibacterial activity with increasing Na doping content towards gram-positive, and gram-negative bacteria. Further, the antifungal analysis against C. albicans, and A. niger authenticate that Na+ substituted CdO nanoparticles shows excellent antifungal activity. The mechanism of the above observed results is examined in detail in this article.

Construction of HaloTag-based macromolecular probe for multiple logic gates and photoactivatable bioimaging

Protein bioconjugation has emerged as one of the most valuable tools for the development of protein-based biochemical assays. Herein, we report a fluorescent macromolecular probe RF12_POI, in which the coumarin derivative RF12 is specifically conjugated onto the HaloTag fused protein of interest (POI) to achieve a dual stimuli-mediated fluorescence response. RF12 is first obtained by installing a photo-cleavable 1-ethyl-2-nitrobenzyl group onto the C7 hydroxy moiety of coumarin fluorophore with a HaloTag ligand attaching to the acid-labile 1,3-dioxane moiety. Upon stimulation, RF12_Halo exhibits a sequential fluorescence response to photon/H+ on both liquid and solid interfaces. Through the conjugation of RF12 onto the GFP_Halo protein, RF12_GFP_Halo presents a fluorescence resonance energy transfer (FRET) from photo-cleaved RF12 to GFP in the protein complex. Furthermore, by utilizing the stimuli-responsive fluorescence characteristics of coumarin derivatives RF12 (photon/H+) and RF16 (H2O2/H+), we construct RF12/RF16_POI based protein films and achieve multiple applications of logic circuits, including AND, OR, XOR, INHIBIT, Half-adder or Half-subtractor. In these circuits, the output value of I/I0 is dependent on the input sequence of photon, H2O2, and H+. Additionally, we evaluate the fluorescence labeling ability of RF12 to intracellular IRE1_Halo protein and demonstrate that RF12 containing the HaloTag ligand could be precisely retained in cells to track IRE1_Halo protein. Hence, we provide a unique structural design strategy to construct fluorescence dual-responsive macromolecules for information encryption and cellular protein visualization.

Photothermal Enhancement of Ion Current for Red Blood Cell Flow Cytometry.

Blood cell counting typically requires complex machinery. Flow cytometers used for this purpose involve precise optical alignment, costly detectors, and pretreatment with fluorescent labels. Coulter countertype devices, which monitor ion current, are simpler. However, conventional Coulter counters provide only information about size, making it impossible to distinguish similarly sized lymphocytes from red blood cells (RBCs). Inspired by the fact that RBCs have an exceptionally high propensity to absorb light and convert it to heat, i.e., photothermal effect, this study proposes integrating photothermal phenomena into a microfluidic Coulter counting chip. Photothermal heat selectively amplifies the ion current from RBCs over other components including lymphocytes. The combination of ion current monitoring and the photothermal effect for RBC counting suggests an evolution toward versatile flow cytometers.

Hydrogen Bond-Associated Photofluorochromism for Time-Resolved Information Encryption and Anti-counterfeiting.

Time-resolved photofluorochromism constitutes a powerful approach to enhance information encryption security but remains challenging. Herein, we report a strategy of using hydrogen bonds to regulate the time for initiating photofluorochromism. In our strategy, copolymers containing negative photochromic spiropyran (NSP), naphthalimide, and multiple hydrogen-bonding (UPy) units are designed, which display photo-switchable fluorescence resonance energy transfer (FRET) process from naphthalimide donor to the NSP acceptor. Interestingly, the FRET is locked via the dynamic hydrogen-bonding interaction between ring-opened NSP and UPy moieties, resulting in time-dependent fluorescence. The change in fluorescence can be finely regulated via UPy fraction in the polymers. Besides the novel time-dependent fluorescence, the polymers also take advantage of visible-light triggerable, excellent photostability, photoreversibility, and processability. We demonstrate that these properties enable them many application opportunities such as fluorescent security labels and multilevel information encryption patterns.

Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization

AbstractBeing able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late‐stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early‐stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real‐time precision opto‐control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito‐Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions.

Cesium lead bromide perovskite nanocrystals as fluorescent taggants for detecting fluid leaks

Fluorescence tagging represents a low cost, fast, and reliable method for leak detection in the chemical industry. Here, the use of halide perovskites as fluorescent taggants is demonstrated to detect piping leakages. To this end, cesium lead bromide (CsPbBr3) nanocrystals were synthesized at room temperature and dissolved in silicon oil as a green luminophore (530 ± 5 nm). The resulting system had a photoluminescence quantum yield of 48 ± 2 % while retaining key optical properties (emission linewidth and lifetime) over the timescale required for typical leak detection (2–30 minutes), even under strongly acidic/basic conditions (pH 1–13) and high pressures (up to 7 atm). Crucially, the operating dose of CsPbBr3 required for leak detection is an order of magnitude lower than those used for typical commercial fluorescent taggants (0.03 versus 0.003 oz mL−1). These results strongly suggest the great potential of halide perovskites towards industrial leak detection applications.

Effect of active loop extrusion on the two-contact correlations in the interphase chromosome.

The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work, we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows us to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin.

Fluorescence labeling strategies for cell surface expression of TRPV1.

Regulation of ion channel expression on the plasma membrane is a major determinant of neuronal excitability, and identifying the underlying mechanisms of this expression is critical to our understanding of neurons. Here, we present two orthogonal strategies to label extracellular sites of the ion channel TRPV1 that minimally perturb its function. We use the amber codon suppression technique to introduce a non-canonical amino acid (ncAA) with tetrazine click chemistry, compatible with a trans-cyclooctene coupled fluorescent dye. Additionally, by inserting the circularly permutated HaloTag (cpHaloTag) in an extracellular loop of TRPV1, we can incorporate a fluorescent dye of our choosing. Optimization of ncAA insertion sites was accomplished by screening residue positions between the S1 and S2 transmembrane domains with elevated missense variants in the human population. We identified T468 as a rapid labeling site (∼5 min) based on functional and biochemical assays in HEK293T/17 cells. Through adapting linker lengths and backbone placement of cpHaloTag on the extracellular side of TRPV1, we generated a fully functional channel construct, TRPV1exCellHalo, with intact wild-type gating properties. We used TRPV1exCellHalo in a single molecule experiment to track TRPV1 on the cell surface and validate studies that show decreased mobility of the channel upon activation. The application of these extracellular label TRPV1 (exCellTRPV1) constructs to track surface localization of the channel will shed significant light on the mechanisms regulating its expression and provide a general scheme to introduce similar modifications to other cell surface receptors.

A novel live DNA tagging system for African swine fever virus shows that bisbenzimide Hoechst 33342 can effectively block its replication

African swine fever virus (ASFV) infection causes a frequently fatal disease in domestic swine that has affected more than 50 countries worldwide since 2021, with a major impact on animal welfare and economy. The development of effective vaccines or antivirals against this disease are urgently required for its effective control. Live detection of viral replication has been used as a tool for the screening and characterization of antiviral compounds in other dsDNA genome containing viruses. Here, we have adapted the ANCHOR fluorescent DNA labelling system to ASFV by constructing and characterizing a novel recombinant virus. We show that this virus is viable and effectively tags viral DNA replication sites, which can be detected and quantified in real time. Further, we have used high content cell microscopy to test the antiviral activity of bisbenzimide compounds and show that Hoechst 33342 has specific anti-ASFV activity. We expect this novel tool to be useful both in the further study of ASFV replication as in the screening of new specific antiviral compounds.

AlphaFold2-guided engineering of split-GFP technology enables labeling of endogenous tubulins across species while preserving function.

Dynamic properties are essential for microtubule (MT) physiology. Current techniques for in vivo imaging of MTs present intrinsic limitations in elucidating the isotype-specific nuances of tubulins, which contribute to their versatile functions. Harnessing the power of the AlphaFold2 pipeline, we engineered a strategy for the minimally invasive fluorescence labeling of endogenous tubulin isotypes or those harboring missense mutations. We demonstrated that a specifically designed 16-amino acid linker, coupled with sfGFP11 from the split-sfGFP system and integration into the H1-S2 loop of tubulin, facilitated tubulin labeling without compromising MT dynamics, embryonic development, or ciliogenesis in Caenorhabditis elegans. Extending this technique to human cells and murine oocytes, we visualized MTs with the minimal background fluorescence and a pathogenic tubulin isoform with fidelity. The utility of our approach across biological contexts and species set an additional paradigm for studying tubulin dynamics and functional specificity, with implications for understanding tubulin-related diseases known as tubulinopathies.

Fluorescence Lifetime Multiplexing (FLEX) for simultaneous high dimensional spatial biology in 3D

Immunohistochemistry is a crucial method for detecting specific proteins within tissue samples, yet constrained to one biomarker per tissue section. Multiplexed immunofluorescence, while allowing simultaneous visualization of multiple proteins, faces limitations in the number of simultaneous fluorescent labels due to spectral overlap. Although cyclic immunofluorescence techniques have successfully broadened antibody staining capacities in a single tissue sample, they are plagued by time-consuming and labor-intensive procedures, sample degradation risks, and inability to scale beyond thin sections. In this study, we introduce the use of 3D confocal Fluorescence Lifetime Imaging Microscopy as a high-throughput, multiplexed immunofluorescence platform that can differentiate 11 or more biomarkers in 3D tissue volumes. Leveraging both spectral and lifetime information, this approach allows for practical spatial biology in thin sections that can readily scale to larger volumes of tissue. We believe that this highly multiplexed and versatile biomarker imaging platform will significantly expedite cancer research and enable new translational approaches in the future.

Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.

The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins, and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular fluorescent proteins and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cell analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.

A Nitroreductase-Activatable Metabolic Reporter for Covalent Labeling of Pathological Hypoxic Cells in Tumorigenesis.

Aberrant hypoxic stress will initiate a cascade of pathological consequence observed prominently in tumorigenesis. Understanding of hypoxia's role in tumorigenesis is highly essential for developing effective therapeutics, which necessitates reliable tools to specifically distinguish hypoxic tumor cells (or tissues) and correlate their dynamics with the status of disease in complex living settings for precise theranostics. So far, disparate hypoxia-responsive probe molecules and prodrugs were designed via chemical or enzymatic reactions, yet their capability in real-time reporting pathogenesis development is often compromised due to unrestricted diffusion and less selectivity towards the environmental responsiveness. Herein we present an oxygen-insensitive nitroreductase (NTR)-activatable glycan metabolic reporter (pNB-ManNAz) capable of covalently labeling hypoxic tumor cells and tissues. Under pathophysiological hypoxic environments, the caged non-metabolizable precursor pNB-ManNAz exhibited unique responsiveness to cellular NTR, culminating in structural self-immolation and the resultant ManNAz could incorporate onto cell surface glycoproteins, thereby facilitating fluorescence labeling via bioorthogonal chemistry. This NTR-responsive metabolic reporter demonstrated broad applicability for multicellular hypoxia labeling, particularly in the dynamic monitoring of orthotopic tumorigenesis and targeted tumor phototherapy in vivo. We anticipate that this approach holds promise for investigating hypoxia-related pathological progression, offering valuable insights for accurate diagnosis and treatment.

Electrospun Janus film: Innovative design of “macro + micro” to achieve thermochromic-anisotropic conductive-fluorescent tri-functionality

Multi-functionalized thermochromic materials will greatly expand their application scopes. In this work, two functions of electrical conductivity and fluorescence are innovatively integrated into a thermochromic material by designing specific “macro + micro” Janus structures. Tri-functional thermochromic-anisotropic conductive-fluorescent thermochromic microcapsules-45 °C (TCM-45)/polymethyl methacrylate (PMMA) microfibers non-array&{[polypyrrole (PPy)/PMMA]//[Coumarin/PMMA] Janus microfibers array} up-down Janus film (named as TCFJAJF) is constructed by two-step electrospinning techniques of “single axis + parallel axis”. The up layer of TCFJAJF is TCM-45/PMMA microfibers non-array film (defined as U-TCFJAJF, viz. thermochromic layer) and the down layer of TCFJAJF is [PPy/PMMA]//[Coumarin/PMMA] Janus microfibers array film (denoted as D-TCFJAJF, viz. anisotropic conductive-fluorescent layer). The macroscopic up-down Janus structure eliminates the mutual influences between D-TCFJAJF and U-TCFJAJF. U-TCFJAJF has excellent color conversion and fading/coloring performances, achieving a reversible and multiple colors conversion from blue to white upon heating from 25 to 45 °C. A new concept of “transient thermal printing” is proposed based on fast thermal coloring/fading conversion of thermally printed patterns on film. Meanwhile, the microscopic Janus microfiber structure of D-TCFJAJF largely alleviates absorption to the excitation light and emission light of Coumarin by PPy and influence of Coumarin on conduction of PPy, ensuring the intense fluorescence and high conductivity. Due to the ordered arrangement of Janus microfibers, D-TCFJAJF has excellent anisotropic conductivity. As a demo application, TCFJAJF as a conductor can light up LED bulbs in a microcircuit and emit bright blue fluorescence under UV light excitation, achieving the working state visualization of the conductive microcircuit in dark surroundings. The multi-functionalized thermochromic film will have huge application prospects in fields of temperature monitoring, transient information reading and displaying, flexible electronics, fluorescent labeling and thermal-fluorescent dual encryption anti-counterfeiting, etc.

Label free tracking to quantify nanoparticle diffusion through biological media

Nanotechnology is a rapidly evolving field and has been extensively studied in biological applications. An understanding of the factors that influence nanoparticle diffusion in biofluids can aid in the development of diverse technologies. The development of real-time, label-free tracking technologies would allow the expansion of current knowledge of the diffusion and activity of nanoparticles. Fluorescence-based microscopy is one of the most widespread tools to monitor and track nanoparticle dynamics; however, the influence of fluorescent tags on diffusion and biological activity is still unclear. In this study, we experimentally determined the diffusion coefficient of gold nanoparticles using a label-free, optical tracking technique and evaluated the influence of protein concentration, charge and diameter on nanoparticle diffusion through biological media. We dispersed positively- and negatively-charged nanoparticles with diameters varying from 10 to 100 nm in a common cell culture media with different concentrations of serum proteins. Our results show that dynamic protein interactions influence nanoparticle diffusion in the range of serum concentrations tested. Experimental regimes to obtain quantitative information on the factors that influence the dynamics of nanoparticles in biological media have been developed.

Synthesis of bifunctional lipophilic constructs

An ability of glycolipids to embed membrane of living cells opens an opportunity to modify cellular surface via insertion of synthetic lipophilic constructs carrying given glycan (or any other molecular fragment). Detection of thus inserted glycans by fluorescent microscopy requires treatment with corresponding fluorescently labeled antibodies. Di- (IgG) and decavalent (IgM) antibodies can significantly affect the distribution of glycolipids in the membrane, therefore direct visualization of embedded lipophilic constructs is required. To achieve this, fluorescent tag must be included in the composition of the lipophilic constructs and at the same time be located at a sufficient distance from glycan part. Here we propose two approaches to the synthesis of these compounds and describe obtaining of two constructs carrying A (type 2) tetrasaccharide and either fluorescein or sulfo-cyanine-3.

Expanding the transgene expression toolbox of the malaria vector Anopheles stephensi.

Anopheles stephensi Liston, 1901 (Diptera: culicidae) is a competent vector of Plasmodium falciparum (Haemosporida: plasmodiidae) malaria, and its expansion in the African continent is of concern due to its viability in urban settings and resistance to insecticides. To enhance its genetic tractability, we determined the utility of a ~2 kb An. stephensi lipophorin (lp) promoter fragment in driving transgene expression. Lipophorin genes are involved in lipid transport in insects, and an orthologous promoter in An. gambiae (AGAP001826) was previously demonstrated to successfully express a transgene. In the present study, we qualitatively characterised the expression of a ZsYellow fluorescent marker protein, expressed by An. stephensi lp promoter fragment. Our study indicated that the lp promoter fragment was effective, generating a distinct expression pattern in comparison to the commonly utilised 3xP3 promoter. The lp:ZsYellow fluorescence was largely visible in early instar larvae and appeared more intense in later instar larvae, pupae and adults, becoming especially conspicuous in adult females after a blood meal. Different isolines showed some variation in expression pattern and intensity. Aside from general transgene expression, as the lp promoter produces a suitable fluorescent protein marker expression pattern, it may facilitate genotypic screening and aid the development of more complex genetic biocontrol systems, such as multi-component gene drives. This study represents an expansion of the An. stephensi genetic toolbox, an important endeavour to increase the speed of An. stephensi research and reach public health milestones in combating malaria.