A multipurpose mitochondrial NIR probe for imaging ferroptosis and mitophagy.

This paper explores the use of a di-cationic fluorophore for visualizing mitochondria in live cells independent of membrane potential. Through the synthesized di-cationic fluorophore, we investigate the monitoring of viscosity, ferroptosis, stress-induced mitophagy, and lysosomal uptake of damaged mitochondria. The designed fluorophore is based on DQAsomes, cationic vesicles responsible for transporting drugs and DNA to mitochondria. The symmetric fluorophores possess two charge centres separated by an alkyl chain and are distinguished by a pyridinium group for mitochondrial selectivity, the C-12 alkyl substitution for membrane affinity, and an electron donor-π-acceptor fluorescent scaffold for intramolecular charge transfer. The synthesized fluorophores, PP and NP, emit wavelengths exceeding 600 nm, with a significant Stokes shift (130-211 nm), and NP demonstrates near-infrared emission (∼690 nm). Our study underscores the potential of these fluorophores for live-cell imaging, examining physiological responses such as viscosity and ferroptosis, and highlights their utility in investigating mitophagy damage and lysosomal uptake.

Fluorescent styrenes for mitochondrial imaging and viscosity sensing.

Fluorophores bearing cationic pendants, such as the pyridinium group, tend to preferentially accumulate in mitochondria, whereas those with pentafluorophenyl groups display a distinct affinity for the endoplasmic reticulum. In this study, we designed fluorophores incorporating pyridinium and pentafluorophenyl pendants and examined their impact on sub-cellular localization. Remarkably, the fluorophores exhibited a notable propensity for the mitochondrial membrane. Furthermore, these fluorophores revealed dual functionality by facilitating the detection of viscosity changes within the sub-cellular environment and serving as heavy-atom-free photosensitizers. With easy chemical tunability, wash-free imaging, and a favorable signal-to-noise ratio, these fluorophores are valuable tools for imaging mitochondria and investigating their cellular processes.

A two-in-one probe: imaging lipid droplets and endoplasmic reticulum in tandem.

The endoplasmic reticulum (ER) and lipid droplets (LDs) intricately interact in cellular processes, with the ER serving as a hub for lipid synthesis and LDs acting as storage organelles for lipids. Developing fluorescent probes that can simultaneously visualise the ER and LDs provides a means for real-time and specific visualisation of these subcellular organelles and elucidating their interaction. Herein, we present synthetically simple and novel donor-π-acceptor styryl fluorophores (PFC, PFN and PFB) incorporating pentafluorophenyl (PFP) to demonstrate exquisite discriminative imaging of ER and LD with a single excitation wavelength. The PFP moiety aids the ER selectivity, while the overall hydrophobicity of the molecule aids in the LD targeting. Furthermore, the fluorophores are utilised in studying the changes in size, distribution, and biogenesis of LDs within ER regions after treatment with oleic acid. Strong emission, lower concentrations ∼100 nM requirement, minimal cytotoxicity, and photostability make these fluorophores excellent tools for probing sub-cellular dynamics.

Lipid Droplets Specific Fluorophore for Demarcation of Normal and Diseased Tissues.

Using high-fidelity, permeable, lipophilic, and bright fluorophores for imaging lipid droplets (LDs) in tissues holds immense potential in diagnosing conditions such as diabetic or alcoholic fatty liver disease. In this work, we utilized linear and Λ-shaped polarity-sensitive fluorescent probes for imaging LDs in both cellular and tissue environments, specifically in rats with diabetic and alcoholic fatty liver disease. The fluorescent probes possess several key characteristics, including high permeability, lipophilicity, and brightness, which make them well-suited for efficient LD imaging. Notably, the probes exhibit a substantial Stokes shift, with 143 nm for DCS and 201 nm for DCN with selective targeting of the lipid droplets. Our experimental investigations successfully differentiated morphological variations between diseased and normal tissues in three distinct tissue types: liver, adipose, and small intestine. They could help provide pointers for improved detection and understanding of LD-related pathologies.

Fluorescent styryl pyridine-N-oxide probes for imaging lipid droplets.

Lipid droplets (LDs) have emerged as major regulators of cellular metabolism, encompassing lipid storage, membrane synthesis, viral replication, and protein degradation. Exclusive studies have suggested a direct link between LDs and cancer, as a notable abundance of LDs is found in cancerous cells. Therefore, monitoring the location, distribution, and movements of LDs is of paramount importance for understanding their involvement in biological processes. To target LDs, we designed and synthesized fluorophores with a styryl scaffold bearing electron-donating amino groups and pyridine-N-oxide, a zwitterionic acceptor moiety. We explored their photophysical properties in various solvents and conducted systematic DFT calculations on the synthesized fluorescent molecules, comparing them with neutral pyridine and cationic pyridinium styryl dyes. The results demonstrate that diphenylaminostyryl pyridine-N-oxide (TNO) shows excellent imaging of LDs, in contrast to the behavior of cationic styrylpyridinium (TNC), which primarily localizes within the mitochondria. Notably, pyridine N-oxide offers several benefits: an increased dipole moment facilitating charge separation between donors and acceptors, substantial HOMO and LUMO stabilization, improved water solubility, favorable redox properties, and bathochromic-shifted absorption/emission spectra, showing promise as a fluorescent tool for probing the cellular-biological realm.

Improved lipophilic probe for visualizing lipid droplets in erastin-induced ferroptosis.

Studying the viscosity of lipid droplets (LDs) provides insights into various diseases associated with LD viscosity. Ferroptosis is one such process in which LD viscosity increases due to the abnormal accumulation of lipid ROS (reactive oxygen species) caused by peroxidation. For investigating the LD imaging and ferroptosis, we developed two molecules (NNS and DNS) that show significant Stokes shifts (182-232 nm) and utilized them for sub-cellular imaging. Excellent localization is noted with the lipid droplets. Subsequently, DNS was used to monitor the variations in the LD viscosity during erastin-induced ferroptosis followed by ferroptosis inhibition. Additionally, we explored variations in the LD quantity, size, and accumulation when subjected to oleic acid stimulation. Extensive DFT and TDDFT investigations have been employed to understand the effect of NO2 substitution on the linear and branched molecular derivatives. Our results with the improved lipophilic fluorophore, exhibiting excellent colocalization with LDs, offer valuable insights into sensing erastin-induced ferroptosis and have the potential for real-time diagnostic applications.

N-Functionalized fluorophores: detecting urinary albumin and imaging lipid droplets.

A series of novel N-sulfonyl pyridinium fluorophores were designed, synthesized, and explored in terms of their ability to bind with serum albumins. Upon binding the fluorophores with BSA, noticeable emission wavelength or intensity changes accompanied by color changes were observed. Competitive binding studies revealed that the fluorophore selectively binds to the warfarin site, but the binding affinity also depends on the nature of the scaffold. Additionally, the fluorophores were employed to detect spiked serum albumin in artificial urine. Cellular imaging experiments indicated that the fluorophores accumulate within lipid droplets (LDs), suggesting their potential as promising biomarkers for lipid droplets. Furthermore, the fluorescence intensity, number, and size of LDs increased upon serum starvation.

Styryl-NIR Mitochondrial Probes with Rapid HOCl Detection in Live-Cells.

Hypochlorous acid (HOCl) is critical for maintaining immune system balance, but it can harm mitochondria by hindering enzyme activity, leading to decreased ATP and increased cell death. In this study, we have designed a fluorophore with a pyridinium scaffold for selective staining of the mitochondria and to detect hypochlorite. The fluorophore exhibits strong solvatochromic emission due to intramolecular charge transfer and excellent sub-cellular localization in the mitochondria. Additionally, it shows a rapid response to HOCl with high selectivity among different reactive oxygen/nitrogen compounds with a detection limit of 2.31 µM. Moreover, it is also utilized for the exogenous and endogenous detection of HOCl in live cells, which may help study the role of hypochlorite in organelles at the cellular level. DFT and TDDFT calculations have been carried out to understand the relationship between the structure and properties of the cationic probes with respect to the α-cyano substitution and extension of π-conjugation. The selective detection of HOCl by C4 over other cationic probes has also been well-demonstrated, showing how the binding of HOCl affects the electronic properties of C4 through the analysis of non-bonding orbitals (NBO) population, electrostatic potential surface (ESP), and density of states (DOS) projected DOS investigations.

Imaging of mitochondria/lysosomes in live cells and C. elegans.

Two rhodamine-phenothiazine conjugates, RP1 and RP2, were synthesized, and their photophysical properties, subcellular localization, and photocytotoxicity were investigated. We observed robust localization of RP1 in mitochondria and dual localization in mitochondria and lysosomes with RP2 in live cells. Live cell imaging with these probes allowed us to track the dynamics of mitochondria and lysosomes during ROS-induced mitochondrial damage and the subsequent lysosomal digestion of the damaged mitochondria. The fluorophores also demonstrated preferential accumulation in cancer cells compared to normal cells and had strong photo-cytotoxicity. However, no cytotoxicity was observed in the dark. The mitochondrial staining and light-induced ROS production were not limited to mammalian cell lines, but were also observed in the animal model C. elegans. The study demonstrated the potential applications of these probes in visualizing the mitochondria-lysosome cross-talk after ROS production and for photodynamic therapy.

Synbiotic Intervention Ameliorates Oxidative Stress and Gut Permeability in an In Vitro and In Vivo Model of Ethanol-Induced Intestinal Dysbiosis.

Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial components to enter the portal vein and induce oxidative stress-induced inflammation in the liver. Only corticosteroids and liver transplants are treatment options for severe alcoholic hepatitis. ALD's pathophysiology is unknown. However, acetaldehyde's toxic effects cause oxidative stress and intestinal permeability. This study investigates the influence of a synbiotic (a combination of aged garlic extract (AGE) and Lactobacillus rhamnosus MTCC1423) on colonic oxidative stress and inflammation in ALD male Wistar rats and Caco2 cells. MDA measurement by HPLC in CaCo2 cells, blood serum, and colon tissue demonstrated that synbiotic treatment in the ALD model reduces oxidative stress. Further, fecal high-throughput 16S rRNA gene sequencing revealed the microbiome's shift towards Firmicutes in the synbiotic group compared to ethanol. In addition, DCFDA labeling and H/E staining demonstrate that the synbiotic is beneficial in inhibiting the development of ALD. In the colon, the synbiotic reduces the activation of CYP2E1 and the inflammatory markers TNF-a and IL-6 while elevating the mRNA expression of ZO-1, occludin, and IL-10. Synbiotics colonize Lactobacillus to restore barrier function and microbiota and reduce colon oxidative stress. Thus, a synbiotic combination can be used in ALD treatment.

Imaging of lipid droplets using coumarin fluorophores in live cells and C. elegans.

Fluorescent probes offer incredibly effective tools for visualizing the dynamic morphology of lipid droplets (LDs) and investigating their physiological interactions. In this work, we have utilized solvatochromic coumarin probes bearing nitrile and ester substituents for live-cell imaging. The fluorescence probes are characterized by a donor (diethylamino) and acceptor (nitrile and/or ester) substituents and a rotatable double bond. The designed architecture allows investigation of environmental sensitivity apart from providing excellent ability to target sub-cellular organelles. The synthesized fluorophores showed low cytotoxicity and excellent localization within the lipid droplets. Further, the fluorophores were also utilized to study viscosity changes within the LDs induced by Nystatin. More importantly, we also demonstrate imaging of LDs in multi-cellular animal models such as C. elegans.

Kinesin-3 motors are fine-tuned at the molecular level to endow distinct mechanical outputs.

BACKGROUND: Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. RESULTS: We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B > KIF16B) show an inverse correlation with their microtubule-binding affinities (KIF1A < KIF13A < KIF13B < KIF16B). We demonstrate that this differential microtubule-binding affinity is largely contributed by the positively charged residues in loop8 of the kinesin-3 motor domain. Furthermore, microtubule gliding and cellular expression studies displayed significant microtubule bending that is influenced by the positively charged insert in the motor domain, K-loop, a hallmark of kinesin-3 family. CONCLUSIONS: Together, we propose that a fine balance between the rate of ATP hydrolysis and microtubule affinity endows kinesin-3 motors with distinct mechanical outputs. The K-loop, a positively charged insert in the loop12 of the kinesin-3 motor domain promotes microtubule bending, an interesting phenomenon often observed in cells, which requires further investigation to understand its cellular and physiological significance.

Single-Molecule Analysis of Sf9 Purified Superprocessive Kinesin-3 Family Motors.

A complex cellular environment poses challenges for single-molecule motility analysis. However, advancement in imaging techniques have improved single-molecule studies and has gained immense popularity in detecting and understanding the dynamic behavior of fluorescent-tagged molecules. Here, we describe a detailed method for in vitro single-molecule studies of kinesin-3 family motors using Total Internal Reflection Fluorescence (TIRF) microscopy. Kinesin-3 is a large family that plays critical roles in cellular and physiological functions ranging from intracellular cargo transport to cell division to development. We have shown previously that constitutively active dimeric kinesin-3 motors exhibit fast and superprocessive motility with high microtubule affinity at the single-molecule level using cell lysates prepared by expressing motor in mammalian cells. Our lab studies kinesin-3 motors and their regulatory mechanisms using cellular, biochemical and biophysical approaches, and such studies demand purified proteins at a large scale. Expression and purification of these motors using mammalian cells would be expensive and time-consuming, whereas expression in a prokaryotic expression system resulted in significantly aggregated and inactive protein. To overcome the limitations posed by bacterial purification systems and mammalian cell lysate, we have established a robust Sf9-baculovirus expression system to express and purify these motors. The kinesin-3 motors are C-terminally tagged with 3-tandem fluorescent proteins (3xmCitirine or 3xmCit) that provide enhanced signals and decreased photobleaching. In vitro single-molecule and multi-motor gliding analysis of Sf9 purified proteins demonstrate that kinesin-3 motors are fast and superprocessive akin to our previous studies using mammalian cell lysates. Other applications using these assays include detailed knowledge of oligomer conditions of motors, specific binding partners paralleling biochemical studies, and their kinetic state.

Toxicological Impact and in Vivo Tracing of Rhodamine Functionalised ZIF-8 Nanoparticles.

Metal Organic Frameworks (MOFs) are extensively used for a wide range of applications due to their exceptionally high surface area. MOF particles are conventionally in micron size, but the nanosized MOFs show good transportation/mobility due to their small size, and when combined with the high surface area of MOFs, it makes MOF nanoparticles an ideal candidate to study for environmental remediation. Therefore, it is important to study the ecotoxicological impact of these MOFs. In this study, we developed rhodamine labelled nanoparticles of zinc imidazolate metal organic framework (ZIF-8 MOFs) as a means of in vivo tracing the MOF translocation in C. elegans. Rhodamine B isothiocyanate functionalized ZIF-8 MOFs nanoparticles (RBITC@ZIF-8 MOF nanoparticles; size 44 ± 7 nm) were fed to the worms naturally within a concentration range of 0.16-16.4 µg mg-1. Fluorescence was detected in the pharyngeal and gut lumen regions of the worms after 4 h of treatment, for exposure concentrations >0.163 µg mg-1. A higher intensity of fluorescence was observed at the end of 24 h for all exposure concentrations. Worms treated with RBITC@ZIF-8 MOF concentrations of ≥1.63 µg mg-1 for 24 h showed a bright stable fluorescence signal at the tail region. The uptake of RBITC@ZIF-8 MOF for an exposure concentration of 0.163, 1.63, and 8.2 µg mg-1 was found to be 52.1, 11.4 and 28.6%, respectively. Through this study, we showed that RBITC@ZIF-8 MOFs can be exposed to C. elegans and imaged at low concentrations of ∼0.16 µg mg-1.

Lutidine derivatives for live-cell imaging of the mitochondria and endoplasmic reticulum.

The mitochondria and endoplasmic reticulum (ER) are highly dynamic subcellular structures essential for several biological functions. The development of non-toxic, wash-free fluorophores to visualize these structures inside cells aid in understanding their localization and dynamics in diverse cellular processes. In this paper, we report the synthesis and characterization of lutidine-based cationic fluorophores bearing push-pull substituents exhibiting emission in green and red wavelength regions and their subcellular localization in living cells. The confocal imaging of the molecules in a cellular domain reveals the robust localization of three molecules (2, 4 and 5) in the mitochondria and two molecules with polyfluorophenyl substituents (6 and 7) in the ER. At the same time, the other two molecules (1 and 3) showed non-specific imaging. These molecules can also be used to sense the altered viscosity of the stressed ER and investigate its dynamics.

Effect of Binding-Affinity and ATPase Activity on the Velocities of Kinesins Using Ratchet Models.

We use two-state ratchet models containing single and coupled Brownian motors to understand the role of motor-microtubule binding, ATPase reaction rate and dimerisation on the translational velocities of Kinesin motors. We use model parameters derived from the experimental measurements on KIF1A, KIF13A, KIF13B, and KIF16B motors to compute velocities in µm/s. We observe that both the models show the same trend in velocities (KIF1A > KIF13A > KIF13B > KIF16B) as the experimental results. However, the models significantly underpredict the velocities when compared with the experiments. The predictions of the coupled-motor model are closer to the experiments than those of the single-motor model. Our results indicate that the variation of ATPase reaction rate governs the trend in velocities for the above four motors. The variation of motor-microtubule binding affinity and the coupling strength between the motor domains may only have a secondary effect. More rigorous models that incorporate the power-stroke mechanism are necessary for better quantitative compliance with the experiments.

Novel dual labelled nanoprobes for nanosafety studies: Quantification and imaging experiment of CuO nanoparticles in C. elegans.

Metal oxide nanoparticles have been extensively studied for their toxicological impacts. However, accurate tracing/quantification of the nanomaterials and their biological responses are difficult to measure at low concentrations. To overcome the challenge, we developed a dual-labelling technique of CuO nanoparticles with a stable isotope of 65Cu, and with rhodamine dye. In vivo experiments on C. elegans were performed using natural feeding of Rhodamine B isothiocyanate-(3 aminopropyl) triethoxysilane functionalized 65CuO nanoprobes (RBITC-APTES@65CuO) (size = 7.41 ± 1 nm) within the range of Predicted Environmental Concentration (PEC) of CuO nanoparticles in soil and sediments. Fluorescence emission (570 nm) was detected in the lumen of the intestine and the pharynx of C. elegans with no impact of nanoparticle exposure on the brood size and life span of worms. The ingested fluorescent labelled RBITC-APTES@65CuO nanoprobes did not enter the reproductive system and were distributed in the alimentary canal of C. elegans. Strong fluorescent signals from the ingested RBITC-APTES@65CuO nanoprobes were achieved even after 24 h of exposure demonstrating the high stability of these nanoprobes in vivo. The net accumulation measured of 65Cu in C. elegans after background subtraction was 0.001 µg mg-1 (3.52 %), 0.005 µg mg-1 (1.76 %) and 0.024 µg mg-1 (1.69 %) for an exposure concentration of 0.0284 µg mg-1, 0.284 µg mg-1, and 1.42 µg mg-1 of 65Cu, respectively. Using C. elegans as a model organism, we demonstrated that RBITC-APTES tagged 65CuO nanoparticles acted as novel nanoprobes for measuring the uptake, accumulation, and biodistribution through quantification and imaging the nanoprobes at a very low exposure concentration (65CuO concentration: 0.033 µg mg-1).

Stress-responsive rhodamine bioconjugates for membrane-potential-independent mitochondrial live-cell imaging and tracking.

The 'powerhouses' of cell, mitochondria have seen an upsurge of interest in investigations pertaining to the imaging and mapping of physiological processes. By utilizing sterol-modified rhodamine, we have performed the live-cell imaging of mitochondria without dependence on a membrane potential. The sterol probes are highly biocompatible, and they can track the mitochondrial live-cell dynamics in a background-free manner with improved brightness and impressive contrast. This is the first attempt to study the stress response using a direct fluorescence readout with bio-conjugates of rhodamine inside mitochondria. The results pave the way for developing different sterol markers for understanding cellular responses and function.

KIF13A motors are regulated by Rab22A to function as weak dimers inside the cell.

Endocytic recycling is a complex itinerary, critical for many cellular processes. Membrane tubulation is a hallmark of recycling endosomes (REs), mediated by KIF13A, a kinesin-3 family motor. Understanding the regulatory mechanism of KIF13A in RE tubulation and cargo recycling is of fundamental importance but is overlooked. Here, we report a unique mechanism of KIF13A dimerization modulated by Rab22A, a small guanosine triphosphatase, during RE tubulation. A conserved proline between neck coil-coiled-coil (NC-CC1) domains of KIF13A creates steric hindrance, rendering the motors as inactive monomers. Rab22A plays an unusual role by binding to NC-CC1 domains of KIF13A, relieving proline-mediated inhibition and facilitating motor dimerization. As a result, KIF13A motors produce balanced motility and force against multiple dyneins in a molecular tug-of-war to regulate RE tubulation and homeostasis. Together, our findings demonstrate that KIF13A motors are tuned at a single-molecule level to function as weak dimers on the cellular cargo.