Visualizing the endocytic and exocytic processes of wheat germ agglutinin by quantum dot-based single-particle tracking

Twisted Intramolecular Charge Transfer-Based Viscosity-Responsive Probe Reveals Lysosomal Degradation Process of Endocytosed Foreign Bodies

The optimization of nanomedicines requires a thorough understanding of nanocarrier attrition during lysosome-mediated biological processes. Real-time monitoring of endocytosis provides valuable insights into the lysosomal effects on nanocarriers and the release of nanodrugs. We report the development of a coresponsive probe that detects changes in the spatial viscosity of the intracellular domain caused by lysosomal degradation of foreign bodies. The probe, based on a benzofuro[2,3-d]pyrimidine structure, exhibits torsional intramolecular charge transfer (TICT) and responds to ambient viscosity changes with a sensitive fluorescence intensity. The antidiffused fluorescence transition of the probe in the spatially restricted domain serves as a key indicator for real-time monitoring. When encapsulated with diverse foreign bodies and emitted into macrophages by endocytosis, the probe forms nanoparticles. Lysosomes uptake these materials for intracellular digestion, causing alterations in the aggregation or depolymerization state of the nanoparticles, leading to viscosity changes manifested by the probe's fluorescence. By studying the spatial viscosity changes caused by lysosomal degradation of foreign bodies, our monitoring strategy contributes to understanding the digestion or escape capabilities of potential pharmaceutical-carrying nanocarriers, providing guidelines to design more effective nanocarriers that navigate lysosomal degradation to achieve precise drug payloads and release.

Quantitative single-virus tracking for revealing the dynamics of SARS-CoV-2 fusion with plasma membrane

Viral envelope fusion with the host plasma membrane (PM) for genome release is a hallmark step in the life cycle of many enveloped viruses. This process is regulated by a complex network of biomolecules on the PM, but robust tools to precisely elucidate the dynamic mechanisms of virus-PM fusion events are still lacking. Here, we developed a quantitative single-virus tracking approach based on highly efficient dual-color labelling of viruses and batch trajectory analysis to achieve the spatiotemporal quantification of fusion events. This approach allows us to comprehensively analyze the membrane fusion mechanism utilized by pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the single-virus level and precisely elucidate how the relevant biomolecules synergistically regulate the fusion process. Our results revealed that SARS-CoV-2 may promote the formation of supersaturated clusters of cholesterol to facilitate the initiation of the membrane fusion process and accelerate the viral genome release.

Wheat germ agglutinin conjugated chitosan nanoparticles for gemcitabine delivery in MCF-7 cells; synthesis, characterisation and in vitro cytotoxicity studies

OBJECTIVE AND AIM

Numerous clinical trials indicated combination regimens containing gemcitabine could extend progression-free survival of breast cancer patients without increasing the incidence of serious adverse effects. Orally administered gemcitabine is being metabolized by enzymes present in intestinal cells rapidly; thereupon, the current study was aimed to preparing, optimizing, and evaluating cytotoxicity of wheat germ agglutinin conjugated gemcitabine-chitosan nanoparticles (WGA-Gem-CNPs) in MCF-7 and HEK293 cells and to determining their cellular uptake by Caco-2 cells.

METHODS

Gem-CNPs were prepared by Ionic Gelation method and optimum formulation was implied for WGA conjugation optimisation. Nanoparticles formation was approved by FTIR and DSC analyses; then particles were characterized by DLS and release profile was prepared. MTT assay was performed in MCF-7 and HEK293.

RESULTS

Optimized Gem-CNPs and WGA-Gem-CNPs particle size were estimated as 126.6 ± 21.8 and 144.8 ± 36.1 nm, respectively. WGA conjugation efficacy was calculated as 50.98 ± 2.32 percent and encapsulation efficiency in WGA-Gem-CNPs was 69.44 ± 3.41 percent. Three-hour Caco-2 cellular uptake from Gem-CNPs and WGA-Gem-CNPs were estimated as averagely 3.5 and 4.5 folds higher than free drug, respectively. Gem-CNPs and WGA-Gem-CNPs reduced IC50 in MCF-7 cells by 2 and 2.5 folds, respectively; such decrease for HEK293 cells was as much as 2.4 and 6.3 folds, in same order.

CONCLUSION

Demonstrated significant in vitro uptake of WGA-Gem-CNPs and cytotoxicity might be considered for more studies as a potential carrier for oral delivery of gemcitabine.

Spatiotemporally controlled drug delivery via photothermally driven conformational change of self-integrated plasmonic hybrid nanogels

BACKGROUND

Spatiotemporal regulation is one of the major considerations for developing a controlled and targeted drug delivery system to treat diseases efficiently. Light-responsive plasmonic nanostructures take advantage due to their tunable optical and photothermal properties by changing size, shape, and spatial arrangement.

RESULTS

In this study, self-integrated plasmonic hybrid nanogels (PHNs) are developed for spatiotemporally controllable drug delivery through light-driven conformational change and photothermally-boosted endosomal escape. PHNs are easily synthesized through the simultaneous integration of gold nanoparticles (GNPs), thermo-responsive poly (N-isopropyl acrylamide), and linker molecules during polymerization. Wave-optic simulations reveal that the size of the PHNs and the density of the integrated GNPs are crucial factors in modulating photothermal conversion. Several linkers with varying molecular weights are inserted for the optimal PHNs, and the alginate-linked PHN (A-PHN) achieves more than twofold enhanced heat conversion compared with others. Since light-mediated conformational changes occur transiently, drug delivery is achieved in a spatiotemporally controlled manner. Furthermore, light-induced heat generation from cellular internalized A-PHNs enables pinpoint cytosolic delivery through the endosomal rupture. Finally, the deeper penetration for the enhanced delivery efficiency by A-PHNs is validated using multicellular spheroid.

CONCLUSION

This study offers a strategy for synthesizing light-responsive nanocarriers and an in-depth understanding of light-modulated site-specific drug delivery.

Intracellular Dynamics of Extracellular Vesicles by Segmented Trajectory Analysis

The analysis of nanoparticle (NP) dynamics in live cell studies by video tracking provides detailed information on their interactions and trafficking in the cells. Although the video analysis is not yet routinely used in NP studies, the equipment suitable for the experiments is already available in most laboratories. Here, we compare trajectory patterns, diffusion coefficients, and particle velocities of NPs in A549 cells with a rather simple experimental setup consisting of a fluorescence microscope and openly available trajectory analysis software. The studied NPs include commercial fluorescent polymeric particles and two subpopulations of PC-3 cell-derived extracellular vesicles (EVs). As bioderived natural nanoparticles, the fluorescence intensities of the EVs limited the recording speed. Therefore, we studied the effect of the recording frame rate and analysis parameters to the trajectory results with bright fluorescent commercial NPs. We show that the trajectory classification and the apparent particle velocities are affected by the recording frame rate, while the diffusion constants stay comparable. The NP trajectory patterns were similar for all NP types and resembled intracellular vesicular transport. Interestingly, the EV movements were faster than the commercial NPs, which contrasts with their physical sizes and may indicate a greater role of the motor proteins in their intracellular transports.

Choosing the Probe for Single-Molecule Fluorescence Microscopy

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.

Biogenesis of Exosomes Laden with Metallic Silver-Copper Nanoparticles Liaised by Wheat Germ Agglutinin for Targeted Delivery of Therapeutics to Breast Cancer

The anticancer property of silver-copper metallic nanoparticles (AgCu-NPs) is of greater interest in cancer therapeutics; however, its off-target toxicity limits its therapeutic application. Exosomes emerge as one of the leading idiosyncratic nanocarrier choices for cancer therapeutics due to their size, stability, and phenotypic diversity; however, to encapsulate NPs in extracellular vesicles (EVs) without disrupting their inherited functions is far from the expectations. Here, the loading strategy of AgCu-NP conjugated with wheat germ agglutinin (AgCu-NP-WGA) in exosomes during biogenesis for the targeted delivery of anticancer therapeutics to breast cancer is reported. Based on the intrinsic mechanism of endocytosis of WGA, results show that internalization of WGA or AgCu-NP-WGA bypasses the lysosomal pathway and recycles in EVs. On the contrary, the transport of naked AgCu-NPs to lysosomes; mechanistically, an acidic environment causes oxidation of AgCu-NP. Next, the analysis of EVs harvested by differential centrifugation shows that only AgCu-NPs-WGA (Exo-NP) retain their metallic state. Furthermore, Exo-NP cytotoxicity results manifest that MCF10A-derived Exo-NPs are toxic to its homologous breast cancer cells (MCF-7 and MDA-MB 231) and nontoxic to heterologous cancers NC1-1975 and MCF 10A. In conclusion, this study shows the self-assembly of AgCu-NP in exosomes to target and deliver therapeutics for breast cancer.

Quantum Dots Tracking Endocytosis and Transport of Proteins Displayed by Mammalian Cells

Mammalian cell display technology uses eukaryotic protein expression system to display proteins on cell surfaces and has become an important method in biological research. Although mammalian cell display technology has many advantages and development potential, certain attributes of the displayed protein remain uncharacterized, such as whether the displayed proteins re-enter the cell and how displayed proteins move into the cell. Here, we present the endocytosis mechanism, motility behavior, and transport kinetics of displayed proteins determined using HaloTag as the displayed protein and quantum dot-based single-particle tracking. The displayed protein enters the cell through clathrin-mediated endocytosis and is transported through the cell in three stages, which is dependent on microfilaments and microtubules. The dynamic information obtained in this study provides answers to questions about endocytosis and postendocytosis transport of displayed proteins and, therefore, is expected to facilitate the development of surface display technology.

Activation of Non-Canonical Autophagic Pathway through Inhibition of Non-Integrin Laminin Receptor in Neuronal Cells

To fight neurodegenerative diseases, several therapeutic strategies have been proposed that, to date, are either ineffective or at the early preclinical stages. Intracellular protein aggregates represent the cause of about 70% of neurodegenerative disorders, such as Alzheimer’s disease. Thus, autophagy, i.e., lysosomal degradation of macromolecules, could be employed in this context as a therapeutic strategy. Searching for a compound that stimulates this process led us to the identification of a 37/67kDa laminin receptor inhibitor, NSC48478. We have analysed the effects of this small molecule on the autophagic process in mouse neuronal cells and found that NSC48478 induces the conversion of microtubule-associated protein 1A/1B-light chain 3 (LC3-I) into the LC3-phosphatidylethanolamine conjugate (LC3-II). Interestingly, upon NSC48478 treatment, the contribution of membranes to the autophagic process derived mainly from the non-canonical m-TOR-independent endocytic pathway, involving the Rab proteins that control endocytosis and vesicle recycling. Finally, qRT-PCR analysis suggests that, while the expression of key genes linked to canonical autophagy was unchanged, the main genes related to the positive regulation of endocytosis (pinocytosis and receptor mediated), along with genes regulating vesicle fusion and autolysosomal maturation, were upregulated under NSC48478 conditions. These results strongly suggest that 37/67 kDa inhibitor could be a useful tool for future studies in pathological conditions.

Measurements and characterization of the dynamics of tracer particles in an actin network

The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks. Surprisingly, the diffusion of a tracer particle in a network of a purified protein, actin, was found to conform to the continuous time random walk type (CTRW). We set out to resolve this discrepancy by studying the tracer particle diffusion using two different tracer particle sizes, in actin networks of different mesh sizes. We find that the ratio of tracer particle size to the characteristic length scale of a bio-polymer network plays a crucial role in determining the type of diffusion it performs. We find that the diffusion of the tracer particles has features of fBm when the particle is large compared to the mesh size, of normal diffusion when the particle is much smaller than the mesh size, and of the CTRW in between these two limits. Based on our findings, we propose and verify numerically a new model for the motion of the tracer in all regimes. Our model suggests that diffusion in actin networks consists of fBm of the tracer particle coupled with caging events with power-law distributed escape times.

Revealing Microtubule-Dependent Slow-Directed Motility by Single-Particle Tracking

Microtubules (MTs) are the main component of cytoskeletons, providing long tracks for cargo trafficking across the cytoplasm. In the past years, transport along MTs was frequently reported to be rapid directed motions with speeds of several micrometers per second, but is that all the truth? Using single-particle tracking, we roundly and precisely analyzed the dynamic behaviors of three kinds of cargoes transported along MTs in two types of cells. It was found that during the transport processes, the directed motions of the cargoes were frequently interrupted by nondirected motions which greatly reduced the translocation rate toward the nucleus. What is more, in addition to the widely reported rapid directed motions, a type of directed motions with most speeds below 0.5 μm/s occurred more frequently. On the whole, these slow directed motions took longer than the rapid directed motions and resulted in displacements same as those of the rapid ones. To sum up, while travelling along MTs toward the cell interior, endocytosed cargoes moved alternately in rapid-directed, slow-directed and nondirected modes. In this process, the rapid- and the slow-directed motions contributed almost equally to the cargoes' translocation. This work provides original insights into the transport on MTs, facilitating a more comprehensive understanding of intracellular trafficking.

Wheat Germ Agglutinin—From Toxicity to Biomedical Applications

Wheat germ agglutinin is a hevein class N-Acetylglucosamine–binding protein with specific toxicity and biomedical potential. It is extractable from wheat germ—a low-value byproduct of the wheat industry—using well–established extraction methods based on salt precipitation and affinity chromatography. Due to its N-Acetylglucosamine affinity, wheat germ agglutinin exhibits antifungal properties as well as cytotoxic properties. Its anticancer properties have been demonstrated for various cancer cells, and toxicity mechanisms are well described. Wheat germ agglutinin has been demonstrated as a viable solution for various biomedical and therapeutic applications, such as chemotherapy, targeted drug delivery, antibiotic-resistant bacteria monitoring and elimination. This is performed mostly in conjunction with nanoparticles, liposomes, and other carrier mechanisms via surface functionalization. Combined with abundant wheat byproduct sources, wheat germ agglutinin has the potential to improve the biomedical field considerably.

Real-Time Dissecting the Dynamics of Drug Transportation in the Live Brain

Brain diseases are becoming a more and more serious threat to human health. Many critical properties of the transport mechanisms of drugs in live brains remain poorly understood. In this work, single-particle tracking was used to dissect the transport dynamics of wheat germ agglutinin (WGA) in live brain and characterize the geometry and rheology of the extracellular space (ECS). The results revealed that the movements of WGA were influenced by the specific-binding molecules and the nature of the ECS. We further analyzed the mobility behaviors of WGA globally and quantitatively and found that movement of WGA in brain cells of acute slices was an active transport process associated with actin filaments and microtubules. This work paves the way for studies aiming at characterizing the biophysics of drug transport in the context of live brains, which may contribute to developing potential new therapeutic applications for brain diseases.

Inhibitory synaptic transmission tuned by Ca2+ and glutamate through the control of GABAA R lateral diffusion dynamics

The GABAergic synapses, a primary inhibitory synapse in the mammalian brain, is important for the normal development of brain circuits, and for the regulation of the excitation‐inhibition balance critical for brain function from the developmental stage throughout life. However, the molecular mechanism underlying the formation, maintenance, and modulation of GABAergic synapses is less understood compared to that of excitatory synapses. Quantum dot‐single particle tracking (QD‐SPT), a super‐resolution imaging technique that enables the analysis of membrane molecule dynamics at single‐molecule resolution, is a powerful tool to analyze the behavior of proteins and lipids on the plasma membrane. In this review, we summarize the recent application of QD‐SPT in understanding of GABAergic synaptic transmission. Here we introduce QD‐SPT experiments that provide further insights into the molecular mechanism supporting GABAergic synapses. QD‐SPT studies revealed that glutamate and Ca²⁺ signaling is involved in (a) the maintenance of GABAergic synapses, (b) GABAergic long‐term depression, and GABAergic long‐term potentiation, by specifically activating signaling pathways unique to each phenomenon. We also introduce a novel Ca²⁺ imaging technique to describe the diversity of Ca²⁺ signals that may activate the downstream signaling pathways that induce specific biological output.

Quantum Dot Labelling of Tepary Bean (Phaseolus acutifolius) Lectins by Microfluidics

Lectins are bioactive proteins with the ability to recognize cell membrane carbohydrates in a specific way. Diverse plant lectins have shown diagnostic and therapeutic potential against cancer, and their cytotoxicity against transformed cells is mediated through the induction of apoptosis. Previous works have determined the cytotoxic activity of a Tepary bean (Phaseolus acutifolius) lectin fraction (TBLF) and its anti-tumorigenic effect on colon cancer. In this work, lectins from the TBLF were additionally purified by ionic-exchange chromatography. Two peaks with agglutination activity were obtained: one of them was named TBL-IE2 and showed a single protein band in two-dimensional electrophoresis; this one was thus selected for coupling to quantum dot (QD) nanoparticles by microfluidics (TBL-IE2-QD). The microfluidic method led to low sample usage, and resulted in homogeneous complexes, whose visualization was achieved using multiphoton and transmission electron microscopy. The average particle size (380 nm) and the average zeta potential (-18.51 mV) were determined. The cytotoxicity of the TBL-IE2 and TBL-IE2-QD was assayed on HT-29 colon cancer cells, showing no differences between them (p ≤ 0.05), where the LC50 values were 1.0 × 10-3 and 1.7 × 10-3 mg/mL, respectively. The microfluidic technique allowed control of the coupling between the QD and the protein, substantially improving the labelling process, providing a rapid and efficient method that enabled the traceability of lectins. Future studies will focus on the potential use of the QD-labelled lectin to recognize tumor tissues.

Single Virus Tracking with Quantum Dots Packaged into Enveloped Viruses Using CRISPR

Labeling viruses with high-photoluminescence quantum dots (QDs) for single virus tracking provides a visual tool to aid our understanding of viral infection mechanisms. However, efficiently labeling internal viral components without modifying the viral envelope and capsid remains a challenge, and existing strategies are not applicable to most viruses. Here, we have devised a strategy using the clustered regularly interspaced short palindromic repeats (CRISPR) imaging system to label the nucleic acids of Pseudorabies virus (PRV) with QDs. In this strategy, QDs were conjugated to viral nucleic acids with the help of nuclease-deactivated Cas9/gRNA complexes in the nuclei of living cells and then packaged into PRV during virion assembly. The processes of PRV-QD adsorption, cytoplasmic transport along microtubules, and nuclear entry were monitored in real time in both Vero and HeLa cells, demonstrating the utility and efficiency of the strategy in the study of viral infection.

Single-Virus Tracking: From Imaging Methodologies to Virological Applications

Uncovering the mechanisms of virus infection and assembly is crucial for preventing the spread of viruses and treating viral disease. The technique of single-virus tracking (SVT), also known as single-virus tracing, allows one to follow individual viruses at different parts of their life cycle and thereby provides dynamic insights into fundamental processes of viruses occurring in live cells. SVT is typically based on fluorescence imaging and reveals insights into previously unreported infection mechanisms. In this review article, we provide the readers a broad overview of the SVT technique. We first summarize recent advances in SVT, from the choice of fluorescent labels and labeling strategies to imaging implementation and analytical methodologies. We then describe representative applications in detail to elucidate how SVT serves as a valuable tool in virological research. Finally, we present our perspectives regarding the future possibilities and challenges of SVT.

NanoPaint: A Tool for Rapid and Dynamic Imaging of Membrane Structural Plasticity at the Nanoscale

Single-particle tracking with quantum dots (QDs) constitutes a powerful tool to track the nanoscopic dynamics of individual cell membrane components unveiling their membrane diffusion characteristics. Here, the nano-resolved population dynamics of QDs is exploited to reconstruct the topography and structural changes of the cell membrane surface with high temporal and spatial resolution. For this proof-of-concept study, bright, small, and stable biofunctional QD nanoconstructs are utilized recognizing the endogenous neuronal cannabinoid receptor 1, a highly expressed and fast-diffusing membrane protein, together with a commercial point-localization microscope. Rapid QD diffusion on the axonal plasma membrane of cultured hippocampal neurons allows precise reconstruction of the membrane surface in less than 1 min with a spatial resolution of tens of nanometers. Access of the QD nanoconstructs to the synaptic cleft enables rapid 3D topological reconstruction of the entire presynaptic component. Successful reconstruction of membrane nano-topology and deformation at the second time-scale is also demonstrated for HEK293 cell filopodia and axons. Named "nanoPaint," this super-resolution imaging technique amenable to any endogenous transmembrane target represents a versatile platform to rapidly and accurately reconstruct the cell membrane nano-topography, thereby enabling the study of the rapid dynamic phenomena involved in neuronal membrane plasticity.

Wheat germ agglutinin liposomes with surface grafted cyclodextrins as bioadhesive dual-drug delivery nanocarriers to treat oral cells

Topical management of oral infection requires combined use of multiple classes of drugs and frequent dosing due to low drug retention rates. The sustained, co-delivery of drugs with different solubilities to cells using nanoparticle drug delivery systems remains a challenge. Here, we developed wheat germ agglutinin (WGA) conjugated liposomes with surface grafted cyclodextrin (WGA-liposome-CD) as bioadhesive dual-drug nanocarriers. We effectively encapsulated two physiochemically different drugs (ciprofloxacin and betamethasone) and demonstrated sustained co-drug release in saliva over a 24 h period in vitro. As proof of therapeutic utility in oral cells, we infected oral keratinocytes with Aggregatibacter actinomycetemcomitans, a bacterial pathogen responsible for chronic periodontal disease. Drug release, resulting from nanocarrier cell binding, produced a significant increase in oral cell survival and synergistically reduced inflammation. These results suggest that WGA-liposome-CD nanocarriers are novel cyto-adhesive candidates for delivering multiple drugs with sustained therapeutic activity for localized drug delivery to oral cells.

Real-time analysis of quantum dot labeled single porcine epidemic diarrhea virus moving along the microtubules using single particle tracking

In order to study the infection mechanism of porcine epidemic diarrhea virus (PEDV), which causes porcine epidemic diarrhea, a highly contagious enteric disease, we combined quantum dot labeled method, which could hold intact infectivity of the labeled viruses to the largest extent, with the single particle tracking technique to dynamically and globally visualize the transport behaviors of PEDVs in live Vero cells. Our results were the first time to uncover the dynamic characteristics of PEDVs moving along the microtubules in the host cells. It is found that PEDVs kept restricted motion mode with a relatively stable speed in the cell membrane region; while performed a slow-fast-slow velocity pattern with different motion modes in the cell cytoplasm region and near the microtubule organizing center region. In addition, the return movements of small amount of PEDVs were also observed in the live cells. Collectively, our work is crucial for understanding the movement mechanisms of PEDV in the live cells, and the proposed work also provided important references for further analysis and study on the infection mechanism of PEDVs.

Single-Particle Tracking Reveals the Sequential Entry Process of the Bunyavirus Severe Fever with Thrombocytopenia Syndrome Virus

The Bunyavirales is one of the largest groups of RNA viruses, which encompasses many strains that are highly pathogenic to animals and humans. Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne bunyavirus that causes severe disease in humans, with a high fatality rate of up to 30%. To date, the entry process of bunyavirus infection remains obscure. Here, using quantum dot (QD)-based single-particle tracking and multicolor imaging, the dynamic molecular process of SFTSV entry and penetration is systematically dissected. The results show that internalization of SFTSV into host cells is initiated by recruiting clathrin onto the cell membrane for the formation of clathrin-coated pits and further pinching off from the plasma membrane to form discrete vesicles. These vesicular carriers further deliver virions to Rab5+ early endosomes, and then to Rab7+ late endosomes. The intracellular transport of virion-carrying endocytic vesicles is dependent first on actin filaments at the cell periphery, and then on microtubules toward the cell interior. The final fusion events occur at ≈15-60 min post-entry, and are triggered by the acidic environment at ≈pH5.6 within the late endosomes. These results reveal the multistep SFTSV entry process and the dynamic virus-host interactions involved.

Uncovering the Rab5-Independent Autophagic Trafficking of Influenza A Virus by Quantum-Dot-Based Single-Virus Tracking

Autophagy is closely related to virus-induced disease and a comprehensive understanding of the autophagy-associated infection process of virus will be significant for developing more effective antiviral strategies. However, many critical issues and the underlying mechanism of autophagy in virus entry still need further investigation. Here, this study unveils the involvement of autophagy in influenza A virus entry. The quantum-dot-based single-virus tracking technique assists in real-time, prolonged, and multicolor visualization of the transport process of individual viruses and provides unambiguous dissection of the autophagic trafficking of viruses. These results reveal that roughly one-fifth of viruses are ferried into cells for infection by autophagic machineries, while the remaining are not. A comprehensive overview of the endocytic- and autophagic-trafficking process indicates two distinct trafficking pathway of viruses, either dependent on Rab5-positive endosomes or autophagosomes, with striking similarities. Expressing dominant-negative mutant of Rab5 suggests that the autophagic trafficking of viruses is independent on Rab5. The present study provides dynamic, precise, and mechanistic insights into the involvement of autophagy in virus entry, which contributes to a better understanding of the relationship between autophagy and virus entry. The quantum-dot-based single-virus tracking is proven to hold promise for autophagy-related fundamental research.

A "Driver Switchover" Mechanism of Influenza Virus Transport from Microfilaments to Microtubules

When infecting host cells, influenza virus must move on microfilaments (MFs) at the cell periphery and then move along microtubules (MTs) through the cytosol to reach the perinuclear region for genome release. But how viruses switch from the actin roadway to the microtubule highway remains obscure. To settle this issue, we systematically dissected the role of related motor proteins in the transport of influenza virus between cytoskeletal filaments in situ and in real-time using quantum dot (QD)-based single-virus tracking (SVT) and multicolor imaging. We found that the switch between MF- and MT-based retrograde motor proteins, myosin VI (myoVI) and dynein, was responsible for the seamless transport of viruses from MFs to MTs during their infection. After virus entry by endocytosis, both the two types of motor proteins are attached to virus-carrying vesicles. MyoVI drives the viruses on MFs with dynein on the virus-carrying vesicle hitchhiking. After role exchanges at actin-microtubule intersections, dynein drives the virus along MTs toward the perinuclear region with myoVI remaining on the vesicle moving together. Such a "driver switchover" mechanism has answered the long-pending question of how viruses switch from MFs to MTs for their infection. It will also facilitate in-depth understanding of endocytosis.

NIR-I-to-NIR-II fluorescent nanomaterials for biomedical imaging and cancer therapy

This review discusses the recent development of nanomaterials with NIR-I-to-NIR-II fluorescence and their applications in biomedical imaging and cancer therapy.

Retrograde interferon-gamma signaling induces major histocompatibility class I expression in human-induced pluripotent stem cell-derived neurons

Objective

Injury-associated axon-intrinsic signals are thought to underlie pathogenesis and progression in many neuroinflammatory and neurodegenerative diseases, including multiple sclerosis (MS). Retrograde interferon gamma (IFN γ) signals are known to induce expression of major histocompatibility class I (MHC I) genes in murine axons, thereby increasing the susceptibility of these axons to attack by antigen-specific CD8⁺ T cells. We sought to determine whether the same is true in human neurons.

Methods

A novel microisolation chamber design was used to physically isolate and manipulate axons from human skin fibroblast-derived induced pluripotent stem cell (iPSC)-derived neuron-enriched neural aggregates. Fluorescent retrobeads were used to assess the fraction of neurons with projections to the distal chamber. Axons were treated with IFN γ for 72 h and expression of MHC class I and antigen presentation genes were evaluated by RT-PCR and immunofluorescence.

Results

Human iPSC-derived neural stem cells maintained as 3D aggregate cultures in the cell body chamber of polymer microisolation chambers extended dense axonal projections into the fluidically isolated distal chamber. Treatment of these axons with IFN γ resulted in upregulation of MHC class I and antigen processing genes in the neuron cell bodies. IFN γ-induced MHC class I molecules were also anterogradely transported into the distal axon.

Interpretation

These results provide conclusive evidence that human axons are competent to express MHC class I molecules, suggesting that inflammatory factors enriched in demyelinated lesions may render axons vulnerable to attack by autoreactive CD8⁺ T cells in patients with MS. Future work will be aimed at identifying pathogenic anti-axonal T cells in these patients.

A new role for human dyskerin in vesicular trafficking

Dyskerin is an essential, conserved, multifunctional protein found in the nucleolus, whose loss of function causes the rare genetic diseases X‐linked dyskeratosis congenita and Hoyeraal‐Hreidarsson syndrome. To further investigate the wide range of dyskerin's biological roles, we set up stable cell lines able to trigger inducible protein knockdown and allow a detailed analysis of the cascade of events occurring within a short time frame. We report that dyskerin depletion quickly induces cytoskeleton remodeling and significant alterations in endocytic Ras‐related protein Rab‐5A/Rab11 trafficking. These effects arise in different cell lines well before the onset of telomere shortening, which is widely considered the main cause of dyskerin‐related diseases. Given that vesicular trafficking affects many homeostatic and differentiative processes, these findings add novel insights into the molecular mechanisms underlining the pleiotropic manifestation of the dyskerin loss‐of‐function phenotype.

Single-molecule fluorescence microscopy review: shedding new light on old problems

Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called 'green revolution', has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called 'super-resolution' fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques.

Bioelectric and Morphological Response of Liquid-Covered Human Airway Epithelial Calu-3 Cell Monolayer to Periodic Deposition of Colloidal 3-Mercaptopropionic-Acid Coated CdSe-CdS/ZnS Core-Multishell Quantum Dots

Lung epithelial cells are extensively exposed to nanoparticles present in the modern urban environment. Nanoparticles, including colloidal quantum dots (QDs), are also considered to be potentially useful carriers for the delivery of drugs into the body. It is therefore important to understand the ways of distribution and the effects of the various types of nanoparticles in the lung epithelium. We use a model system of liquid-covered human airway epithelial Calu-3 cell cultures to study the immediate and long-term effects of repeated deposition of colloidal 3-mercaptopropionic-acid coated CdSe-CdS/ZnS core-multishell QDs on the lung epithelial cell surface. By live confocal microscope imaging and by QD fluorescence measurements we show that the QD permeation through the mature epithelial monolayers is very limited. At the time of QD deposition, the transepithelial electrical resistance (TEER) of the epithelial monolayers transiently decreased, with the decrement being proportional to the QD dose. Repeated QD deposition, once every six days for two months, lead to accumulation of only small amounts of the QDs in the cell monolayer. However, it did not induce any noticeable changes in the long-term TEER and the molecular morphology of the cells. The colloidal 3-mercaptopropionic-acid coated CdSe-CdS/ZnS core-multishell QDs could therefore be potentially used for the delivery of drugs intended for the surface of the lung epithelia during limited treatment periods.

Simultaneous Visualization of Parental and Progeny Viruses by a Capsid-Specific HaloTag Labeling Strategy

Real-time, long-term, single-particle tracking (SPT) provides us an opportunity to explore the fate of individual viruses toward understanding the mechanisms underlying virus infection, which in turn could lead to the development of therapeutics against viral diseases. However, the research focusing on the virus assembly and egress by SPT remains a challenge because established labeling strategies could neither specifically label progeny viruses nor make them distinguishable from the parental viruses. Herein, we have established a temporally controllable capsid-specific HaloTag labeling strategy based on reverse genetic technology. VP26, the smallest pseudorabies virus (PrV) capsid protein, was fused with HaloTag protein and labeled with the HaloTag ligand during virus replication. The labeled replication-competent recombinant PrV harvested from medium can be applied directly in SPT experiments without further modification. Thus, virus infectivity, which is critical for the visualization and analysis of viral motion, is retained to the largest extent. Moreover, progeny viruses can be distinguished from parental viruses using diverse HaloTag ligands. Consequently, the entire course of virus infection and replication can be visualized continuously, including virus attachment and capsid entry, transportation of capsids to the nucleus along microtubules, docking of capsids on the nucleus, endonuclear assembly of progeny capsids, and the egress of progeny viruses. In combination with SPT, the established strategy represents a versatile means to reveal the mechanisms and dynamic global picture of the life cycle of a virus.

Nanoparticle-assisted optical tethering of endosomes reveals the cooperative function of dyneins in retrograde axonal transport

Dynein-dependent transport of organelles from the axon terminals to the cell bodies is essential to the survival and function of neurons. However, quantitative knowledge of dyneins on axonal organelles and their collective function during this long-distance transport is lacking because current technologies to do such measurements are not applicable to neurons. Here, we report a new method termed nanoparticle-assisted optical tethering of endosomes (NOTE) that made it possible to study the cooperative mechanics of dyneins on retrograde axonal endosomes in live neurons. In this method, the opposing force from an elastic tether causes the endosomes to gradually stall under load and detach with a recoil velocity proportional to the dynein forces. These recoil velocities reveal that the axonal endosomes, despite their small size, can recruit up to 7 dyneins that function as independent mechanical units stochastically sharing load, which is vital for robust retrograde axonal transport. This study shows that NOTE, which relies on controlled generation of reactive oxygen species, is a viable method to manipulate small cellular cargos that are beyond the reach of current technology.

Threshold Dose of Three Types of Quantum Dots (QDs) Induces Oxidative Stress Triggers DNA Damage and Apoptosis in Mouse Fibroblast L929 Cells

Although it has been reported that fluorescent quantum dots (QDs) have obvious acute toxic effects in vitro, their toxic effects at low doses or threshold doses are still unknown. Therefore, we evaluated the biological histocompatibility and in vitro toxicity of three types of QDs at threshold doses. Also, we compared the toxic effects of QDs with different raw chemical compositions and sizes. The results showed that low concentrations of QDs (≤7 μg/mL) had no obvious effect on cell viability and cell membrane damage, oxidative damage, cell apoptosis or DNA damage. However, QD exposure led to a significant cytotoxicity at higher doses (≥14 μg/mL) and induced abnormal cellular morphology. In addition, when comparing the three types of QDs, 2.2 nm CdTe QDs exposure showed a significantly increased proportion of apoptotic cells and significant DNA damage, suggesting that size and composition contribute to the toxic effects of QDs. Based on these discussions, it was concluded that the concentration (7 μg/mL) may serve as a threshold level for these three types of QDs only in L929 fibroblasts, whereas high concentrations (above 14 μg/mL) may be toxic, resulting in inhibition of proliferation, induction of apoptosis and DNA damage in L929 fibroblasts.

Rapid and Quantitative Detection of Avian Influenza A(H7N9) Virions in Complex Matrices Based on Combined Magnetic Capture and Quantum Dot Labeling

Avian influenza A(H7N9) virus, which emerged in China in the spring of 2013, has infected hundreds of people and resulted in many deaths. Herein, a rapid and quantitative assay is proposed for the one-step detection of H7N9 virions. Immunomagnetic nanospheres (IMNs) and antibody-conjugated quantum dots (Ab-QDs) are simultaneously employed to capture and identify the target virus, leading to a high efficiency, good specificity, and strong anti-interference ability. Moreover, this reliable detection assay, which combines the efficient magnetic enrichment and the unique photophysical properties of QDs, can achieve a high sensitivity for a low detection limit. At the same time, this detection strategy shows great flexibility for employment in a variety of fluorescence detectors, including fluorescence spectrometry, microscope assays, and handheld UV lamp tests. Furthermore, our one-step detection strategy induces very little change in the integrity of the vulnerable virions, which enables additional genotyping testing following the fluorescence detection. The present study, thus, reports a rapid and quantitative approach for the detection of H7N9 virions based on simultaneous magnetic capture and QD labeling, thereby providing a higher probability for detection and therefore faster diagnosis of H7N9-infected patients.

Quantum dots for quantitative imaging: from single molecules to tissue

Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes.

Cytotoxicity of nucleus-targeting fluorescent gold nanoclusters

Gold nanoclusters (AuNCs) with ultra small sizes and unique fluorescence properties have shown promising potential for imaging the nuclei of living cells. However, little is known regarding the potential cytotoxicity of AuNCs after they enter the cell nucleus. The aim of this study is to investigate whether and how nucleus-targeting AuNCs affect the normal functioning of cells. Highly stable, water-soluble and bright fluorescent Au25NCs (the core of each nanocluster is composed of 25 gold atoms) were synthesized. Specific targeting of Au25NCs to the cell nucleus was achieved by conjugating the TAT peptide to the Au25NCs. Cell viability, cell morphology, cell apoptosis/necrosis, reactive oxygen species (ROS) level and mitochondrial membrane potential examinations were performed on different cell lines exposed to the nucleus-targeting Au25NCs. We found that the nucleus-targeting Au25NCs caused cell apoptosis in a dose-dependent manner. A possible mechanism for the cytotoxicity of the nucleus-targeting Au25NCs was proposed as follows: the nucleus-targeting Au25NCs induce the production of ROS, resulting in the oxidative degradation of mitochondrial components, in turn leading to apoptosis via a mitochondrial damage pathway. This work facilitates a better understanding of the toxicity of AuNCs, especially nucleus-targeting AuNCs.

Three-dimensional tracking of Rab5- and Rab7-associated infection process of influenza virus

Three-dimensional (3D) single-particle tracking (SPT) techniques have been widely reported. However, the 3D SPT technique remains poorly used for solving actual biological problems. In this work, a quantum dots (QDs)-based single-particle tracking technique is utilized to explore the Rab5- and Rab7-associated infection behaviors of influenza virus in three dimensions with a set of easily-attained equipment by the fast and accurate centroid method for 3D SPT. The experimental results indicate that Rab5 protein takes part in the virus infection process from the cell periphery to the perinuclear region, while Rab7 protein is mainly involved in the intermittent and confined movements of the virus in the perinuclear region. Evidently, the transition process of the virus-containing vesicles from early to late endosomes might occur during the intermittent movement in the perinuclear region. These findings reveal distinct dynamic behaviors of Rab5- and Rab7-positive endosomes in the course of the intracellular transport of viruses. This work is helpful in understanding the intracellular transport of cargoes.

Real-time visualizing and tracing of HSV-TK/GCV suicide gene therapy by near-infrared fluorescent quantum dots

Exploring intracellular behavior of suicide gene is significant for improving the efficacy and safety of herpes simplex virus thymidine kinase gene/ganciclovir (HSV-TK/GCV) system in cancer therapy. Molecular imaging represents a powerful tool to understand gene transportation and function dynamics. In this work, we reported a quantum-dot-based technique for revealing the procedure of HSV-TK/GCV suicide gene therapy by constructing covalent linkage between near-infrared fluorescent quantum dots (QDs) and TK gene. This stable QD labeling did not influence either the QDs fluorescence or the biological activity of TK gene. Furthermore, we visualized and dynamically traced the intracellular behavior antitumor effect of TK gene in vitro and in vivo. It is demonstrated that TK gene was shuttled to the nucleus after a-24 h treatment; at that time the single dose of GCV administration exerts the gradually increasing lethal effect until to 72 h. Real-time tracing the formation of hepatocellular carcinoma treated with HSV-TK/GCV suicide gene system in vivo by QD-based NIR fluorescence imaging provides useful insight toward QD-based theranostics in future cancer therapy.

Exploring sialic acid receptors-related infection behavior of avian influenza virus in human bronchial epithelial cells by single-particle tracking

Human respiratory tract epithelial cells are the portals of human infection with influenza viruses. However, the infection pathway of individual avian influenza viruses in human respiratory cells remains poorly reported so far. The single-particle tracking technique (SPT) is a powerful tool for studying the transport mechanism of biomolecules in live cells. In this work, we use quantum dots to label avian influenza H9N2 virus and elaborate on the infection mechanism of the virus in human bronchial epithelial (HBE) cells using a three-dimensional SPT technique. We have found that the H9N2 virus can infect HBE cells directly and the virus infection follows an actin filament- and microtubule-dependent process with a three-stage pattern. The transport behaviors show a high degree of consistency between the sialic acid receptors and the influenza virus. Real-time SPT provides dynamic evidence of the sialic acid receptors-related infection behavior of the avian influenza virus in live cells. The study of the influence of sialic acid receptors on virus infection may contribute to a better understanding of the cross-species transmission of the avian influenza virus.

Counterion-enhanced cyanine dye loading into lipid nano-droplets for single-particle tracking in zebrafish

Superior brightness of fluorescent nanoparticles places them far ahead of the classical fluorescent dyes in the field of biological imaging. However, for in vivo applications, inorganic nanoparticles, such as quantum dots, are limited due to the lack of biodegradability. Nano-emulsions encapsulating high concentrations of organic dyes are an attractive alternative, but classical fluorescent dyes are inconvenient due to their poor solubility in the oil and their tendency to form non-fluorescent aggregates. This problem was solved here for a cationic cyanine dye (DiI) by substituting its perchlorate counterion for a bulky and hydrophobic tetraphenylborate. This new dye salt, due to its exceptional oil solubility, could be loaded at 8 wt% concentration into nano-droplets of controlled size in the range 30-90 nm. Our 90 nm droplets, which contained >10,000 cyanine molecules, were >100-fold brighter than quantum dots. This extreme brightness allowed, for the first time, single-particle tracking in the blood flow of live zebrafish embryo, revealing both the slow and fast phases of the cardiac cycle. These nano-droplets showed minimal cytotoxicity in cell culture and in the zebrafish embryo. The concept of counterion-based dye loading provides a new effective route to ultra-bright lipid nanoparticles, which enables tracking single particles in live animals, a new dimension of in vivo imaging.

Fast and high-accuracy localization for three-dimensional single-particle tracking

We report a non-iterative localization algorithm that utilizes the scaling of a three-dimensional (3D) image in the axial direction and focuses on evaluating the radial symmetry center of the scaled image to achieve the desired single-particle localization. Using this approach, we analyzed simulated 3D particle images by wide-field microscopy and confocal microscopy respectively, and the 3D trajectory of quantum dots (QDs)-labeled influenza virus in live cells. Both applications indicate that the method can achieve 3D single-particle localization with a sub-pixel precision and sub-millisecond computation time. The precision is almost the same as that of the iterative nonlinear least-squares 3D Gaussian fitting method, but with two orders of magnitude higher computation speed. This approach can reduce considerably the time and costs for processing the large volume data of 3D images for 3D single-particle tracking, which is especially suited for 3D high-precision single-particle tracking, 3D single-molecule imaging and even new microscopy techniques.

Functionalized quantum dots induce proinflammatory responses in vitro: the role of terminal functional group-associated endocytic pathways

PEGylation has been applied as an effective strategy of surface functionalization to improve the stability and reduce non-specific binding of quantum dots (QDs). However, its effects on the proinflammatory properties of QDs and the underlying mechanism have not been well elucidated yet. Herein, the proinflammatory effects of PEGylated CdSe/ZnS QDs with an amphiphilic polymer coating (PEG-pQDs) were investigated in human pulmonary epithelial cells and macrophages by evaluating the cytokine/chemokine production. The results showed that the proinflammatory effects of PEG-pQDs were strongly associated with the functional groups (-COOH, -NH2, -OH, and -OCH3) at the end of PEG chain. COOH-PEG-pQDs demonstrated the most proinflammatory effects followed by NH2-PEG-pQDs and HO-PEG-pQDs with CH3O-PEG-pQDs exhibiting the least proinflammatory effects. The proinflammatory effects of PEG-pQDs relied on lipid raft- and class A scavenger receptor (SRA)-dependent endocytic pathways as well as the downstream NF-κB and MAPK signaling cascades. COOH-PEG-pQDs were selectively internalized by lipid raft- and SRA-mediated endocytosis, which consequently activated NF-κB signaling pathway. On the other hand, NH2-PEG-pQDs and HO-PEG-pQDs were mostly internalized via lipid raft-mediated endocytosis, thereby activating p38 MAPK/AP-1 signaling cascades. These data revealed a critical role of terminal functional group-associated endocytic pathways in the proinflammatory responses induced by PEGylated QDs in human pulmonary epithelial cells and macrophages.

Self-biotinylation and site-specific double labeling of baculovirus using quantum dots for single-virus in-situ tracking

Single-virus labeling and tracking represent a powerful tool to study virus-cell interactions. Using baculovirus as a model, here we developed a biochemical method for labeling both the viral envelope and the viral capsid of a virus. Viral envelope of the baculovirus AcMNPV was self-biotinylated and site-specifically conjugated with quantum dots (QDs) following one-step binding reaction, while the viral nucleocapsid was site-specifically labeled with green fluorescent protein (GFP) during viral replication. The established procedure of labeling did not affect viral infectivity, showing that the double-labeled virus retained functional structure and could be tracked for viral localization and movement in the host cells. The double-labeled virus also demonstrated the potential to be used for in-situ and real-time visualizing the internalization of a single viral particle into the host cells. Furthermore, the disassembly processes of the viral envelope and the viral nucleocapsid could be monitored for a long period of time (up to 2 h). Using the established method, several interaction details between the labeled baculoviruses and the host cells have been revealed. Given its advantages in high efficiency, high specificity, convenience and the maintenance of viral infectivity, the established approach provides a promising means for elucidating virus-cell interactions.

In vitro translocation experiments with RxLR-reporter fusion proteins of Avr1b from Phytophthora sojae and AVR3a from Phytophthora infestans fail to demonstrate specific autonomous uptake in plant and animal cells

Plant-pathogenic oomycetes have a large set of secreted effectors that can be translocated into their host cells during infection. One group of these effectors are the RxLR effectors for which it has been shown, in a few cases, that the RxLR motif is important for their translocation. It has been suggested that the RxLR-leader sequences alone are enough to translocate the respective effectors into eukaryotic cells through binding to surface-exposed phosphoinositol-3-phosphate. These conclusions were primary based on translocation experiments conducted with recombinant fusion proteins whereby the RxLR leader of RxLR effectors (i.e., Avr1b from Phytophthora sojae) were fused to the green fluorescent protein reporter-protein. However, we failed to observe specific cellular uptake for a comparable fusion protein where the RxLR leader of the P. infestans AVR3a was fused to monomeric red fluorescent protein. Therefore, we reexamined the ability of the reported P. sojae AVR1b RxLR leader to enter eukaryotic cells. Different relevant experiments were performed in three independent laboratories, using fluorescent reporter fusion constructs of AVR3a and Avr1b proteins in a side-by-side comparative study on plant tissue and human and animal cells. We report that we were unable to obtain conclusive evidence for specific RxLR-mediated translocation.

Single molecule methods with applications in living cells

Our knowledge about dynamic processes in biological cells systems has been obtained roughly on two levels of detail; molecular level experiments with purified components in test tubes and system wide experiments with indirect readouts in living cells. However, with the development of single molecule methods for application in living cells, this partition has started to dissolve. It is now possible to perform detailed biophysical experiments at high temporal resolution and to directly observe processes at the level of molecules in living cells. In this review we present single molecule methods that can easily be implemented by readers interested to venture into this exciting and expanding field. We also review some recent studies where single molecule methods have been used successfully to answer biological questions as well as some of the most common pitfalls associated with these methods.