Quantitative determination of fluorescence labeling implemented in cell cultures.

BACKGROUND: Labeling efficiency is a crucial parameter in fluorescence applications, especially when studying biomolecular interactions. Current approaches for estimating the yield of fluorescent labeling have critical drawbacks that usually lead them to be inaccurate or not quantitative. RESULTS: We present a method to quantify fluorescent-labeling efficiency that addresses the critical issues marring existing approaches. The method operates in the same conditions of the target experiments by exploiting a ratiometric evaluation with two fluorophores used in sequential reactions. We show the ability of the protocol to extract reliable quantification for different fluorescent probes, reagents concentrations, and reaction timing and to optimize labeling performance. As paradigm, we consider the labeling of the membrane-receptor TrkA through 4'-phosphopantetheinyl transferase Sfp in living cells, visualizing the results by TIRF microscopy. This investigation allows us to find conditions for demanding single and multi-color single-molecule studies requiring high degrees of labeling. CONCLUSIONS: The developed method allows the quantitative determination and the optimization of staining efficiency in any labeling strategy based on stable reactions.

Fast-diffusing p75NTR monomers support apoptosis and growth cone collapse by neurotrophin ligands.

The p75 neurotrophin (NT) receptor (p75NTR) plays a crucial role in balancing survival-versus-death decisions in the nervous system. Yet, despite 2 decades of structural and biochemical studies, a comprehensive, accepted model for p75NTR activation by NT ligands is still missing. Here, we present a single-molecule study of membrane p75NTR in living cells, demonstrating that the vast majority of receptors are monomers before and after NT activation. Interestingly, the stoichiometry and diffusion properties of the wild-type (wt) p75NTR are almost identical to those of a receptor mutant lacking residues previously believed to induce oligomerization. The wt p75NTR and mutated (mut) p75NTR differ in their partitioning in cholesterol-rich membrane regions upon nerve growth factor (NGF) stimulation: We argue that this is the origin of the ability of wt p75NTR , but not of mut p75NTR, to mediate immature NT (proNT)-induced apoptosis. Both p75NTR forms support proNT-induced growth cone retraction: We show that receptor surface accumulation is the driving force for cone collapse. Overall, our data unveil the multifaceted activity of the p75NTR monomer and let us provide a coherent interpretative frame of existing conflicting data in the literature.

Impact of electrostatic doping on carrier concentration and mobility in InAs nanowires.

We fabricate dual-gated electric double layer (EDL) field effect transistors based on InAs nanowires gated with an ionic liquid, and we perform electrical transport measurements in the temperature range from room temperature to 4.2 K. By adjusting the spatial distribution of ions inside the ionic liquid employed as gate dielectric, we electrostatically induce doping in the nanostructures under analysis. We extract low-temperature carrier concentration and mobility in very different doping regimes from the analysis of current-voltage characteristics and transconductances measured exploiting global back-gating. In the liquid gate voltage interval from -2 to 2 V, carrier concentration can be enhanced up to two orders of magnitude. Meanwhile, the effect of the ionic accumulation on the nanowire surface turns out to be detrimental to the electron mobility of the semiconductor nanostructure: the electron mobility is quenched irrespectively to the sign of the accumulated ionic species. The reported results shine light on the effective impact on crucial transport parameters of EDL gating in semiconductor nanodevices and they should be considered when designing experiments in which electrostatic doping of semiconductor nanostructures via electrolyte gating is involved.

Orbital Tuning of Tunnel Coupling in InAs/InP Nanowire Quantum Dots.

We report results on the control of barrier transparency in InAs/InP nanowire quantum dots via the electrostatic control of the device electron states. Recent works demonstrated that barrier transparency in this class of devices displays a general trend just depending on the total orbital energy of the trapped electrons. We show that a qualitatively different regime is observed at relatively low filling numbers, where tunneling rates are rather controlled by the axial configuration of the electron orbital. Transmission rates versus filling are further modified by acting on the radial configuration of the orbitals by means of electrostatic gating, and the barrier transparency for the various orbitals is found to evolve as expected from numerical simulations. The possibility to exploit this mechanism to achieve a controlled continuous tuning of the tunneling rate of an individual Coulomb blockade resonance is discussed.

Morphology control of single-crystal InSb nanostructures by tuning the growth parameters.

Research interest in indium antimonide (InSb) has increased significantly in recent years owing to its intrinsic properties and the consequent opportunities to implement next-generation quantum devices. Hence, the precise, reproducible control over morphology and crystalline quality becomes of paramount importance for a practical quantum-device technology. Here, we investigate the growth of InSb nanostructures with different morphologies on InAs stems without pre-growth efforts (patterning). InSb nanostructures such as nanowires (1D), nanoflags (2D) and nanocubes (3D) have been realized by means of Au-assisted chemical beam epitaxy by tailoring the growth parameters like growth temperature, precursor fluxes, sample rotation and substrate orientation. Through morphological and crystallographic characterization, all the as-grown InSb 2D nanostructures are found to be single-crystalline with zinc blende structure, free from any defects such as stacking faults and twin planes. The existence of two families of 2D nanostructures, characterised by an aperture angle at the base of 145° and 160°, is observed and modelled. This study provides useful guidelines for the controlled growth of high-quality InSb nanostructures with different shape.

Simultaneous two-photon imaging of intracellular chloride concentration and pH in mouse pyramidal neurons in vivo.

Intracellular chloride ([Cl-]i) and pH (pHi) are fundamental regulators of neuronal excitability. They exert wide-ranging effects on synaptic signaling and plasticity and on development and disorders of the brain. The ideal technique to elucidate the underlying ionic mechanisms is quantitative and combined two-photon imaging of [Cl-]i and pHi, but this has never been performed at the cellular level in vivo. Here, by using a genetically encoded fluorescent sensor that includes a spectroscopic reference (an element insensitive to Cl- and pH), we show that ratiometric imaging is strongly affected by the optical properties of the brain. We have designed a method that fully corrects for this source of error. Parallel measurements of [Cl-]i and pHi at the single-cell level in the mouse cortex showed the in vivo presence of the widely discussed developmental fall in [Cl-]i and the role of the K-Cl cotransporter KCC2 in this process. Then, we introduce a dynamic two-photon excitation protocol to simultaneously determine the changes of pHi and [Cl-]i in response to hypercapnia and seizure activity.

Thermoelectric Conversion at 30 K in InAs/InP Nanowire Quantum Dots.

We demonstrate high-temperature thermoelectric conversion in InAs/InP nanowire quantum dots by taking advantage of their strong electronic confinement. The electrical conductance G and the thermopower S are obtained from charge transport measurements and accurately reproduced with a theoretical model accounting for the multilevel structure of the quantum dot. Notably, our analysis does not rely on the estimate of cotunnelling contributions, since electronic thermal transport is dominated by multilevel heat transport. By taking into account two spin-degenerate energy levels we are able to evaluate the electronic thermal conductance K and investigate the evolution of the electronic figure of merit ZT as a function of the quantum dot configuration and demonstrate ZT ≈ 35 at 30 K, corresponding to an electronic efficiency at maximum power close to the Curzon-Ahlborn limit.

Conductometric Sensing with Individual InAs Nanowires.

In this work, we isolate individual wurtzite InAs nanowires and fabricate electrical contacts at both ends, exploiting the single nanostructures as building blocks to realize two different architectures of conductometric sensors: (a) the nanowire is drop-casted onto-supported by-a SiO2/Si substrate, and (b) the nanowire is suspended at approximately 250 nm from the substrate. We test the source-drain current upon changes in the concentration of humidity, ethanol, and NO2, using synthetic air as a gas carrier, moving a step forward towards mimicking operational environmental conditions. The supported architecture shows higher response in the mid humidity range (50% relative humidity), with shorter response and recovery times and lower detection limit with respect to the suspended nanowire. These experimental pieces of evidence indicate a minor role of the InAs/SiO2 contact area; hence, there is no need for suspended nanostructures to improve the sensing performance. Moreover, the sensing capability of single InAs nanowires for detection of NO2 and ethanol in the ambient atmosphere is reported and discussed.

Workers' Exposure to Nano-Objects with Different Dimensionalities in R&D Laboratories: Measurement Strategy and Field Studies.

With the increasing interest in the potential benefits of nanotechnologies, concern is still growing that they may present emerging risks for workers. Various strategies have been developed to assess the exposure to nano-objects and their agglomerates and aggregates (NOAA) in the workplace, integrating different aerosol measurement instruments and taking into account multiple parameters that may influence NOAA toxicity. The present study proposes a multi-metric approach for measuring and sampling NOAA in the workplace, applied to three case studies in laboratories each dedicated to materials with different shapes and dimensionalities: graphene, nanowires, and nanoparticles. The study is part of a larger project with the aim of improving risk management tools in nanomaterials research laboratories. The harmonized methodology proposed by the Organization for Economic Cooperation and Development (OECD) has been applied, including information gathering about materials and processes, measurements with easy-to-use and hand-held real-time devices, air sampling with personal samplers, and off-line analysis using scanning electron microscopy. Significant values beyond which an emission can be attributed to the NOAA production process were identified by comparison of the particle number concentration (PNC) time series and the corresponding background levels in the three laboratories. We explored the relations between background PNC and microclimatic parameters. Morphological and elemental analysis of sampled filters was done to identify possible emission sources of NOAA during the production processes: rare particles, spherical, with average diameter similar to the produced NOAA were identified in the nanoparticles laboratory, so further investigation is recommended to confirm the potential for worker exposure. In conclusion, the information obtained should provide a valuable basis for improving risk management strategies in the laboratory at work.

Peptide-Based Stealth Nanoparticles for Targeted and pH-Triggered Delivery.

Stealth agents are extensively investigated as a means by which to prolong nanostructure residence time in the bloodstream by avoiding uptake by the reticuloendothelial system. Unfortunately, commonly used agents such as poly(ethylene glycol) can adversely impact targeting efficiency and promote immune reaction by the host organism. Therefore, there is an increasing interest in developing biocompatible, non-PEGylated organic nanostructures able to perform targeted delivery to increase the efficacy of liposomal technology. Here, a lipopeptide is presented that can be mixed with lipids commonly used in liposomal formulations in percentages ranging from 20% to 60% w/w. The resulting vesicles are thermally and chemically stable. The peptide coating limits serum-protein adsorption even upon prolonged incubation in pure serum in physiological conditions, outperforming PEGylated liposomes. This architecture can be easily modified to allow straightforward derivatization by standard bio-orthogonal conjugation. Upon derivatization with an anti-transferrin receptor aptamer, these vesicles show highly selective cellular internalization with minimal nonspecific uptake and pH-triggered doxorubicin release.

Local anodic oxidation on hydrogen-intercalated graphene layers: oxide composition analysis and role of the silicon carbide substrate.

We investigate nanoscale local anodic oxidation (LAO) on hydrogen-intercalated graphene grown by controlled sublimation of silicon carbide (SiC). Scanning probe microscopy was used as a lithographic and characterization tool in order to investigate the local properties of the nanofabricated structures. The anomalous thickness observed after the graphene oxidation process is linked to the impact of LAO on the substrate. Micro-Raman (µ-Raman) spectroscopy was employed to demonstrate the presence of two oxidation regimes depending on the applied bias. We show that partial and total etching of monolayer graphene can be achieved by tuning the bias voltage during LAO. Finally, a complete compositional characterization was achieved by scanning electron microscopy and energy dispersive spectroscopy.

Self-aggregation propensity of the Tat peptide revealed by UV-Vis, NMR and MD analyses.

By a combination of UV-Vis analyses, NMR-based diffusion measurements and MD simulations we have demonstrated for the first time that the HIV-1 Tat arginine-rich peptide (Tat11) is able to self-aggregate in both its fluorescently labeled and unlabeled variants. We propose Tat11 dimerization as the dominant aggregation process and show that the associated equilibrium constant increases ten-fold by labeling with the standard TAMRA dye. Also, we extend similar conclusions to other cationic cell penetrating peptides (CPPs), such as Antennapedia (Ant) and nona-arginine (R9).

GHz Electroluminescence Modulation in Nanoscale Subwavelength Emitters.

We investigate light emission from nanoscale point-sources obtained in hybrid metal-GaAs nanowires embedding two sharp axial Schottky barriers. Devices are obtained via the formation of Ni-rich metallic alloy regions in the nanostructure body thanks to a technique of controlled thermal annealing of Ni/Au electrodes. In agreement with recent findings, visible-light electroluminescence can be observed upon suitable voltage biasing of the junctions. We investigate the time-resolved emission properties of our devices and demonstrate an electrical modulation of light generation up to 1 GHz. We explore different drive configurations and discuss the intrinsic bottlenecks of the present device architecture. Our results demonstrate a novel technique for the realization of fast subwavelength light sources with possible applications in sensing and microscopy beyond the diffraction limit.

Gate-Tunable Spatial Modulation of Localized Plasmon Resonances.

We demonstrate localization and field-effect spatial control of the plasmon resonance in semiconductor nanostructures, using scattering-type scanning near-field optical microscopy in the mid-infrared region. We adopt InAs nanowires embedding a graded doping profile to modulate the free carrier density along the axial direction. Our near-field measurements have a spatial resolution of 20 nm and demonstrate the presence of a local resonant feature whose position can be controlled by a back-gate bias voltage. In the present implementation, field-effect induces a modulation of the free carrier density profile yielding a spatial shift of the plasmon resonance of the order of 100 nm. We discuss the relevance of our electrically tunable nanoplasmonic architectures in view of innovative optoelectronic devices concepts.

Spatiotemporal Fluctuation Analysis: A Powerful Tool for the Future Nanoscopy of Molecular Processes.

The enormous wealth of information available today from optical microscopy measurements on living samples is often underexploited. We argue that spatiotemporal analysis of fluorescence fluctuations using multiple detection channels can enhance the performance of current nanoscopy methods and provide further insight into dynamic molecular processes of high biological relevance.

Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells.

In a living cell, the movement of biomolecules is highly regulated by the cellular organization into subcompartments that impose barriers to diffusion, can locally break the spatial isotropy, and ultimately guide these molecules to their targets. Despite the pivotal role of these processes, experimental tools to fully probe the complex connectivity (and accessibility) of the cell interior with adequate spatiotemporal resolution are still lacking. Here, we show how the heterogeneity of molecular dynamics and the location of barriers to molecular motion can be mapped in live cells by exploiting a two-dimensional (2D) extension of the pair correlation function (pCF) analysis. Starting from a time series of images collected for the same field of view, the resulting 2D pCF is calculated in the proximity of each point for each time delay and allows us to probe the spatial distribution of the molecules that started from a given pixel. This 2D pCF yields an accurate description of the preferential diffusive routes. Furthermore, we combine this analysis with the image-derived mean-square displacement approach and gain information on the average nanoscopic molecular displacements in different directions. Through these quantities, we build a fluorescence-fluctuation-based diffusion tensor that contains information on speed and directionality of the local dynamical processes. Contrary to classical fluorescence correlation spectroscopy and related methods, this combined approach can distinguish between isotropic and anisotropic local diffusion. We argue that the measurement of this iMSD tensor will contribute to advance our understanding of the role played by the intracellular environment in the regulation of molecular diffusion at the nanoscale.

Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes.

Spatial distribution and dynamics of plasma-membrane proteins are thought to be modulated by lipid composition and by the underlying cytoskeleton, which forms transient barriers to diffusion. So far this idea was probed by single-particle tracking of membrane components in which gold particles or antibodies were used to individually monitor the molecules of interest. Unfortunately, the relatively large particles needed for single-particle tracking can in principle alter the very dynamics under study. Here, we use a method that makes it possible to investigate plasma-membrane proteins by means of small molecular labels, specifically single GFP constructs. First, fast imaging of the region of interest on the membrane is performed. For each time delay in the resulting stack of images the average spatial correlation function is calculated. We show that by fitting the series of correlation functions, the actual protein "diffusion law" can be obtained directly from imaging, in the form of a mean-square displacement vs. time-delay plot, with no need for interpretative models. This approach is tested with several simulated 2D diffusion conditions and in live Chinese hamster ovary cells with a GFP-tagged transmembrane transferrin receptor, a well-known benchmark of membrane-skeleton-dependent transiently confined diffusion. This approach does not require extraction of the individual trajectories and can be used also with dim and dense molecules. We argue that it represents a powerful tool for the determination of kinetic and thermodynamic parameters over very wide spatial and temporal scales.

Ligand signature in the membrane dynamics of single TrkA receptor molecules.

The neurotrophin receptor TrkA (also known as NTRK1) is known to be crucially involved in several physio-pathological processes. However, a clear description of the early steps of ligand-induced TrkA responses at the cell plasma membrane is missing. We have exploited single particle tracking and TIRF microscopy to study TrkA membrane lateral mobility and changes of oligomerization state upon binding of diverse TrkA agonists (NGF, NGF R100E HSANV mutant, proNGF and NT-3). We show that, in the absence of ligands, most of the TrkA receptors are fast moving monomers characterized by an average diffusion coefficient of 0.47 µm(2)/second; about 20% of TrkA molecules move at least an order of magnitude slower and around 4% are almost immobile within regions of about 0.6 µm diameter. Ligand binding results in increased slow and/or immobile populations over the fast one, slowing down of non-immobile trajectories and reduction of confinement areas, observations that are consistent with the formation of receptor dimeric and oligomeric states. We demonstrate that the extent of TrkA lateral mobility modification is strictly ligand dependent and that each ligand promotes distinct trajectory patterns of TrkA receptors at the cell membrane (ligand 'fingerprinting' effect). This ligand signature of receptor dynamics results from a differential combination of receptor-binding affinity, intracellular effectors recruited in the signalling platforms and formation of signalling and/or recycling endosome precursors. Thus, our data uncover a close correlation between the initial receptor membrane dynamics triggered upon binding and the specific biological outcomes induced by different ligands for the same receptor.

Ligand-induced dynamics of neurotrophin receptors investigated by single-molecule imaging approaches.

Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.

Acoustofluidics and whole-blood manipulation in surface acoustic wave counterflow devices.

On-chip functional blocks for sample preprocessing are necessary elements for the implementation of fully portable micrototal analysis systems (µTAS). We demonstrate and characterize the microparticle and whole-blood manipulation capabilities of surface acoustic wave (SAW) driven counterflow micropumps. The motion of suspended cells in this system is governed by the two dominant acoustic forces associated with the scattered SAW (of wavelength λf): acoustic-radiation force and acoustic-streaming Stokesian drag force. We show that by reducing the microchannel height (h) beyond a threshold value the balance of these forces is shifted toward the acoustic-radiation force and that this yields control of two different regimes of microparticle dynamics. In the regime dominated by the acoustic radiation force (h ≲ λf), microparticles are collected in the seminodes of the partial standing sound-wave arising from reflections off microchannel walls. This enables the complete separation of plasma and corpuscular components of whole blood in periodical predetermined positions without any prior sample dilution. Conversely, in the regime dominated by acoustic streaming (h ≫ λf), the microbeads follow vortical streamlines in a pattern characterized by three different phases during microchannel filling. This makes it possible to generate a cell-concentration gradient within whole-blood samples, a behavior not previously reported in any acoustic-streaming device. By careful device design, a new class of SAW pumping devices is presented that allows the manipulation and pretreatment of whole-blood samples for portable and integrable biological chips and is compatible with hand-held battery-operated devices.