A prism combination for near isotropic fluorescence excitation by total internal reflection

FluoroTensor: Identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning

The identification of photobleaching steps in single molecule fluorescence imaging is a well-established procedure for analysing the stoichiometries of molecular complexes. Nonetheless, the method is challenging with protein fluorophores because of the high levels of noise, rapid bleaching and highly variable signal intensities, all of which complicate methods based on statistical analyses of intensities to identify bleaching steps. It has recently been shown that deep learning by convolutional neural networks can yield an accurate analysis with a relatively short computational time. We describe here an improved use of such an approach that detects bleaching events even in the first time point of observation, and we have included this within an integrated software package incorporating fluorescence spot detection, colocalisation, tracking, FRET and photobleaching step analyses of single molecules or complexes. This package, known as FluoroTensor, is written in Python with a self-explanatory user interface.

Controlling Water Delivery to an Electrochemical Interface with Surfactants

Most electrochemical reactions require delivery of protons, often from water, to surface-adsorbed species. However, water also acts as a competitor to many such processes by directly reacting with the electrode, which necessitates using water in small amounts. Controlling the water content and structure near the surface is an important frontier in directing the reactivity and selectivity of electrochemical reactions. Surfactants accumulate near surfaces, and therefore, they can be used as agents to control interfacial water. Using mid-IR spectro-electrochemistry, we show that a modest concentration (1 mM) of the cationic surfactant CTAB in mixtures of 10 M water in an organic solvent (dDMSO) has a large effect on the interfacial water concentration, changing it by up to ∼35% in the presence of an applied potential. The major cause of water content change is displacement due to the accumulation or depletion of surfactants driven by potential. Two forces drive the surfactants to the electrode: the applied potential and the hydrophobic interactions with the water in the bulk. We have quantified their competition by varying the water content in the bulk. To our knowledge, for the first time, we have identified the electrochemical equivalent of the hydrophobic drive. For our system, a change in applied potential of 1 V has the same effect as adding a 0.55 mole fraction of water to the bulk. This work illustrates the significance of surfactants in the partitioning of water between the bulk and the surface and paves the way toward engineering interfacial water structures for controlling electrochemical reactions.

High-robustness intravascular photoacoustic endoscope with a hermetically sealed opto-sono capsule

The prevailing open-structure intravascular photoacoustic (IVPA) endoscope emits a gradually deformed laser beam with exposed optical or acoustical components bearing pollution and damage in arterial lumen. Deformed laser beam scanning, which causes a low excitation efficiency and serious deterioration of the transverse resolution, is a current big obstacle to the application of photoacoustic endoscopy in intravascular imaging. Hence, the stable and reliable IVPA endoscope is indispensable. In this letter, we designed a high-robustness intravascular photoacoustic (HR-IVPA) endoscope with a hermetically sealed opto-sono capsule. The distal end of the opto-sono capsule was integrated with miniaturized optics, including a customized C-Lens and a customized total-reflection prism (TRP). The TRP was first applied to a side-viewing IVPA endoscope, featuring a high-throughput energy coupling efficiency of 90% and a cut-off free damage threshold. The optical path structure of the endoscope, optimized using optical simulation tools, overcame the ambiguous focus shift caused by chromatic dispersion and achieved a waist size of 20 µm as well as a focus depth of 4 mm in water at the wavelength of 1200 nm. The mass phantom experiments demonstrated that the HR-IVPA endoscope afforded repeatable IVPA images with a relatively constant signal-to-noise ratio (SNR) of about ∼41.8 dB and a transverse resolution of about ∼23 µm. The imaging experiments of the stent and lipid further demonstrated the robustness and validated the imaging ability of the HR-IVPA endoscope, which opens a new avenue for improving the endoscopic imaging capability, strengthening the credible detection of atherosclerotic cardiovascular disease.

Tuning fluorophore excitation in a total-internal-reflection-fluorescence microscopy

In a total-internal-reflection-fluorescence-microscopy method, there is anisotropy in the polarized evanescent wave. Since the evanescent wave is used as an excitation field, the mentioned anisotropy is a disadvantage in using the total-internal-reflection-fluorescence-microscopy technique. Therefore, by theoretical and analytical approaches, and based on the Fresnel coefficients, the effect of three dielectrics media on the anisotropy of the evanescent wave is investigated. Following that, a proper combination of the cover glass, oil immersion, and prism for both living and non-living samples is suggested that not only enhances the intensity of the evanescent wave, but also and importantly, decreases the essential anisotropy of the evanescent wave.

A surface-bound molecule that undergoes optically biased Brownian rotation

Developing molecular systems with functions analogous to those of macroscopic machine components, such as rotors, gyroscopes and valves, is a long-standing goal of nanotechnology. However, macroscopic analogies go only so far in predicting function in nanoscale environments, where friction dominates over inertia. In some instances, ratchet mechanisms have been used to bias the ever-present random, thermally driven (Brownian) motion and drive molecular diffusion in desired directions. Here, we visualize the motions of surface-bound molecular rotors using defocused fluorescence imaging, and observe the transition from hindered to free Brownian rotation by tuning medium viscosity. We show that the otherwise random rotations can be biased by the polarization of the excitation light field, even though the associated optical torque is insufficient to overcome thermal fluctuations. The biased rotation is attributed instead to a fluctuating-friction mechanism in which photoexcitation of the rotor strongly inhibits its diffusion rate.

Chapter 7: Total internal reflection fluorescence microscopy

Total internal reflection fluorescence microscopy (TIRFM), also known as evanescent wave microscopy, is used in a wide range of applications, particularly to view single molecules attached to planar surfaces and to study the position and dynamics of molecules and organelles in living culture cells near the contact regions with the glass coverslip. TIRFM selectively illuminates fluorophores only in a very thin (less than 100 nm deep) layer near the substrate, thereby avoiding excitation of fluorophores outside this subresolution optical section. This chapter reviews the history, current applications in cell biology and biochemistry, basic optical theory, combinations with numerous other optical and spectroscopic approaches, and a range of setup methods, both commercial and custom.

Multidimensional single-molecule imaging in live cells using total-internal-reflection fluorescence microscopy

We have developed a wide-field total-internal-reflection fluorescence microscope capable of imaging single molecules in live cells, resolved in both wavelength and polarization. We show fluorescence resonance energy transfer between single pairs of fluorescent molecules bound to signaling receptors in the plasma membrane of live cells and demonstrate the importance of polarization discrimination in addition to wavelength separation.

Dynamics of actomyosin interactions in relation to the cross-bridge cycle

Transient kinetic measurements of the actomyosin ATPase provided the basis of the Lymn-Taylor model for the cross-bridge cycle, which underpins current models of contraction. Following the determination of the structure of the myosin motor domain, it has been possible to introduce probes at defined sites and resolve the steps in more detail. Probes have been introduced in the Dicytostelium myosin II motor domain via three routes: (i) single tryptophan residues at strategic locations throughout the motor domain; (ii) green fluorescent protein fusions at the N and C termini; and (iii) labelled cysteine residues engineered across the actin-binding cleft. These studies are interpreted with reference to motor domain crystal structures and suggest that the tryptophan (W501) in the relay loop senses the lever arm position, which is controlled by the switch 2 open-to-closed transition at the active site. Actin has little effect on this process per se. A mechanism of product release is proposed in which actin has an indirect effect on the switch 2 and lever arm position to achieve mechanochemical coupling. Switch 1 closing appears to be a key step in the nucleotide-induced actin dissociation, while its opening is required for the subsequent activation of product release. This process has been probed with F239W and F242W substitutions in the switch 1 loop. The E706K mutation in skeletal myosin IIa is associated with a human myopathy. To simulate this disease we investigated the homologous mutation, E683K, in the Dictyostelium myosin motor domain.

Protonation, Photobleaching, and Photoactivation of Yellow Fluorescent Protein (YFP 10C): A Unifying Mechanism

Yellow fluorescent protein (YFP 10C) is widely used as a probe in biology, but its complex photochemistry gives rise to unusual behavior that requires fuller definition. Here we characterize the kinetics of protonation and reversible bleaching over time scales of picoseconds to hours. Stopped-flow and pressure-jump techniques showed that protonation of the fluorescent YFP(-) anion state is two-step with a slow transition that accounts for blinking of 527 nm emission at the single molecule level on the seconds time scale. Femtosecond spectroscopy revealed that the protonated excited-state (YFPH*) decayed predominantly by a radiationless mechanism, but emission at 460 nm was detected within the first picosecond. Limited excited-state proton transfer leads to 527 nm emission characteristic of the YFP(-*) anion. Prolonged continuous wave illumination at the peak of YFP(-) absorbance (514 nm) yields, irreversibly, a weakly fluorescent product that absorbs at 390 nm. This "photobleaching" process also gives a different species (YFPHrb) that absorbs at 350/430 nm and spontaneously regenerates YFP(-) in the dark on the time scale of hours but can be photoactivated by UV light to regenerate YFP(-) within seconds, via a ground-state protonated intermediate. Using a pulsed laser for photobleaching resulted in decarboxylation of YFP as indicated by the mass spectrum. These observations are accounted for in a unifying kinetic scheme.

Total internal reflection fluorescence microscopy: technical innovations and novel applications

Recent years have seen the introduction of novel techniques and applications of total internal reflection fluorescence microscopy (TIRFM). Key technical achievements include miniaturization, enhanced depth resolution, reduction of detection volumes and the combination of TIRFM with other microscopic techniques. Novel applications have concentrated on single-molecule detection (e.g. of cellular receptors), imaging of exocytosis or endocytosis, measurements of adhesion foci of microtubules, and studies of the localization, activity and structural arrangement of specific ion channels. In addition to conventional fluorescent dyes, genetically engineered fluorescent proteins are increasingly being used to measure molecular conformations or intermolecular distances by fluorescence resonance energy transfer.