Second-harmonic generation of biological interfaces: probing the membrane protein bacteriorhodopsin and imaging membrane potential around GFP molecules at specific sites in neuronal cells of C. elegans

On Effect of Chloroform on Electrical Activity of Proteinoids

Proteinoids, or thermal proteins, produce hollow microspheres in aqueous solutions. Ensembles of the microspheres produce endogenous spikes of electrical activity, similar to that of neurons. To make the first step toward the evaluation of the mechanisms of such electrical behaviour, we decided to expose proteinoids to chloroform. We found that while chloroform does not inhibit the electrical oscillations of proteinoids, it causes substantial changes in the patterns of electrical activity. Namely, incremental chloroform exposure strongly affects proteinoid microsphere electrical activity across multiple metrics. As chloroform levels rise, the spike potential drops from 0.9 mV under control conditions to 0.1 mV at 25 mg/mL. This progressive spike potential decrease suggests chloroform suppresses proteinoid electrical activity. The time between spikes, the interspike period, follows a similar pattern. Minimal chloroform exposure does not change the average interspike period, while higher exposures do. It drops from 23.2 min under control experiments to 3.8 min at 25 mg/mL chloroform, indicating increased frequency of the electrical activity. These findings might lead to a deeper understanding of the electrical activity of proteinoids and their potential application in the domain of bioelectronics.

Digital pathology and spatial omics in steatohepatitis: Clinical applications and discovery potentials

Steatohepatitis with diverse etiologies is the most common histological manifestation in patients with liver disease. However, there are currently no specific histopathological features pathognomonic for metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, or metabolic dysfunction-associated steatotic liver disease with increased alcohol intake. Digitizing traditional pathology slides has created an emerging field of digital pathology, allowing for easier access, storage, sharing, and analysis of whole-slide images. Artificial intelligence (AI) algorithms have been developed for whole-slide images to enhance the accuracy and speed of the histological interpretation of steatohepatitis and are currently employed in biomarker development. Spatial biology is a novel field that enables investigators to map gene and protein expression within a specific region of interest on liver histological sections, examine disease heterogeneity within tissues, and understand the relationship between molecular changes and distinct tissue morphology. Here, we review the utility of digital pathology (using linear and nonlinear microscopy) augmented with AI analysis to improve the accuracy of histological interpretation. We will also discuss the spatial omics landscape with special emphasis on the strengths and limitations of established spatial transcriptomics and proteomics technologies and their application in steatohepatitis. We then highlight the power of multimodal integration of digital pathology augmented by machine learning (ML)algorithms with spatial biology. The review concludes with a discussion of the current gaps in knowledge, the limitations and premises of these tools and technologies, and the areas of future research.

Label-Free Imaging of Membrane Potentials by Intramembrane Field Modulation, Assessed by Second Harmonic Generation Microscopy

Optical interrogation of cellular electrical activity has proven itself essential for understanding cellular function and communication in complex networks. Voltage-sensitive dyes are important tools for assessing excitability but these highly lipophilic sensors may affect cellular function. Label-free techniques offer a major advantage as they eliminate the need for these external probes. In this work, it is shown that endogenous second-harmonic generation (SHG) from live cells is highly sensitive to changes in transmembrane potential (TMP). Simultaneous electrophysiological control of a living human embryonic kidney (HEK293T) cell, through a whole-cell voltage-clamp reveals a linear relation between the SHG intensity and membrane voltage. The results suggest that due to the high ionic strengths and fast optical response of biofluids, membrane hydration is not the main contributor to the observed field sensitivity. A conceptual framework is further provided that indicates that the SHG voltage sensitivity reflects the electric field within the biological asymmetric lipid bilayer owing to a nonzero χeff(2) tensor. Changing the TMP without surface modifications such as electrolyte screening offers high optical sensitivity to membrane voltage (≈40% per 100 mV), indicating the power of SHG for label-free read-out. These results hold promise for the design of a non-invasive label-free read-out tool for electrogenic cells.

All-Atom Quantum Mechanical Calculation of the Second-Harmonic Generation of Fluorescent Proteins

Fluorescent proteins (FPs) are biotags of choice for second-harmonic imaging microscopy (SHIM). Because of their large size, computing their second-harmonic generation (SHG) response represents a great challenge for quantum chemistry. In this contribution, we propose a new all-atom quantum mechanics methodology to compute SHG of large systems. This is now possible because of two recent implementations: the tight-binding GFN2-xTB method to optimize geometries and a related version of the simplified time-dependent density functional theory (sTD-DFT-xTB) to evaluate quadratic response functions. In addition, a new dual-threshold configuration selection scheme is introduced to reduce the computational costs while retaining overall similar accuracy. This methodology was tested to evaluate the SHG of the proteins iLOV and bacteriorhodopsin (bR). In the case of bR, quantitative agreement with respect to experiment was reached for the out-of-resonance low-energy part of the β_HRS frequency dispersion. This work paves the way toward an accurate prediction of the SHG of large structures-a requirement for the design of new and improved SHIM biotags.

Harmonic Generation Microscopy 2.0: New Tricks Empowering Intravital Imaging for Neuroscience

Optical harmonic generation, e.g., second- (SHG) and third-harmonic generation (THG), provides intrinsic contrasts for three-dimensional intravital microscopy. Contrary to two-photon excited fluorescence (TPEF), however, they have found relatively specialized applications, such as imaging collagenous and non-specific tissues, respectively. Here we review recent advances that broaden the capacity of SHG and THG for imaging the central nervous system in particular. The fundamental contrast mechanisms are reviewed as they encode novel information including molecular origin, spectroscopy, functional probes, and image analysis, which lay foundations for promising future applications in neuroscience.

Challenging compounds for calculating molecular second hyperpolarizabilities: the triplet state of the trimethylenemethane diradical and two derivatives

The second hyperpolarizability γ of trimethylenemethane (TMM) and two 1,3-dipole derivatives (NXA and OXA) in their triplet ground state has been evaluated at the UCCSD(T) level with the d-aug-cc-pVDZ extended basis set, highlighting that γ decreases from TMM to NXA and OXA, following the opposite order of their permanent dipole moments. These results are then used to benchmark a broad range of levels of approximation. So, the UMP2, UMP4, and UCCSD methods can be used to characterize γ of TMM and NXA but not of OXA. In that case, the large field-induced charge transfer contribution is difficult to handle using the MPn methods and only the UCCSD method provides values close to the UCCSD(T) reference. Turning to the performance of DFT with typical exchange-correlation functionals, the UM06-2X functional, which contains 54% of HF exchange, performs very well with a maximum of 4.5% of difference with respect to the reference values. On the other hand, employing less HF exchange leads to an overestimation of the responses whereas range-separated hybrids generally underestimate the second hyperpolarizabilities. Finally, the use of spin-projected methods for these 1,3-dipole triplet molecules has a little impact since the spin contamination is almost negligible.

Engineering a genetically-encoded SHG chromophore by electrostatic targeting to the membrane

Although second harmonic generation (SHG) microscopy provides unique imaging advantages for voltage imaging and other biological applications, genetically-encoded SHG chromophores remain relatively unexplored. SHG only arises from non-centrosymmetric media, so an anisotropic arrangement of chromophores is essential to provide strong SHG signals. Here, inspired by the mechanism by which K-Ras4B associates with plasma membranes, we sought to achieve asymmetric arrangements of chromophores at the membrane-cytoplasm interface using the fluorescent protein mVenus. After adding a farnesylation motif to the C-terminus of mVenus, nine amino acids composing its β-barrel surface were replaced by lysine, forming an electrostatic patch. This protein (mVe9Knus-CVIM) was efficiently targeted to the plasma membrane in a geometrically defined manner and exhibited SHG in HEK293 cells. In agreement with its design, mVe9Knus-CVIM hyperpolarizability was oriented at a small angle (~7.3°) from the membrane normal. Genetically-encoded SHG chromophores could serve as a molecular platform for imaging membrane potential.

Excited state electronic structures of 5,10-methenyltetrahydrofolate and 5,10-methylenetetrahydrofolate determined by Stark spectroscopy

Folates are ubiquitous cofactors that participate in a wide variety of critical biological processes. 5,10-Methenyltetrahydrofolate and its photodegradation product 5,10-methylenetetrahydrofolate are both associated with the light-driven DNA repair protein DNA photolyase and its homologues (e.g., cryptochromes). The excited state electronic properties of these folate molecules have been studied here using Stark spectroscopy and complementary quantum calculations. The tetrahydrofolates have relatively large difference dipole moments (ca. 6-8 Debye) and difference polarizabilities (ca. 100 Å(3)). This extensive excited state charge redistribution appears to be due largely to the pendant p-aminobenzoic acid group, which helps shuttle charge over the entirety of the molecule. Simple calculations based on the experimental difference dipole moments suggest that tetrahydrofolates should have large two photon cross sections sufficient to enable two photon microscopy to selectively detect and follow folate-containing proteins both in vitro and in vivo.

SECOND-HARMONIC GENERATION OF FLUORESCENT PROTEINS

We theoretically study the second-order nonlinear optical properties of six fluorescent proteins (FPs), such as green fluorescent protein (GFP), BFP, enhanced BFP (eBFP), CFP, YFP, and DsRed. To begin with, the geometries of all these FP chromophores are optimized at B3LYP/6-311++G** level in a water medium and the polarized continuum model (PCM in water) method is adopted. Using a time-dependent density functional theory (TDDFT) method, the electronic structures and excited-state properties of chromophores are determined. Here we employ TDDFT combining with the sum-over-states (SOS) method to calculate the first-order hyperpolarizability for second-harmonic generation (SHG) optical process. Moreover, we discuss the origin of the nonlinear optical response and determine what caused the variation of first-order hyperpolarizability. Our calculations show that the charge transfers of π → π* in the central conjugated structure and p → π* charge transfers from the side chain R1 to conjugated structure of chromophores markedly affect the first-order hyperpolarizability.

Excited state charge redistribution and dynamics in the donor-π-acceptor flavin derivative ABFL

Chromophores containing a donor-π-acceptor (D-π-A) motif have been shown to exhibit many interesting photophysical properties. The lowest electronic transition of a flavin derivative containing this motif, azobenzylflavin (ABFL), has previously been shown to be highly sensitive to solvent environment and hydrogen bonding ligands. To better understand this sensitivity, we have investigated the excited state charge redistribution and dynamics of ABFL in a low-dielectric, non-hydrogen bonding solvent by steady-state Stark and femtosecond optical transient absorption spectroscopies. The Stark measurements reveal the difference dipole moment, Δμ01, between the ground and first excited states to be 22.3 ± 0.9 D. The direction of Δμ01 in the molecular frame was assigned with the aid of TD-DFT and finite field calculations, verifying the hypothesis that electron density moves from the diethylaniline donor to the flavin acceptor in the excited state. The magnitude of the difference dipole moment was used to estimate the hyperpolarizability of ABFL, β0 = 720 × 10(-30) esu. Subsequent excited state decay via charge recombination was shown to take place in a few picoseconds. The data was best fit to a kinetic model composed of a sub-picosecond internal conversion step from S2→S1, followed by a 5 ps decay to the ground state. A competing process involving formation of an additional long-lived state from S1 was also observed. Cyclic voltammetry shows one oxidation and two reduction waves and is completely reversible. This analysis lays the groundwork for developing new flavin dyads with the desired excited electronic state properties for applications such as nonlinear optical devices, molecular electronics applications, or dye-sensitized solar cells.

Imaging voltage in neurons

In the last decades, imaging membrane potential has become a fruitful approach to study neural circuits, especially in invertebrate preparations with large, resilient neurons. At the same time, particularly in mammalian preparations, voltage imaging methods suffer from poor signal to noise and secondary side effects, and they fall short of providing single-cell resolution when imaging of the activity of neuronal populations. As an introduction to these techniques, we briefly review different voltage imaging methods (including organic fluorophores, SHG chromophores, genetic indicators, hybrid, nanoparticles, and intrinsic approaches) and illustrate some of their applications to neuronal biophysics and mammalian circuit analysis. We discuss their mechanisms of voltage sensitivity, from reorientation, electrochromic, or electro-optical phenomena to interaction among chromophores or membrane scattering, and highlight their advantages and shortcomings, commenting on the outlook for development of novel voltage imaging methods.

Second-harmonic generation in GFP-like proteins

The second-order nonlinear optical properties of green fluorescent proteins (GFPs), such as the photoswitchable Dronpa and enhanced GFP (EGFP), have been studied at both the theoretical and experimental levels. In the case of Dronpa, both approaches are consistent in showing the rather counterintuitive result of a larger second-order nonlinear polarizability (or first hyperpolarizability, beta) for the protonated state, which has a higher transition energy, than for the deprotonated, fluorescent state with its absorption at lower energy. Moreover, the value of beta for the protonated form of Dronpa is among the highest reported for proteins. In addition to the pH dependence, we have found a wavelength dependence in the beta values. These properties are essential for the practical use of Dronpa or other GFP-like fluorescent proteins as second-order nonlinear fluorophores for symmetry-sensitive nonlinear microscopy imaging and as nonlinear optical sensors for electrophysiological processes. An accurate value of the first hyperpolarizability is also essential for any qualitative analysis of the nonlinear images.

Synthesis of chromophores combining second harmonic generation and two photon induced fluorescence properties

The design of new chromophores presenting simultaneous SHG and TPEF properties is reported.

Upper limits of dielectric permittivity modulation in bacteriorhodopsin films

A theoretical study of light-induced modulation of the dielectric permittivity in bacteriorhodopsin films has been done (including B--> M and B --> Q transitions). Analysis of dielectric permittivity modulation enables us to determine the fundamental limits of BR to be used in a holographic data storage system, together with the optimum experimental and material conditions. In order to carry out this analysis, the macroscopic dielectric permittivity was related to the microscopic polarizability of the three states of BR considered (B, M and Q). This parameter was calculated using a modelization procedure that includes the effect of ASP85, TRP86, and TYR185 amino acid residues (the B3LYP/6-31+ G(*) method was used for the calculations). Good concordance between theoretical calculations and experimental data was found for the linear optical properties (absorption wavelength, transition dipole moment, and dielectric permittivity modulation). The theoretical upper limits of Deltaepsilson at 750 nm (far from the resonance of the molecule) in a randomly oriented material are about 0.01 and 0.012 for B--> M and B--> Q transitions, respectively. The values of Deltaepsilon obtained were used to simulate diffraction efficiencies (eta) of a volume phase hologram recorded in a BR film. The high absorptive losses at low wavelengths (about 625 nm ) cause an interesting behavior, since the highest Deltaepsilom do not produce the greatest eta. The highest eta is produced for a hologram thickness in the range of 900-1000 microm and working wavelength of 700-750 nm.

Imaging of Caenorhabditis elegans neurons by second-harmonic generation and two-photon excitation fluorescence

Second-harmonic generation (SHG) and two-photon excitation fluorescence (TPEF) are relatively new and promising tools for the detailed imaging of biological samples and processes at the microscopic level. By exploiting these nonlinear phenomena phototoxicity and photobleaching effects on the specimens are reduced dramatically. The main target of this work was the development of a compact inexpensive and reliable experimental apparatus for nonlinear microscopy measurements. Femtosecond laser pulses were utilized for excitation. We achieved high-resolution imaging and mapping of Caenorhabditis elegans (C. elegans) neurons and muscular structures of the pharynx, at the microscopic level by performing SHG and TPEF measurements. By detecting nonlinear phenomena such as SHG and TPEF it is feasible to extract valuable information concerning the structure and the function of nematode neurons.

Second harmonic imaging of membrane potential of neurons with retinal

We present a method to optically measure and image the membrane potential of neurons, using the nonlinear optical phenomenon of second harmonic generation (SHG) with a photopigment retinal as the chromophore [second harmonic retinal imaging of membrane potential (SHRIMP)]. We show that all-trans retinal, when adsorbed to the plasma membrane of living cells, can report on the local electric field via its change in SHG. Using a scanning mode-locked Ti-sapphire laser, we collect simultaneous two-photon excited fluorescence (TPEF) and SHG images of retinal-stained kidney cells and cultured pyramidal neurons. Patch clamp experiments on neurons stained with retinal show an increase of 25% in SHG intensity per 100-mV depolarization. Our data are the first demonstration of optical measurements of membrane potential of mammalian neurons with SHG. SHRIMP could have wide applicability in neuroscience and, by modifying rhodopsin, could in principle be subject for developing genetically engineered voltage sensors.

Video-rate nonlinear microscopy of neuronal membrane dynamics with genetically encoded probes

Biological membranes decorated with suitable contrast agents give rise to nonlinear optical signals such as two-photon fluorescence and harmonic up-conversion when illuminated with ultra-short, high-intensity pulses of infrared laser light. Microscopic images based on these nonlinear contrasts were acquired at video or higher frame rates by scanning a focused illuminating spot rapidly across neural tissues. The scan engine relied on an acousto-optic deflector (AOD) to produce a fast horizontal raster and on corrective prisms to offset the AOD-induced dispersion of the ultra-short excitation light pulses in space and time. Two membrane-bound derivatives of the green fluorescent protein (GFP) were tested as nonlinear contrast agents. Synapto-pHluorin, a pH-sensitive GFP variant fused to a synaptic vesicle membrane protein, provided a time-resolved fluorescent read-out of neurotransmitter release at genetically specified synaptic terminals in the intact brain. Arrays of dually lipidated GFP molecules at the plasma membrane generated intense two-photon fluorescence but no detectable second-harmonic power. Comparison with second-harmonic generation by membranes stained with a synthetic styryl dye suggested that the genetically encoded chromophore arrangement lacked the orientational anisotropy and/or dipole density required for efficient coherent scattering of the incident optical field.

Near-field optics: from subwavelength illumination to nanometric shadowing

Near-field optics uniquely addresses problems of x, y and z resolution by spatially confining the effect of a light source to nanometric domains. The problems in using far-field optics (conventional optical imaging through a lens) to achieve nanometric spatial resolution are formidable. Near-field optics serves a bridging role in biology between optical imaging and scanned probe microscopy. The integration of near-field and scanned probe imaging with far-field optics thus holds promise for solving the so-called inverse problem of optical imaging.

A two-photon and second-harmonic microscope

Two-photon microscopy has revolutionized life sciences by enabling long-term imaging of living preparations in highly scattering tissue while minimizing photodamage. At the same time, commercial two-photon microscopes are expensive and this has prevented the widespread application of this technique to the biological community. As an alternative to commercial systems, we provide an update of our efforts designing custom-built two-photon instruments by modifying the Olympus FluoView laser scanning confocal microscope. With the newer version of our instrument we modulate the intensity of the laser beam in arbitrary spatiotemporal patterns using a Pockels cell and software control over the scanning. We can also perform simultaneous optical imaging and optical stimulation experiments and combine them with second harmonic generation measurements.

Optimization of second-harmonic generation microscopy

We describe the principles and characteristics of second-harmonic generation imaging (SHGI) and explore various methods for optimization of the technique. Second-harmonic imaging is optimized for ultrashort laser pulses, high numerical aperture microscope objectives, a highly sensitive non-descanned large area detector, pseudo-phase-matching, and specimens with large second-order non linearity or which exhibit surface plasmon enhanced phenomena. We also compare and contrast the techniques of SHGI and two-photon excited fluorescence imaging.

Coherent scattering in multi-harmonic light microscopy

By focusing a pulsed laser beam into a sample, harmonic up-conversion can be generated as well as multi-photon excited fluorescence. Whereas multi-photon excited fluorescence microscopy is well established, the use of multi-harmonic generation for three-dimensional image contrast is very recent. Both techniques can provide similar resolution and, for adequate radiating source density, comparable signal levels, allowing them to be combined in a single versatile instrument. However, harmonic generation differs fundamentally from fluorescence generation in that it is coherent and produces radiation patterns that are highly sensitive to phase. As such, multi-harmonic generation microscopy provides a unique window into molecular spatial organization that is inaccessible to fluorescence.

GFP is a selective non-linear optical sensor of electrophysiological processes in Caenorhabditis elegans

Electrophysiology of the nematode Caenorhabditis elegans has the potential to bridge the wealth of information on the molecular biology and anatomy of this organism with the responses of selected cells and cellular neural networks associated with a behavioral response. In this paper we report that the nonlinear optical phenomenon of second harmonic generation (SHG) can be detected using green fluorescent protein (GFP) chimeras expressed in selected cells of living animals. Alterations in the SHG signal as a result of receptor ligand interactions and mechanical stimulation of the mechanosensory cells indicate that this signal is very sensitive to membrane potential. The results suggest that this approach to membrane potential measurements in C. elegans and in other biological systems could effectively couple data on selective locations within specific cells with functional responses that are associated with behavioral and sensory processes.

High-resolution nonlinear optical imaging of live cells by second harmonic generation

By adapting a laser scanning microscope with a titanium sapphire femtosecond pulsed laser and transmission optics, we are able to produce live cell images based on the nonlinear optical phenomenon of second harmonic generation (SHG). Second harmonic imaging (SHIM) is an ideal method for probing membranes of living cells because it offers the high resolution of nonlinear optical microscopy with the potential for near-total avoidance of photobleaching and phototoxicity. The technique has been implemented on three cell lines labeled with membrane-staining dyes that have large nonlinear optical coefficients. The images can be obtained within physiologically relevant time scales. Both achiral and chiral dyes were used to compare image formation for the case of single- and double-leaflet staining, and it was found that chirality plays a significant role in the mechanism of contrast generation. It is also shown that SHIM is highly sensitive to membrane potential, with a depolarization of 25 mV resulting in an approximately twofold loss of signal intensity.