Simple super-resolution live-cell imaging based on diffusion-assisted Förster resonance energy transfer

PySOFI: an open source Python package for SOFI

Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution without requirement of sophisticated imaging instruments. Easy-to-use open-source packages for SOFI are important to support the utilization and community adoption of the SOFI method, they also encourage the participation and further development of SOFI by new investigators. In this work, we developed PySOFI, an open-source Python package for SOFI analysis that offers the flexibility to inspect, test, modify, improve, and extend the algorithm. We provide complete documentation for the package and a collection of Jupyter Notebooks to demonstrate the usage of the package. We discuss the architecture of PySOFI and illustrate how to use each functional module. A demonstration on how to extend the PySOFI package with additional modules is also included in the PySOFI package. We expect PySOFI to facilitate efficient adoption, testing, modification, dissemination, and prototyping of new SOFI-relevant algorithms.

Super-resolution FRET measurements

Super-resolution fluorescence microscopy and Förster Resonance Energy Transfer (FRET) form a well-established family of techniques that has provided unique tools to study the dynamic architecture and functionality of biological systems, as well as to investigate nanomaterials. In the last years, the integration of super-resolution methods with FRET measurements has generated advances in two fronts. On the one hand, FRET-based probes have enhanced super-resolution imaging. On the other, the development of super-resolved FRET imaging methods has allowed the visualization of molecular interaction patterns with higher spatial resolution, less averaging and higher dynamic range. Here, we review these advances and discuss future perspectives, including the possible integration of FRET with next generation super-resolution techniques capable of reaching true molecular-scale spatial resolution.

Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET

Förster resonance energy transfer (FRET) imaging methods provide unique insight into the spatial distribution of energy transfer and (bio)molecular interaction events, though they deliver average information for an ensemble of events included in a diffraction-limited volume. Coupling super-resolution fluorescence microscopy and FRET has been a challenging and elusive task. Here, we present STED-FRET, a method of general applicability to obtain super-resolved energy transfer images. In addition to higher spatial resolution, STED-FRET provides a more accurate quantification of interaction and has the capacity of suppressing contributions of noninteracting partners, which are otherwise masked by averaging in conventional imaging. The method capabilities were first demonstrated on DNA-origami model systems, verified on uniformly double-labeled microtubules, and then utilized to image biomolecular interactions in the membrane-associated periodic skeleton (MPS) of neurons.

Active-modulated, random-illumination, super-resolution optical fluctuation imaging

Super-resolution optical fluctuation imaging (SOFI) provides subdiffraction resolution based on the analysis of temporal stochastic intensity fluctuations. However, conventional SOFI imaging relies on the intrinsic blinking properties of fluorescent markers and suffers from severe artifacts and signal losses owing to the unmatched blinking on-time ratio. Herein, we propose active-modulated, random-illumination, super-resolution optical fluctuation imaging that allows the traditional SOFI to overcome the effect of the intrinsic impertinent blinking characteristic of fluorescent markers. We demonstrate theoretically and experimentally that this method of active-modulated random illumination can generate random illumination patterns with a controllable blinking on-time ratio to match the high-order SOFI reconstruction considerably reducing the generated artifacts and signal losses. High-order, high-quality images can be obtained with increased lateral resolution.

Self-Blinking Dyes Unlock High-Order and Multiplane Super-Resolution Optical Fluctuation Imaging

Most diffraction-unlimited super-resolution imaging critically depends on the switching of fluorophores between at least two states, often induced using intense laser light and specialized buffers or UV radiation. Recently, so-called self-blinking dyes that switch spontaneously between an open, fluorescent "on" state and a closed, colorless "off" state were introduced. Here, we exploit the synergy between super-resolution optical fluctuation imaging (SOFI) and spontaneously switching fluorophores for 2D and 3D imaging. SOFI analyzes higher order statistics of fluctuations in the fluorophore emission instead of localizing individual molecules. It thereby tolerates a broad range of labeling densities, switching behavior, and probe brightness. Thus, even dyes that exhibit spontaneous blinking characteristics that are not suitable or suboptimal for single molecule localization microscopy can be used successfully for SOFI-based super-resolution imaging. We demonstrate 2D imaging of fixed cells with almost uniform resolution up to 50-60 nm in 6th order SOFI and characterize changing experimental conditions. Next, we investigate volumetric imaging using biplane and eight-plane data acquisition. We extend 3D cross-cumulant analysis to 4th order, achieving super-resolution in 3D with up to 29 depth planes. Finally, the low laser excitation intensities needed for single and biplane self-blinking SOFI are well suited for live-cell imaging. We show the perspective for time-resolved imaging by observing slow membrane movements in cells. Self-blinking SOFI thus provides a more robust alternative route for easy-to-use 2D and 3D high-resolution imaging.

Cusp-artifacts in high order superresolution optical fluctuation imaging

Superresolution optical fluctuation imaging (SOFI) is a simple and affordable super-resolution imaging technique, and attracted a growing community over the past decade. However, the theoretical resolution enhancement of high order SOFI is still not fulfilled. In this study, we identify "cusp artifacts" in high order SOFI images, and show that the high-order cumulants, odd-order moments and balanced-cumulants (bSOFI) are highly vulnerable to cusp artifacts. Our study provides guidelines for developing and screening for fluorescence probes, and improving data acquisition for SOFI. The new insight is important to inspire positive utilization of the cusp artifacts.

Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging

Recent advances in super-resolution microscopy allow the localization of single molecules within individual cells but not within multiple whole cells due to weak signals from single molecules and slow acquisition process for point accumulation to reconstruct super-resolution images. Here, we report a fast, large-scale, and three-dimensional super-resolution fluorescence microscope based on single-wavelength Bessel lightsheet to selectively illuminate spontaneous blinking fluorophores tagged to the proteins of interest in space. Critical parameters such as labeling density, excitation power, and exposure time were systematically optimized resulting in a maximum imaging speed of 2.7 × 104 µm3 s-1. Fourier ring correlation analysis revealed a reconstructed image with a lateral resolution of ~75 nm through the accumulation of 250 image volumes on immobilized samples within 15 min. Hence, the designed system could open new insights into the discovery of complex biological structures and live 3D localization imaging.

Moments reconstruction and local dynamic range compression of high order superresolution optical fluctuation imaging

Super-resolution optical fluctuation imaging (SOFI) offers a simple and affordable alternative to other super-resolution (SR) imaging techniques. The theoretical resolution enhancement of SOFI scales linearly with the order of cumulants, while the imaging conditions exhibit less photo-toxicity to the living samples as compared to other SR methods. High order SOFI could, therefore, be a method of choice for dynamic live cell imaging. However, due to the cusp-artifacts and dynamic range expansion of pixel intensities, this promise has not been materialized as of yet. Here we investigated and compared high order moments vs. high order cumulant SOFI reconstructions. We demonstrate that even-order moments reconstructions are intrinsically free of cusp artifacts, allowing for a subsequent deconvolution operation to be performed, hence enhancing the resolution even further. High order moments reconstruction performance was examined for various (simulated) conditions and applied to (experimental) imaging of QD labeled microtubules in fixed cells, and actin stress fiber dynamics in live cells.

Fluorogenic probes for super-resolution microscopy

Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.

SRRF: Universal live-cell super-resolution microscopy

Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide palette of high specificity molecular labels, straightforward sample preparation and live-cell compatibility. Despite this, the application of super-resolution microscopy to dynamic, living samples has thus far been limited and often requires specialised, complex hardware. Here we demonstrate how a novel analytical approach, Super-Resolution Radial Fluctuations (SRRF), is able to make live-cell super-resolution microscopy accessible to a wider range of researchers. We show its applicability to live samples expressing GFP using commercial confocal as well as laser- and LED-based widefield microscopes, with the latter achieving long-term timelapse imaging with minimal photobleaching.

Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device

We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.

Elucidating endotoxin-biomolecule interactions with FRET: extending the frontiers of their supramolecular complexation

Endotoxin has been one of the topical chemical contaminants of major concern to researchers, especially in the field of bioprocessing. This major concern of researchers stems from the fact that the presence of Gram-negative bacterial endotoxin in intracellular products is unavoidable and requires complex downstream purification steps. For instance, endotoxin interacts with recombinant proteins, peptides, antibodies and aptamers and these interactions have formed the foundation for most biosensors for endotoxin detection. It has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove endotoxin, without compromising the quality and quantity of the end-product. However, the underlying mechanism involved during endotoxin-biomolecule interaction is still a gray area. The use of quantitative molecular microscopy that provides high resolution of biomolecules is highly promising, hence, may lead to the development of improved endotoxin detection strategies in biomolecule preparation. Förster resonance energy transfer (FRET) spectroscopy is one of the emerging most powerful tools compatible with most super-resolution techniques for the analysis of molecular interactions. However, the scope of FRET has not been well-exploited in the analysis of endotoxin-biomolecule interaction. This article reviews endotoxin, its pathophysiological consequences and the interaction with biomolecules. Herein, we outline the common potential ways of using FRET to extend the current understanding of endotoxin-biomolecule interaction with the inference that a detailed understanding of the interaction is a prerequisite for the design of strategies for endotoxin identification and removal from protein milieus.

Single-molecule fluorescence resonance energy transfer in molecular biology

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.

Superior performance with sCMOS over EMCCD in super-resolution optical fluctuation imaging

Super-resolution optical fluctuation imaging (SOFI) is a fast and low-cost live-cell optical nanoscopy for extracting subdiffraction information from the statistics of fluorescence intensity fluctuation. As SOFI is based on the fluctuation statistics, rather than the detection of single molecules, it poses unique requirements for imaging detectors, which still lack a systematic evaluation. Here, we analyze the influences of pixel sizes, frame rates, noise levels, and different gains in SOFI with simulations and experimental tests. Our analysis shows that the smaller pixel size and faster readout speed of scientific-grade complementary metal oxide semiconductor (sCMOS) enables SOFI to achieve high spatiotemporal resolution with a large field-of-view, which is especially beneficial for live-cell super-resolution imaging. Overall, as the performance of SOFI is relatively insensitive to the signal-to-noise ratio (SNR), the gain in pixel size and readout speed exceeds the loss in SNR, indicating sCMOS is superior to electron multiplying charge coupled device in context to SOFI in many cases. Super-resolution imaging of cellular microtubule structures with high-order SOFI is experimentally demonstrated at large field-of-view, taking advantage of the large pixel number and fast frame rate of sCMOS cameras.

TRICK: A Single-Molecule Method for Imaging the First Round of Translation in Living Cells and Animals

The life of an mRNA is dynamic within a cell. The development of quantitative fluorescent microscopy techniques to image single molecules of RNA has allowed many aspects of the mRNA lifecycle to be directly observed in living cells. Recent advances in live-cell multicolor RNA imaging, however, have now made it possible to investigate RNA metabolism in greater detail. In this chapter, we present an overview of the design and implementation of the translating RNA imaging by coat protein knockoff RNA biosensor, which allows untranslated mRNAs to be distinguished from ones that have undergone a round of translation. The methods required for establishing this system in mammalian cell lines and Drosophila melanogaster oocytes are described here, but the principles may be applied to any experimental system.

Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution

Stochastic optical fluctuation imaging (SOFI) is a super-resolution fluorescence imaging technique that makes use of stochastic fluctuations in the emission of the fluorophores. During a SOFI measurement multiple fluorescence images are acquired from the sample, followed by the calculation of the spatiotemporal cumulants of the intensities observed at each position. Compared to other techniques, SOFI works well under conditions of low signal-to-noise, high background, or high emitter densities. However, it can be difficult to unambiguously determine the reliability of images produced by any superresolution imaging technique. In this work we present a strategy that enables the estimation of the variance or uncertainty associated with each pixel in the SOFI image. In addition to estimating the image quality or reliability, we show that this can be used to optimize the signal-to-noise ratio (SNR) of SOFI images by including multiple pixel combinations in the cumulant calculation. We present an algorithm to perform this optimization, which automatically takes all relevant instrumental, sample, and probe parameters into account. Depending on the optical magnification of the system, this strategy can be used to improve the SNR of a SOFI image by 40% to 90%. This gain in information is entirely free, in the sense that it does not require additional efforts or complications. Alternatively our approach can be applied to reduce the number of fluorescence images to meet a particular quality level by about 30% to 50%, strongly improving the temporal resolution of SOFI imaging.

AIE Based Coumarin Chromophore - Evaluation and Correlation Between Solvatochromism and Solvent Polarity Parameters

A new class of red emitting extensively conjugated donor-π-acceptor type dyes bearing coumarin units have been synthesized by condensation of 7-(diethylamino)-2-oxo-2 H-chromene-3-carbaldehyde with different active methylenes. All the dyes are characterized by (1)H NMR, (13)C NMR and HRMS spectroscopy. The photophysical behaviour and the relation between structure and properties of the coumarin "push-pull" derivatives were investigated experimentally. The dyes exhibited positive solvatochromism and solvatofluorism in solution of varying polarity. These coumarin dyes show aggregation induced emission properties with red emitting fluorescence. They show absorption in the range of 501-528 and emission in the range of 547-630 nm. We evaluated photophysical properties of coumarin dyes using solvotochromism and solvent dependent shift in the emission wavelength. All the synthesized coumarin dyes COS1-COS4 are showing very good solvatochromic properties.

Superresolution imaging with optical fluctuation using speckle patterns illumination

Superresolution fluorescence microscopy possesses an important role for the study of processes in biological cells with subdiffraction resolution. Recently, superresolution methods employing the emission properties of fluorophores have rapidly evolved due to their technical simplicity and direct applicability to existing microscopes. However, the application of these methods has been limited to samples labeled with fluorophores that can exhibit intrinsic emission properties at a restricted timescale, especially stochastic blinking. Here, we present a superresolution method that can be performed using general fluorophores, regardless of this intrinsic property. Utilizing speckle patterns illumination, temporal emission fluctuation of fluorophores is induced and controlled, from which a superresolution image can be obtained exploiting its statistical property. Using this method, we demonstrate, theoretically and experimentally, the capability to produce subdiffraction resolution images. A spatial resolution of 500 nm, 300 nm and 140 nm with 0.4, 0.5 and 1.4 NA objective lenses respectively was achieved in various samples with an enhancement factor of 1.6 compared to conventional fluorescence microscopy.

Intracellular FRET-based probes: a review

Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.

Novel approach for label free super-resolution imaging in far field

Progress in the emerging areas of science and technology, such as bio- and nano-technologies, depends on development of corresponding techniques for imaging and probing the structures with high resolution. Recently, the far field diffraction resolution limit in the optical range has been circumvented and different methods of super-resolution optical microscopy have been developed. The importance of this breakthrough achievement has been recognized by Nobel Prize for Chemistry in 2014. However, the fluorescence based super-resolution techniques only function with fluorescent molecules (most of which are toxic and can destroy or lead to artificial results in living biological objects) and suffer from photobleaching. Here we show a new way to break the diffraction resolution limit, which is based on nano-sensitivity to internal structure. Instead of conventional image formation as 2D intensity distribution, in our approach images are formed as a result of comparison of the axial spatial frequency profiles, reconstructed for each image point. The proposed approach dramatically increases the lateral resolution even in presence of noise and allows objects to be imaged in their natural state, without any labels.

Anomalous surface diffusion of protons on lipid membranes

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.

Fourier interpolation stochastic optical fluctuation imaging

Stochastic Optical Fluctuation Imaging (SOFI) is a super-resolution fluorescence microscopy technique which allows to enhance the spatial resolution of an image by evaluating the temporal fluctuations of blinking fluorescent emitters. SOFI is not based on the identification and localization of single molecules such as in the widely used Photoactivation Localization Microsopy (PALM) or Stochastic Optical Reconstruction Microscopy (STORM), but computes a superresolved image via temporal cumulants from a recorded movie. A technical challenge hereby is that, when directly applying the SOFI algorithm to a movie of raw images, the pixel size of the final SOFI image is the same as that of the original images, which becomes problematic when the final SOFI resolution is much smaller than this value. In the past, sophisticated cross-correlation schemes have been used for tackling this problem. Here, we present an alternative, exact, straightforward, and simple solution using an interpolation scheme based on Fourier transforms. We exemplify the method on simulated and experimental data.

Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging

Previous stochastic localization-based super-resolution techniques are largely limited by the labeling density and the fidelity to the morphology of specimen. We report on an optical super-resolution imaging scheme implementing joint tagging using multiple fluorescent blinking dyes associated with super-resolution optical fluctuation imaging (JT-SOFI), achieving ultra-high labeling density super-resolution imaging. To demonstrate the feasibility of JT-SOFI, quantum dots with different emission spectra were jointly labeled to the tubulin in COS7 cells, creating ultra-high density labeling. After analyzing and combining the fluorescence intermittency images emanating from spectrally resolved quantum dots, the microtubule networks are capable of being investigated with high fidelity and remarkably enhanced contrast at sub-diffraction resolution. The spectral separation also significantly decreased the frame number required for SOFI, enabling fast super-resolution microscopy through simultaneous data acquisition. As the joint-tagging scheme can decrease the labeling density in each spectral channel, thereby bring it closer to single-molecule state, we can faithfully reconstruct the continuous microtubule structure with high resolution through collection of only 100 frames per channel. The improved continuity of the microtubule structure is quantitatively validated with image skeletonization, thus demonstrating the advantage of JT-SOFI over other localization-based super-resolution methods.

Super-Resolution Single-Molecule Localization Microscopy: Tricks of the Trade

Application of single-molecule fluorescence detection has led to the development of light microscopy techniques that make it possible to study fluorescent samples at spatial resolutions significantly improved upon the diffraction limit of light. The biological and materials science applications of these "super-resolution" microscopy methods are vast, causing current demand for them to be high. However, implementation, execution, and interpretation of these techniques, particularly involving biological samples, require a broad interdisciplinary skillset, not often found in a single laboratory. Those already used to interdisciplinary work as well as navigating communication and collaboration between more pure forms of physics, chemistry, and biology are well-positioned to spearhead such efforts. In this Perspective, we describe various aspects of single-molecule super-resolution imaging, discussing, in particular, the role that physical chemistry has so far played in its development and establishment. We also highlight a selection of some of the remarkable recent research achievements in this vibrant field.

Live-cell multiplane three-dimensional super-resolution optical fluctuation imaging

Super-resolution optical fluctuation imaging (SOFI) provides an elegant way of overcoming the diffraction limit in all three spatial dimensions by computing higher-order cumulants of image sequences of blinking fluorophores acquired with a classical widefield microscope. Previously, three-dimensional (3D) SOFI has been demonstrated by sequential imaging of multiple depth positions. Here we introduce a multiplexed imaging scheme for the simultaneous acquisition of multiple focal planes. Using 3D cross-cumulants, we show that the depth sampling can be increased. The simultaneous acquisition of multiple focal planes significantly reduces the acquisition time and thus the photobleaching. We demonstrate multiplane 3D SOFI by imaging fluorescently labelled cells over an imaged volume of up to 65 × 65 × 3.5 μm³ without depth scanning. In particular, we image the 3D network of mitochondria in fixed C2C12 cells immunostained with Alexa 647 fluorophores and the 3D vimentin structure in living Hela cells expressing the fluorescent protein Dreiklang.

Super-resolution optical fluctuation imaging provides 3D images of biological specimens via blinking fluorophores. Geissbuehler et al. present a multiplexed version of this method that captures images at multiple focal planes simultaneously, reducing the acquisition time compared with standard approaches.

Imaging ER-to-Golgi transport: towards a systems view

Proteins synthesised at the endoplasmic reticulum (ER) have to undergo a number of consecutive and coordinated steps to reach the Golgi complex. To understand the dynamic complexity of ER-to-Golgi transport at the structural and molecular level, light microscopy approaches are fundamental tools that allow in vivo observations of protein dynamics and interactions of fluorescent proteins in living cells. Imaging protein and organelle dynamics close to the ultra-structural level became possible by combining light microscopy with electron microscopy analyses or super-resolution light microscopy methods. Besides, increasing evidence suggests that the early secretory pathway is tightly connected to other cellular processes, such as signal transduction, and quantitative information at the systems level is fundamental to achieve a comprehensive molecular understanding of these connections. High-throughput microscopy in fixed and living cells in combination with systematic perturbation of gene expression by, e.g. RNA interference, will open new avenues to gain such an understanding of the early secretory pathway at the systems level. In this Commentary, we first outline examples that revealed the dynamic organisation of ER-to-Golgi transport in living cells. Next, we discuss the use of advanced imaging methods in studying ER-to-Golgi transport and, finally, delineate the efforts in understanding ER-to-Golgi transport at the systems level.

Phanta: a non-fluorescent photochromic acceptor for pcFRET

We have developed an orange non-fluorescent photochromic protein (quantum yield, 0.003) we call Phanta that is useful as an acceptor in pcFRET applications. Phanta can be repeatedly inter-converted between the two absorbing states by alternate exposure to cyan and violet light. The absorption spectra of Phanta in one absorbing state shows excellent overlap with the emission spectra of a number of donor green fluorescent proteins including the commonly used EGFP. We show that the Phanta-EGFP FRET pair is suitable for monitoring the activation of caspase 3 in live cells using readily available instrumentation and a simple protocol that requires the acquisition of two donor emission images corresponding to Phanta in each of its photoswitched states. This the first report of a genetically encoded non-fluorescent acceptor for pcFRET.

Towards the Physics of Calcium Signalling in Plants

Calcium is an abundant element with a wide variety of important roles within cells. Calcium ions are inter- and intra-cellular messengers that are involved in numerous signalling pathways. Fluctuating compartment-specific calcium ion concentrations can lead to localised and even plant-wide oscillations that can regulate downstream events. Understanding the mechanisms that give rise to these complex patterns that vary both in space and time can be challenging, even in cases for which individual components have been identified. Taking a systems biology approach, mathematical and computational techniques can be employed to produce models that recapitulate experimental observations and capture our current understanding of the system. Useful models make novel predictions that can be investigated and falsified experimentally. This review brings together recent work on the modelling of calcium signalling in plants, from the scale of ion channels through to plant-wide responses to external stimuli. Some in silico results that have informed later experiments are highlighted.

Quantitative phase imaging techniques for the study of cell pathophysiology: from principles to applications

A cellular-level study of the pathophysiology is crucial for understanding the mechanisms behind human diseases. Recent advances in quantitative phase imaging (QPI) techniques show promises for the cellular-level understanding of the pathophysiology of diseases. To provide important insight on how the QPI techniques potentially improve the study of cell pathophysiology, here we present the principles of QPI and highlight some of the recent applications of QPI ranging from cell homeostasis to infectious diseases and cancer.