High-density volumetric super-resolution microscopy

Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce biological throughput and applicability by requiring lower labeling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMLFM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We demonstrate this optical robustness experimentally with high accuracy ( > 99.2 ± 0.1%, 0.1 locs μm-2) and sensitivity ( > 86.6 ± 0.9%, 0.1 locs μm-2) through whole-cell (scan-free) imaging and tracking of single membrane proteins in live primary B cells. We also exemplify high-density volumetric imaging (0.15 locs μm-2) in dense cytosolic tubulin datasets.

resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission

Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.

resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission

Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.

ThX - a next-generation probe for the early detection of amyloid aggregates

Neurodegenerative diseases such as Alzheimer's and Parkinson's are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, the improved optical properties (extinction coefficient, quantum yield and brightness) of ThX can be used to monitor structural differences in oligomeric species, not observed via traditional ThT imaging.

A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane

In terrestrial ecosystems most plant species live in mutualistic symbioses with nutrient-delivering arbuscular mycorrhizal (AM) fungi. Establishment of AM symbioses includes transient, intracellular formation of fungal feeding structures, the arbuscules. A plant-derived peri-arbuscular membrane (PAM) surrounds the arbuscules, mediating reciprocal nutrient exchange. Signaling at the PAM must be well coordinated to achieve this dynamic cellular intimacy. Here, we identify the PAM-specific Arbuscular Receptor-like Kinase 1 (ARK1) from maize and rice to condition sustained AM symbiosis. Mutation of rice ARK1 causes a significant reduction in vesicles, the fungal storage structures, and a concomitant reduction in overall root colonization by the AM fungus Rhizophagus irregularis. Arbuscules, although less frequent in the ark1 mutant, are morphologically normal. Co-cultivation with wild-type plants restores vesicle and spore formation, suggesting ARK1 function is required for the completion of the fungal life-cycle, thereby defining a functional stage, post arbuscule development.

The peri-arbuscular membrane (PAM) mediates mutually-beneficial nutrient exchange between plants and arbuscular mycorrhizal (AM) fungi. Here the authors identify ARK1, a PAM-specific receptor-like kinase from rice that sustains AM symbiosis post-arbuscule development.

Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics

A key feature of Notch signaling is that it directs immediate changes in transcription via the DNA-binding factor CSL, switching it from repression to activation. How Notch generates both a sensitive and accurate response-in the absence of any amplification step-remains to be elucidated. To address this question, we developed real-time analysis of CSL dynamics including single-molecule tracking in vivo. In Notch-OFF nuclei, a small proportion of CSL molecules transiently binds DNA, while in Notch-ON conditions CSL recruitment increases dramatically at target loci, where complexes have longer dwell times conferred by the Notch co-activator Mastermind. Surprisingly, recruitment of CSL-related corepressors also increases in Notch-ON conditions, revealing that Notch induces cooperative or "assisted" loading by promoting local increase in chromatin accessibility. Thus, in vivo Notch activity triggers changes in CSL dwell times and chromatin accessibility, which we propose confer sensitivity to small input changes and facilitate timely shut-down.

Maximizing the field of view and accuracy in 3D Single Molecule Localization Microscopy

Super-resolution techniques that localize single molecules in three dimensions through point spread function (PSF) engineering are very sensitive to aberrations and optical alignment. Here we show how double-helix point spread function is affected by such mis-alignment and aberration. Specifically, we demonstrate through simulation and experiment how misplacement of phase masks in infinity corrected systems is a common source of significant loss of accuracy. We also describe an optimal alignment and calibration procedure to correct for these errors. In combination, these optimizations allow for a maximal field of view with high accuracy and precision. Though discussed with reference to double-helix point spread function (DHPSF), the optimization techniques are equally applicable to other engineered PSFs.

Investigation of the confocal wavefront sensor and its application to biological microscopy

Wavefront sensing in the presence of background light sources is complicated by the need to restrict the effective depth of field of the wavefront sensor. This problem is particularly significant in direct wavefront sensing adaptive optic (AO) schemes for correcting imaging aberrations in biological microscopy. In this paper we investigate how a confocal pinhole can be used to reject out of focus light whilst still allowing effective wavefront sensing. Using a scaled set of phase screens with statistical properties derived from measurements of wavefront aberrations induced by C. elegans specimens, we investigate and quantify how the size of the pinhole and the aberration amplitude affect the transmitted wavefront. We suggest a lower bound for the pinhole size for a given aberration strength and quantify the optical sectioning provided by the system. For our measured aberration data we find that a pinhole of size approximately 3 Airy units represents a good compromise, allowing effective transmission of the wavefront and thin optical sections. Finally, we discuss some of the practical implications of confocal wavefront sensing for AO systems in microscopy.

Polarization effects on contrast in structured illumination microscopy

In this Letter, we present an analysis of the effects of polarization state on the pattern contrast in a structured illumination microscope. Using vectorial ray tracing methods, we show that the contrast varies nonmonotonically with both the numerical aperture of the microscope objective lens and the orientation of the electric field with respect to the meridional plane. By careful selection of these two parameters, high pattern contrast can be obtained without polarization rotation, reducing the cost and complexity of structured illumination imaging systems and increasing light throughput and imaging speed. We present experimental results that show good agreement with theoretical predictions and discuss the implications for super-resolution imaging.

Topology of light's darkness

We numerically study the topology of optical vortex lines (nodal lines) in volumes of optical speckle, modeled as superpositions of random plane waves. It is known that the vortex lines may be infinitely long, or form closed loops. Loops are occasionally threaded by infinite lines, or linked with other loops. We find the probability of a loop not being threaded decays exponentially with the length of the loop. This behavior has a similarity to scaling laws studied in superfluid turbulence, and polymers modeled as random walks.

Polarization singularities in 2D and 3D speckle fields

The 3D structure of randomly polarized light fields is exemplified by its polarization singularities: lines along which the polarization is purely circular (C lines) and surfaces on which the polarization is linear (L surfaces). We visualize these polarization singularities experimentally in vector laser speckle fields, and in numerical simulations of random wave superpositions. Our results confirm previous analytical predictions [M. R. Dennis, Opt. Commun. 213, 201 (2002)] regarding the statistical distribution of types of C points and relate their 2D properties to their 3D structure.

Fractality of light's darkness

Natural light fields are threaded by lines of darkness. For monochromatic light, the phenomenon is familiar in laser speckle, i.e., the black points that appear in the scattered light. These black points are optical vortices that extend as lines throughout the volume of the field. We establish by numerical simulations, supported by experiments, that these vortex lines have the fractal properties of a Brownian random walk. Approximately 73% of the lines percolate through the optical beam, the remainder forming closed loops. Our statistical results are similar to those of vortices in random discrete lattice models of cosmic strings, implying that the statistics of singularities in random optical fields exhibit universal behavior.

Light beams with fractional orbital angular momentum and their vortex structure

Light emerging from a spiral phase plate with a non-integer phase step has a complicated vortex structure and is unstable on propagation. We generate light carrying fractional orbital angular momentum (OAM) not with a phase step but by a synthesis of Laguerre-Gaussian modes. By limiting the number of different Gouy phases in the superposition we produce a light beam which is well characterised in terms of its propagation. We believe that their structural stability makes these beams ideal for quantum information processes utilising fractional OAM states.

Topology of optical vortex lines formed by the interference of three, four, and five plane waves

When three or more plane waves overlap in space, complete destructive interference occurs on nodal lines, also called phase singularities or optical vortices. For super positions of three plane waves, the vortices are straight, parallel lines. For four plane waves the vortices form an array of closed or open loops. For five or more plane waves the loops are irregular. We illustrate these patterns numerically and experimentally and explain the three-, four- and five-wave topologies with a phasor argument.