Published: Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework

K.J.A. Martens, A. Jabermoradi, S. Yang, and J. Hohlbein, Methods, 193, 2021, [link], previously on bioRxiv [link]

In single-molecule localization microscopy (SMLM), the use of engineered point spread functions (PSFs) provides access to three-dimensional localization information. The conventional approach of fitting PSFs with a single 2-dimensional Gaussian profile, however, often falls short in analyzing complex PSFs created by placing phase masks, deformable mirrors or spatial light modulators in the optical detection pathway. Here, we describe the integration of PSF modalities known as double-helix, saddle-point or tetra-pod into the phasor-based SMLM (pSMLM) framework enabling fast CPU based localization of single-molecule emitters with sub- pixel accuracy in three dimensions. For the double-helix PSF, pSMLM identifies the two individual lobes and uses their relative rotation for obtaining z-resolved localizations. For the analysis of saddle-point or tetra-pod PSFs, we present a novel phasor-based deconvolution approach entitled circular-tangent pSMLM. Saddle-point PSFs were experimentally realized by placing a deformable mirror in the Fourier plane and modulating the incoming wavefront with specific Zernike modes. Our pSMLM software package delivers similar precision and recall rates to the best-in-class software package (SMAP) at signal-to-noise ratios typical for organic fluorophores and achieves localization rates of up to 15 kHz (double-helix) and 250 kHz (saddle-point/tetra-pod) on a standard CPU. We further integrated pSMLM into an existing software package (SMALL-LABS) suitable for single-particle imaging and tracking in environments with obscuring backgrounds. Taken together, we provide a powerful hardware and software environment for advanced single-molecule studies.

News: New lab members

For the start of the academic year, we welcome new lab members: Erwin Dijkstra started with his MSc thesis on spectrally resolved super-resolution imaging, Victor Pools will help us as a research assistant with cloning and single-molecule particle tracking, and Konstantin Speckner is taking a short break from his PhD in Bayreuth to learn more about single-molecule and single-cell techniques. Welcome on board!

Published: Probing DNA – transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices

M. Fontana, Š. Ivanovaite , S. Lindhoud, E. van der Wijk, K. Mathwig, W. van den Berg, D. Weijers, and J. Hohlbein, Advanced Biology, 2100953, 2021, [link], preprint: bioRxiv, 2021, [link]

Single-molecule fluorescence detection offers powerful ways to study biomolecules and their complex interactions. Here, nanofluidic devices and camera-based, single-molecule Förster resonance energy transfer (smFRET) detection are combined to study the interactions between plant transcription factors of the auxin response factor (ARF) family and DNA oligonucleotides that contain target DNA response elements. In particular, it is shown that the binding of the unlabeled ARF DNA binding domain (ARF-DBD) to donor and acceptor labeled DNA oligonucleotides can be detected by changes in the FRET efficiency and changes in the diffusion coefficient of the DNA. In addition, this data on fluorescently labeled ARF-DBDs suggest that, at nanomolar concentrations, ARF-DBDs are exclusively present as monomers. In general, the fluidic framework of freely diffusing molecules minimizes potential surface-induced artifacts, enables high-throughput measurements, and proved to be instrumental in shedding more light on the interactions between ARF-DBDs monomers and between ARF-DBDs and their DNA response element

News: Presentation on open microscopy and in-vivo single-molecule CRISPR-Cas

In January 2021, I had the pleasure to present some of our recent work as part of the Imaging ONEWORLD series initiated by the Royal Society of Microscopy. Topics I talked about include: open-source microscopy (#miCube), accelerated single-molecule localisation analysis (#SMLM) using phasor analysis, diffusion distribution analysis (#anaDDA), and in vivo single-particle tracking of CRISPR-Cas9.

Pre-print: Enabling single-molecule localization microscopy in turbid food emulsions

A. Jabermoradi, S. Yang, M. Gobes, J.P.M. van Duynhoven, and J. Hohlbein, bioRxiv, 2021, [link]

Turbidity poses a major challenge for the microscopic characterization of many food systems. In these systems, local mismatches in refractive indices can cause reflection, absorption and scattering of incoming as well as outgoing light leading to significant image deterioration along sample depth. To mitigate the issue of turbidity and to increase the achievable optical resolution, we combined adaptive optics (AO) with single-molecule localization microscopy (SMLM). Building on our previously published open hardware microscopy framework, the miCube, we first added a deformable mirror to the detection path. This element enables both the compensation of aberrations directly from single-molecule data and, by further modulating the emission wavefront, the introduction of various point spread functions (PSFs) to enable SMLM in three dimensions. We further added a top hat beam shaper to the excitation path to obtain an even illumination profile across the field of view (FOV). As a model system for a non-transparent food colloid in which imaging in depth is challenging, we designed an oil-in-water emulsion in which phosvitin, a ferric ion binding protein present in from egg yolk, resides at the oil water interface. We targeted phosvitin with fluorescently labelled primary antibodies and used PSF engineering to obtain 2D and 3D images of phosvitin covered oil droplets with sub 100 nm resolution. Droplets with radii as low as 200 nm can be discerned, which is beyond the range of conventional confocal light microscopy. Our data indicated that in the model emulsion phosvitin is homogeneously distributed at the oil-water interface. With the possibility to obtain super-resolved images in depth of nontransparent colloids, our work paves the way for localizing biomacromolecules at colloidal interfaces in heterogeneous food emulsions.

 

News: NWO Take-off (phase I) granted & new lab members

Happy to share the news that we received a NWO Take-off (phase 1) grant for “Spectrally-resolved single-molecule localization microscopy to go”. Looking forward working with Niels and the people from Cairn Research Ltd, Confocal.nl, Wageningen University & Research on this exciting project to bring more colours into microscopy. 

We further say good bye to Mattia, who will continue working with my new colleague Dr. Sonja Schmid (see her new and shiny webpage here). Hope we can get all those great work of yours published soon!

We also welcome two new BSc students, Mink Neeleman and Casper Peters, who will work on CRISPR-Cas, live cell imaging and microfluidics. Welcome on board!

 

Published: Quantitative spatiotemporal mapping of lipid and protein oxidation in mayonnaise

S. Yang, A.A. Verhoef, D.W.H Merkx, J.P.M. van Duynhoven, and J. Hohlbein, Antioxidants, 9, 1278, 2020, [link]

Lipid oxidation in food emulsions is mediated by emulsifiers in the water phase and at the oil-water interface. To unravel the physico-chemical mechanisms and to obtain local lipid and protein oxidation rates, we used confocal laser scanning microscopy (CLSM), thereby monitoring changes in both the fluorescence emission of a lipophilic dye BODIPY 665/676 and protein auto-fluorescence. Our data show that the removal of lipid-soluble antioxidants from mayonnaises promotes lipid oxidation within oil droplets as well as protein oxidation at the oil-water interface. Furthermore, we demonstrate that ascorbic acid acts as either a lipid antioxidant or pro-oxidant depending on the presence of lipid-soluble antioxidants. The effects of antioxidant formulation on local lipid and protein oxidation rates were all statistically significant (p < 0.0001). The observed protein oxidation at the oil-water interface was spatially heterogeneous, which is in line with the heterogeneous distribution of lipoprotein granules from the egg yolk used for emulsification. The impact of the droplet size on local lipid and protein oxidation rates was significant (p < 0.0001) but minor compared to the effects of ascorbic acid addition and lipid-soluble antioxidant depletion. The presented results demonstrate that CLSM can be applied for unraveling the roles of colloidal structure and transport in mediating lipid oxidation in complex food emulsions.

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Published: Extracting transition rates in particle tracking using analytical diffusion distribution analysis

J. Vink, S.J.J. Brouns, and J. Hohlbein, Biophysical Journal, 119, 1970–83, 2020, [link], preprint: bioRxiv, 2020, [link]

Single-particle tracking is an important technique in the life sciences to understand the kinetics of biomolecules. The analysis of apparent diffusion coefficients in vivo, for example, enables researchers to determine whether biomolecules are moving alone, as part of a larger complex, or are bound to large cellular components such as the membrane or chromosomal DNA. A remaining challenge has been to retrieve quantitative kinetic models, especially for molecules that rapidly switch between different diffusional states. Here, we present analytical diffusion distribution analysis (anaDDA), a framework that allows for extracting transition rates from distributions of apparent diffusion coefficients calculated from short trajectories that feature less than 10 localizations per track. Under the assumption that the system is Markovian and diffusion is purely Brownian, we show that theoretically predicted distributions accurately match simulated distributions and that anaDDA outperforms existing methods to retrieve kinetics, especially in the fast regime of 0.1–10 transitions per imaging frame. AnaDDA does account for the effects of confinement and tracking window boundaries. Furthermore, we added the option to perform global fitting of data acquired at different frame times to allow complex models with multiple states to be fitted confidently. Previously, we have started to develop anaDDA to investigate the target search of CRISPR-Cas complexes. In this work, we have optimized the algorithms and reanalyzed experimental data of DNA polymerase I diffusing in live Escherichia coli. We found that long-lived DNA interaction by DNA polymerase are more abundant upon DNA damage, suggesting roles in DNA repair. We further revealed and quantified fast DNA probing interactions that last shorter than 10 ms. AnaDDA pushes the boundaries of the timescale of interactions that can be probed with single-particle tracking and is a mathematically rigorous framework that can be further expanded to extract detailed information about the behavior of biomolecules in living cells.

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Published: Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis

A. Freire-Rios, K. Tanaka, I. Crespo, E. van der Wijk, Y. Sizentsova, V. Levitsky, S. Lindhoud, M. Fontana, J. Hohlbein, D.R. Boer, V. Mironova, and D. Weijers, Proceedings of the National Academy of Science of the United States of America, 117 (39), 24557, 2020, [link]

The hormone auxin controls many aspects of the plant life cycle by regulating the expression of thousands of genes. The transcriptional output of the nuclear auxin signaling pathway is determined by the activity of AUXIN RESPONSE transcription FACTORs (ARFs), through their binding to cis-regulatory elements in auxin-responsive genes. Crystal structures, in vitro, and heterologous studies have fueled a model in which ARF dimers bind with high affinity to distinctly spaced repeats of canonical AuxRE motifs. However, the relevance of this “caliper” model, and the mechanisms underlying the binding affinities in vivo, have remained elusive. Here we biochemically and functionally interrogate modes of ARF–DNA interaction. We show that a single additional hydrogen bond in Arabidopsis ARF1 confers high-affinity binding to individual DNA sites. We demonstrate the importance of AuxRE cooperativity within repeats in the Arabidopsis TMO5 and IAA11 promoters in vivo. Meta-analysis of transcriptomes further reveals strong genome-wide association of auxin response with both inverted (IR) and direct (DR) AuxRE repeats, which we experimentally validated. The association of these elements with auxin-induced up-regulation (DR and IR) or down-regulation (IR) was correlated with differential binding affinities of A-class and B-class ARFs, respectively, suggesting a mechanistic basis for the distinct activity of these repeats. Our results support the relevance of high-affinity binding of ARF transcription factors to uniquely spaced DNA elements in vivo, and suggest that differential binding affinities of ARF subfamilies underlie diversity in cis-element function.

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News: Goodbye Koen and welcome Cleo, Martijn, Niels and Simon

After recently defending his PhD thesis titled “Pinpointing macromolecular motion. Single-particle tracking fluorescence microscopy advances and applications” with distinction (cum laude!), Koen Martens left the group for a postdoc position in the lab of Dr. Ulrike Endesfelder (CMU, Pittsburgh). All the best, Koen, you will be missed!

A big welcome to Martijn Gobes and Cleo Bagchus who both joined the group for their MSc thesis. Martijn will improve our computational workflow for super-resolution microscopy (his first ImageJ plugin for fast temporal median filtering is available here). Cleo will continue our work on single-particle tracking in live cells together with Simon van de Els, who joined the lab as a (semi) post-doctoral research assistant.

Last but not least, we welcome Niels Zijlstra as a guest scientist from the Cordes lab in Munich. Niels will work on combining the miCube platform with spectrally resolved super-resolution imaging.