Pumpy is out! Perform advanced microscopy experiments thanks to NanoJ-Fluidics

The LEGO Pumpy (or more officially NanoJ-Fluidics) paper is out ! A joint venture with the Henriques lab, this details how to build a fully open-source multi-channel syringe pumps with LEGO and Arduino. We provide examples on how to use it directly on the microscope for complex imaging protocols: live-to-fixed correlative acquisitions, image-analysis triggered fixation, sequential imaging… Check the video we put together showing the possibilities:

In the lab, we used Pumpy to perform complex STORM/PAINT multiplexed acquisitions. Here it’s a 5-color imaging of actin, mitochondria, intermediate filaments, microtubules and clathrin. It’s made with 1 single-color STORM and two 2-color PAINT sequential acquisitions:

Imaging was a breeze thanks to Pumpy, so the main challenge was to optimize the fixation and immunolabeling for 5 distinct targets. Great work from Ghislaine Caillol and Fanny Boroni-Rueda! Check the full article here for more.

Just out: overview of the NanoJ framework for open-source super-resolution

The Henriques lab and its collaborators have a new paper out in the Journal of Physics D: Applied Physics. This is an overview of the NanoJ framework they are developing for open-source super-resolution in ImageJ/Fiji. In includes SRRF, SQUIRREL, NanoJ-Fluidics aka Pumpy, but also utilities for drift correction, chromatic aberration registration and single-article averaging. Have a look at the accepted manuscript here!

New paper out: slow axonal transport of actin via hotspots and trails

Our latest work (previously on bioRxiv) is now published in the Journal of Cell Biology. We collaborated with the Roy lab to reveal a new mechanism of slow axonal transport, based on the previous discovery of actin hotspots and trails. Hotspots are static actin clusters that appear and disappear within minutes every 3-4 µm along the axon. They generate the assembly of trails, long actin filaments that polymerize along the axon and collapse within seconds. Our new article first shows that trails polymerize at their barbed ends, located at the surface of hotspots. Each trail is thus pushed away from the hotspot as as it grows, resulting in a net displacement of actin monomers after trail collapse. In addition, trails grow in both directions (anterograde and retrograde), but with a small bias toward the tip of the axon (58% anterograde vs 42% retrograde).

The combination of these two processes (displacement of actin by trails and anterograde bias) results in the slow progress of actin along the axon. Modeling from the Jung lab allowed to determine the overall actin transport speed resulting from the hotspots and trails dynamics. Strikingly, this slow anterograde transport speed of actin (0.4 mm/day) precisely matches the values obtained by classic radio-labeling studies. This is a fundamentally new mechanism of slow axonal transport for cytoskeletal components, based on a biased assembly/disassembly mechanism rather than processive transport by motor proteins.

In this work, we used STORM imaging of axonal actin to pinpoint the architecture of hotspots, showing that the multi-directional growth of trails make them appear as asters when the axon is thicker (see Figure). Furthermore, we imaged hundreds of hotspots by STORM and quantified their diameter to ~200 nm. This is a first step toward elucidating the molecular organization of hotspots and trails, which will be crucial to understand their cellular functions.

Details of hotspots seen by STORM
Quantification of hotspots diameter from STORM images

Just published: our review on the architecture of axonal actin

Marie-Jeanne and Christophe wrote a review detailing how recent discoveries renewed the understanding of axonal actin organization. In the axon shaft itself, new nano-structures such as rings, hotspots and trails have been described, but their function remains to be elucidated. At presynapses, the precise architecture of actin is still elusive, and contradicting findings have been reported regarding its function. This is an exciting time to study actin in axons!

The review is now published in Molecular and Cellular Neuroscience, and will be part of a special issue on “Membrane Trafficking and Cytoskeletal Dynamics in Neuronal Function”. If you don’t have access to the review, a preprint manuscript is available on Zenodo.

Fig.2 from Papandreou & Leterrier 2018

The SQUIRREL is out!

Our article with the Henriques and Mercer labs is now out in Nature Methods. Previously posted on bioRxiv, it proposes a new metric to measure the quality of super-resolution images called NanoJ-SQUIRREL (Super-resolution Quantitative Image Rating and Reporting of Error Locations). Simply put, it compares the image to a reference diffraction-limited image, allowing to detect  artefacts and missing features in the super-resolved image.

We used SQUIRREL to determine when to stop a STORM acquisition, showing that the longest acquisition was not always the best. In this case of imaging actin rings along axons labeled with phalloïdin, the quality of the STORM image as measured by SQUIRREL peaks after 30,000 frames and slightly drops when reaching 60,000 frames:

Another application of SQUIRREL is to optimize a DNA-PAINT experiment. In DNA-PAINT imaging, the density of the blinking events can be tuned by varying the concentration of the imager strand. We imaged clathrin-coated pits in a glial cell and the blinking sequence were processed with different algorithms. Each algorithm had a specific optimal blinking density (and thus imager strand concentration): SRRF was better with a denser blinking sequence, while pure localization algorithms such as MLE or CoM require a sparser acquisition sequence:

There are a lot more applications in the paper and its hefty supplementary file, go check it! Then try it thanks to the easy to use, open-source plugin for the ImageJ/Fiji plugin software.

Finally, this project is a striking example of open science in action. I (Christophe) met and started to collaborate with Ricardo and Jason on Twitter; the manuscript was posted on bioRxiv, where it got feedback from beta-testers and caught the attention of editors, before being accepted for publication six months later. Congrats to Siân, David, Caron, Pedro, and everyone!


New article out: myosin II at the axon initial segment

Our collaboration with the lab of Jim Salzer (NYU) is just out. We visualized the association of phospho-myosin light chain (pMLC, an activator of the contractile myosin-II) with actin rings along the axon initial segment (AIS). This was done using two-color STORM. Moreover, acute treatment with KCL (mimicking elevated activity) resulted in a disappearance of the phospho-MLC signal before the disorganization of the actin rings. This suggests that myosin-II contractility has a role in setting the AIS shape and position along the axon, and that release of this contractility could be a key remodelling step for the activity-dependant plasticity of the AIS.

Just out: The nano-architecture of the axonal cytoskeleton

Our review on the nano-architecture of the axonal cytoskeleton is out today on the Nature Reviews Neuroscience website. This was a lot of work and a lot of fun to write with Pankaj Dubey and Subhojit Roy. We tried to provide an up-to-date view that discusses recent findings such as the various axonal actin structures visualized along the axon by STORM. We also wanted to highlight the classic EM works that shaped how we think about the axonal cytoskeleton. So it’s chock-full of recent references with fancy techniques, but also beautiful classic papers. We hope it will be a pleasant reading for all!

Two collaborative papers out in the Journal of Neuroscience

In collaboration with Matt Rasband’s lab in Houston, we characterized the α-spectrin that is present along axons at the axon initial segment (AIS) and nodes of Ranvier. This work is out today as two back-to-back paper just pre-published on the Journal of Neuroscience website, here and here. Spectrins are tetramers of two α and two β subunits. It is known that the β-spectrin form at the AIS and nodes is the ßIV-spectrin since 2000, but the identity of the α subunit was unknown. In the axon, spectrins binds submembrane actin rings regularly spaced every 190 nm. As this is just below the resolution limit of conventional fluorescence microscopy (~200 nm), the resulting periodic scaffold is only visible using super-resolutive techniques such as STORM.

The first paper: “αII spectrin forms a periodic cytoskeleton at the axon initial segment and is required for nervous system function” focuses on the identification of αII-spectrin as the ßIV-spectrin partner at the AIS, and the consequences of αII-spectrin depletion in CNS-specific knockout mice. We used super-resolution microscopy to show that αII-spectrin is integrated in the AIS periodic actin/spectrin scaffold that supports the axonal plasma membrane. With the αII-spectrin antibody we used, the periodicity is seen as double bands every 190 nm by STORM. When using 2-color DNA-PAINT to image αII-spectrin together with ßIV-spectrin, the doublet of αII-spectrin labeling appears on both sides of the ßIV-spectrin bands, resolving the organization of the spectrin tetramers in situ. We also showed by STORM that the periodic actin/spectrin complex is disorganized in αII-spectrin-depleted neurons.

The second paper: “An αII spectrin based cytoskeleton protects large diameter Myelinated axons from degeneration” focuses on αII-spectrin in the PNS and nodes of Ranvier. In C. elegans mutants, the submembrane spectrin scaffold is necessary for the mechanical resistance of axons. Here, an αII-spectrin knockout mouse specific to peripheral sensory neurons was used to demonstrate this for in a vertebrate. Using STORM, we showed that loss of αII-spectrin causes a disorganization of the periodic scaffold at and around nodes. This disorganization ultimately results in the degeneration of large-diameter peripheral axons lacking  αII-spectrin.