Imaging Intermediate Filaments and Microtubules with 2-dimensional Direct Stochastic Optical Reconstruction Microscopy

The overall goal of this methodology is to create the optimal experimental conditions from sample preparation to image acquisition and reconstruction in order to perform 2D dual-colored D-STORM imaging of microtubules and intermediate filaments in fixed cells. This method can help characterize the physical interactions between dense and complex cytoskeletal networks such as intermediate filaments and microtubules. The main advantage of this technique is that it allows the observation of cellular structures, which are not resolved with conventional fluorescence microscopy.

Visual demonstration of this method is critical as the control of sample preparation and acquisition of robe-linking data is crucial in order to limit the generation of artifacts. After growing U373 cells according to the text protocol, fix the cells by first using PBS to wash them once. Then, remove the PBS and add one milliliter per well of preheated extraction fixation solution.

Incubate the cells at room temperature for 60 seconds. Then remove the solution and add one milliliter per well of freshly prepared and preheated 4%PFA diluted in cytoskeleton buffer. Place the 12-well plate back into the incubator at 37 degrees Celsius for 10 minutes.

Then remove the PFA and add three milliliters of PBS per well. Use PBS to wash the cells twice. Then remove the PBS and add freshly prepared 10 millimolars sodium borohydride diluted in PBS in order to quench the autofluorescence from the glutaraldehyde.

Incubate the cells at room temperature for seven minutes and transfer the recycled sodium borohydride into a specific bin. Use PBS to wash the wells three times for five minutes each. Then remove the PSB and add 5%BSA in PBS as a blocking solution.

After immunostaining samples and preparing solutions in buffers according to the text protocol, mount the coverslip containing the labeled cells on a magnetic sample holder. And add the imaging buffer to completely fill the chamber. Apply the lid and make sure that there are no air bubbles between the imaging buffer and the lid.

Using absolute ethanol, clean the bottom of the sample and verify that there are no leaks. Then if necessary, use grease to properly seal the sample hold. To carry out imaging, switch on the microscope and the acquisition software.

Set up the acquisition parameters according to the text protocol, using the 100-fold NA 1.46 objective, the 1.6-fold Optivar lens, and the TIRF UHP mode. Create a 647 track to image the vimentin filaments labeled with Alexa Fluor 647. Select the 405 and 642 nanometer laser lines and the LP 655 emission filter.

Then, create a 555 track to image the microtubules labeled with Alexa Fluor 555. Select the 561, 488, and 405 nanometer laser lines to image the fluorophores and the BP 570 to 650 emission filter. Next, add oil to the objective and place the sample on the lens.

Then, select the locate tab and open the shutter of the fluorescence lamp. Find the focus and use the eyepiece to look for the cells to image. Then use the joystick to position the cells in the center of the field.

Click on the acquisition tab to return to acquisition mode. Then select the 647 track and set the 642 laser power to 0.2%and the 405 laser power to its minimal value. Set the exposure time to 50 milliseconds and the gain to 50.

Then choose continuous acquisition mode to observe the cell on the screen. Make sure that there is at least one fluorescent bead in the field of view. Use an autoscale mode for the display and adjust the focus.

Next, take a wide field epifluorescence image of the vimentin network by clicking on snap and save the image. To check TIRF illumination, click on TIRF, press continuous, adjust the acquisition parameters in order to have a homogenous field of illumination. Then press snap and save the image.

Check the 555 track. Uncheck the 647 track, and select the 555 track. Take an epifluorescence image of the microtubule network and save it.

Then take a TIRF image and save it. Now, check the 647 track. Uncheck the 555 track, and select the 647 track.

Set the gain to zero and the exposure time to 10 milliseconds. Then press continuous. Set the 642 nanometer laser power to 100%in order to pump most of the Alexa 647 dyes to the dark state.

Once the fluorophores start blinking, increase the exposure to 15 milliseconds and the gain to 300. Use the range indicator mode to verify that single molecule signals do not saturate the camera as indicated by the red color. In that case, decrease the gain until the saturation disappears.

The beads will remain saturated at the beginning of the acquisition. Press stop to discontinue observation of the cell. Expand the online processing tool and click online processing PALM to visualize the STORM image during acquisition.

Use nine for the peak mask size and six for the peak intensity to noise. Now, press start acquisition. During acquisition, refocus on the cell if necessary.

Adjust the exposure time and eventually switch on the 405 nanometer laser line starting at the 0.001%to keep a medium density of fluorophores with a minimum distance of one micrometer between single molecules. Make sure that the peak of localization precision on the histogram below the reconstructed image is centered around or below 10 nanometers. Press stop to end the movie when more than one million localizations have been reached.

Save the raw data from the STORM acquisition with the CZI format. Then in the channels tool, check track 555, uncheck track 647, and select track 555. Next, press the continuous button.

Set the exposure time to 30 milliseconds and the gain to zero. Then set both 488 and 561 lasers to 100%to pump Alexa 555 dyes to the dark state. Use the HILO mode of illumination.

Once the fluorophores are depleted, press stop. Set the gain to 250 and decrease the 488 laser to 50%Use the range indicator to check that single molecules do not saturate the camera. If that is the case, decrease the gain.

Now, press start acquisition. During acquisition, increase the gain gradually to reach the limit of saturation. Increase step-by-step the 405 nanometer laser power to activate the molecules and reach a medium density in the field of view.

Decrease the 488 nanometer laser power to 30%when the 405 laser is about 15%Then decrease gradually the 488 while increasing the 405 laser power in order to keep the blinking of the molecules as fast as possible and with a medium density. The 488 laser line coupled with the 561 excitation laser at maximal intensity increases both the on and off rates of the fluorophores, whereas the 405 laser line only increases the on rate. Stop the acquisition when 500, 000 localizations or more have been reached or when no more molecules are blinking.

Then save the raw data from the STORM acquisition with the CZI format. To carry out image reconstruction using the PAL-Drift tool, choose the model-based correction type with automatic segments with a maximum size of eight. Press apply multiple times in a row until the drift is corrected.

This model-based correction applies an algorithm based on cross-correlation analysis, which corrects the drift. Using the PAL filter tools, improve the appearance of the STORM image by selecting only the molecules which were best localized. For example, limit the localization precision to 30 nanometers and the PSF to 120 to 180 nanometers.

With the PAL-Render tool, use a pixel resolution of five or 10 nanometers and parameters according to the text protocol. Select render auto dynamic range HR with a 95%value and render auto dynamic range SWF with a 90%value. Then select render best quality.

In the PALM menu of the processing tab, select PALM convert. Press select and then apply. Finally, save the created image with the format LSM and not CZI.

This figure shows a typical example of a D-STORM image of vimentin filaments immuno-labeled with Alexa 647. The increase in resolution can clearly be observed upon comparison with the image acquired with a standard, wide-field microscope. The fluorescence intensity profiles presented in this graph show that super resolution microscopy imaging allows the resolution of vimentin bundles.

The D-STORM resolution is sufficient to count the number of filaments present in the bundles. Shown here is a typical example of the dual-colored D-STORM imaging of vimentin and microtubule networks immuno-labeled with Alexa 647 and Alexa 555, respectively. Good vimentin images should have at least 5, 000 localizations per micrometer squared and 2, 500 per micrometer squared for microtubules.

Once mastered, this technique can be done in three days if it performed properly. While attempting this procedure, it is important to adapt the methods of fixation and parametrization to the protein that would be imaged. For example, fixation with only glutaraldehyde gives poor results for intermediate filaments, but is best for microtubule fixation.

It is important to remember to use freshly prepared samples and solutions, especially MEA, whose pH has to be carefully adjusted. After its development, this technique paved the way for researchers in the field of cell biology to explore the morphology of nanoscopic cellular structures. After watching this video, you should have a good understanding of how to perform sample preparation, image acquisition, and reconstruction of 2D dual-colored D-STORM images of intermediate filaments and microtubules.

Don't forget that working with some solutions, especially PFA, NABH4 can be extremely hazardous and precautions such as wearing gloves, working under the chemical hood, and using specific bins should always been taken while performing this procedure.