We thank Prof. Yuri Korchev (Imperial College, UK) for the long-term support and advice throughout all stages of the project. We also thank Drs. Pavel Novak and Andrew Shevchuk (Imperial College, UK) as well as Oleg Belov (National Research Centre for Audiology, Russia) for their help with software development. The study was supported by NIDCD/NIH (R01 DC008861 and R01 DC014658 to G.I.F.).

The study was performed in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Kentucky (protocol 00903M2005).
1.&#160;Manufacturing and testing the nanopipettes
<ol>
	<li>Create a program in the micropipette puller to obtain pipettes with a resistance between 200 and 400 M&#8486;, which corresponds to inner tip diameters of approximately 50-70 nm. The parameters will depend on the micropipette puller. To obtain short pipettes with non-flexible fine tips, check in the operational manual of the puller.</li>
	<li>Use borosilicate glass capillaries with outer/inner diameters of 1/0.58 mm and an inner filament to facilitate filling. The length of the pipette is crucial because it determines the frequency of the lateral mechanical resonance of the pipette. The longer is the pipette, the lower is the resonant frequency and the harder is to avoid this resonance. 
	NOTE: The user should try to manufacture the shortest pipette the holder can accept. The length of nanopipettes in this experiment is usually 15-25 mm (Figure 2A).</li>
	<li>Fill the nanopipette up to its middle point (Figure 2A) with a bath solution, either Leibovitz&#39;s L-15 or with Hank&#39;s Balanced Salt Solution (HBSS) supplemented with 20 mM D-glucose (to adjust osmolarity). To avoid potential artefacts, use the same solution that will be used in the bath for recordings.</li>
	<li>Using an optical microscope with a magnification of 10x, check for any bubbles at the tip of the pipette (Figure 2B). The bubbles would prevent the current flow. It is harder to remove bubbles in the pipettes that have been pulled several hours before the experiment. Therefore, it is recommended to pull new pipettes with every experiment.</li>
	<li>Once the pipette is free of bubbles, mount it in the HPICM pipette holder (Figure 2C).</li>
	<li>Place the sample (tissue or calibration standard) on the custom-built&#160;chamber and add 4 mL of the above-mentioned bath solution.</li>
	<li>Place the&#160;custom-built&#160;chamber on the HPICM stage and introduce the ground electrode in the solution.</li>
	<li>Make sure that the voltage being applied to the pipette by the patch clamp amplifier is zero.</li>
	<li>Move the pipette in Z until it touches the liquid.</li>
	<li>Set the amplifier offset to zero and then add +100 mV to check the pipette current.</li>
	<li>Calculate the resistance and the diameter of the pipette, based on Ohm&#39;s law: 
	R = V/I 
	where R is the resistance (MOhm), V is the voltage applied to the nanopipette (mV) and I is the current flowing through the nanopipette (nA).
	<ol>
		<li>Calculate the inner diameter of the pipette as described elsewhere according to the following formula12: 
		IDTip&#160;= 1000/ &#8730;R 
		NOTE: The ideal resistance value is between 200 and 400 M&#8486;. Pipettes with a resistance higher than 400 M&#8486; might lead to an unstable current due to their small size (&#60; 50 nm inner diameter). On the contrary, pipettes with resistances smaller than 200 M&#8486; are too large (&#62; 70 nm inner diameter) and would not resolve small features. Its recommended to start imaging with the pipettes of 200 M&#8486; resistance, as they are easier to manufacture and tend to provide less electrical noise.</li>
	</ol>
	</li>
</ol>
2.&#160;Minimizing sample drifts and vibrations
NOTE: To decrease the mechanical noise in the system during imaging, mount the samples on the custom-built chambers that utilize thick glass slides (~1.2 mm):
<ol>
	<li>Remove the glass portion off a 50 mm glass-bottom dish, leaving the plastic walls intact.</li>
	<li>Glue the plastic portion of the cell culture dish on top of the thick glass slide with silicon glue.</li>
	<li>Mount the calibration sample in the middle of the chamber (on top of the glass slide) using either silicon glue or thin double-sided tape.</li>
	<li>Firmly secure the chamber onto the HPICM stage using double-sided tape.</li>
	<li>During imaging, close the Faraday cage and cover it with a blanket to minimize electrical interference and thermal drift, correspondingly.</li>
</ol>
3.Testing the resolution with AFM calibration standards 
NOTE: It is strongly recommended to image AFM standards (see Table of Materials) before imaging live cells in order to troubleshoot the system and test its resolution in the X-Z-Y axes. The calibration standards have silicon dioxide pillars and holes of different shapes but fixed heights/depths (i.e., 20 or 100 nm) on a 5 x 5 mm silicon chip. Starting with the 100 nm calibration standard is recommended, to guarantee that the Z resolution is below 100 nm. After achieving a successful high-resolution image of the pillars or holes in this calibration sample (Figure 3A), move to the 20 nm standard. If the imaging of the latter standard is successful (Figure 3B), the resolution in the Z axis is guaranteed to be below 20 nm and appropriate for the imaging of the hair cell stereocilia bundles12. The following steps are used to image both calibration standards.
<ol>
	<li>Attach the calibration standard to the chamber with silicon glue.</li>
	<li>Add 4 mL of HBSS to the chamber to cover the calibration sample. Then, secure the chamber to the XY stage of the HPICM setup using double-sided tape.</li>
	<li>Clamp the magnetic holder of the ground electrode to the stage near the chamber and immerse the electrode into the bath solution (Figure 1B).</li>
	<li>Mount the nanopipette into the holder, immerse it into the bath solution, and set its current to ~1 nA following the steps described in Section 1.</li>
	<li>Position the nanopipette approximately above the center of the calibration standard using a course patch-clamp manipulator. Visual inspection is usually enough for this positioning, since the area covered by silicon dioxide structures is relatively large (1 x 1 mm). In contrast to the organ of Corti explants (see below), calibration standard is non-transparent and, therefore, a more precise positioning guided by optical imaging is not possible for this sample.</li>
	<li>Increase the setpoint while monitoring the signal from the sensor of the Z piezo actuator on an oscilloscope in real time. After establishing a stable repeatable Z approach cycle (as in Figure 1C, bottom), decrease the setpoint to the value that is just above the point of instability. This procedure would ensure the optimal setpoint for this particular nanopipette.</li>
	<li>Move the pipette down at a speed of ~5 &#181;m/s with a patch clamp micromanipulator until it reaches the sample. At this moment, the bottom level of the real-time Z positioning signal (Figure 1C) will increase, indicating that the nanopipette is withdrawn due to &#34;sensing&#34; the sample surface. Any further movement of the nanopipette will result in further positive shift of Z-positioning signal. 
	NOTE: Be careful not to exceed the upper limit of Z piezo actuator movement.</li>
	<li>Start imaging at low resolution (see Table 1). Due to uneven mounting of the AFM standard, the highest point of the area of interest may be unknown. Therefore, set the amplitude of pipette retraction (hop amplitude) to at least 200-500 nm.
	<ol>
		<li>Once the highest point of the sample in the imaging area is identified, decrease the hop amplitude. A smaller hop amplitude allows faster scanning, which is preferred for high resolution imaging due to diminished effects of the drifts and decreased vibration.</li>
	</ol>
	</li>
	<li>Before moving the pipette to a new X-Y location, retract it about 200 &#181;m in the Z axis to prevent any undesired collisions with the sample. 
	NOTE: In cases when the nanopipette is not aligned with the center of the calibration standard, it is possible that the scanning starts just off the area of surface features.</li>
	<li>After the area of interest is found, start imaging at a higher resolution (see&#160;Table 1).</li>
</ol>
4.&#160;Making custom-built chambers to secure the cochlear explants
NOTE: Mount the cochlear explants in the chambers with custom-built clamping systems that utilize either flexible glass pipettes (step 4.1) (Figure 4A) or dental floss (step 4.2) (Figure 4B). The glass pipette chamber could be sterilized and used for the cultured organs of Corti, while dental floss chamber provides a more secure holding of the sample and a control over stereocilia bundle orientation during mounting. These custom-built chambers need to be prepared in advance, but they can be cleaned and re-used in several imaging sessions.
<ol>
	<li>Make a chamber using flexible glass pipettes
	<ol>
		<li>Pull two thin and flexible glass fibers from glass capillaries using a pipette puller. Our pulled glass fibers typically measure 1 to 2 cm in length and are fairly flexible.</li>
		<li>Place a small drop of the silicone elastomer on top of a glass coverslip. Use coverslips of 2 cm in diameter.</li>
		<li>Place the ends of two glass fibers on the silicone drop and arrange the fibers to have a small degree of separation between them (Figure 4A).</li>
		<li>Place the coverslip on a hot plate to quickly cure the elastomer (1 to 3 min).</li>
		<li>Glue the coverslip onto the glass bottom of the chamber described in Section 2 using a small amount (1-3 &#181;L) of silicone elastomer and allowing it to cure overnight.</li>
	</ol>
	</li>
	<li>Making a chamber using dental floss:
	<ol>
		<li>Remove the glass portion of a 50 mm glass-bottom dish, leaving the plastic walls intact. Then glue the plastic portion of the cell culture dish on top of a 1.2 mm thick glass slide with silicon glue.</li>
		<li>Mount one plastic coverslip (6.5 x 6.5 mm) with the same glue to the center of the chamber. Then repeat the process with another coverslip on top of the previous one.</li>
		<li>Mount two small tungsten or gold-plated wires (12 mm of length and ~0.5 mm in diameter) with silicon glue, each one at opposites sides of the cover slides. Glue them far enough (&#62; 10-15 mm) from the cover slides (Figure 4B).</li>
		<li>Separate two dental floss strands and place them on top of the cover slides and secure them to the wires by making a knot. Leave a small gap between both strands (Figure 4B, short arrows).</li>
	</ol>
	</li>
	<li>Clean the chambers after every use
	<ol>
		<li>Gently remove the tissue from the chamber using fine tweezers and lightly scrape any tissue residues left behind.</li>
		<li>Rinse the chamber first with 70% ethanol and then with distilled water.</li>
		<li>Repeat the rinse cycle if needed.</li>
		<li>Place the chamber upside down on a filter paper to let it dry until next experiment. The chambers do not need to be sterilized, unless culturing of the organ of Corti is planned after the imaging.</li>
	</ol>
	</li>
</ol>
5.&#160;Dissecting the rodent organ of Corti
<ol>
	<li>Perform dissection of the young postnatal cochlear explants as described in detail elsewhere13.</li>
	<li>For HPICM imaging, dissect the organ of Corti from mice between postnatal days 3 and 6 (P3-6), and from rats between postnatal days 3 and 8 (P3-8). 
	NOTE: Older hair cells are more susceptible to the damage during dissection and, therefore, cannot be used for hours-long time lapse HPICM imaging.</li>
	<li>Do not forget to remove the tectorial membrane before HPICM imaging.</li>
	<li>Immediately after dissection, secure the tissue in one of the chambers described in Section 4, either placing it under the flexible glass pipettes or under the two dental floss strands (Figure 4). Pre-fill these chambers with 4 mL of the room temperature bath solution (to minimize bubble formation).</li>
</ol>
6.&#160;Imaging of the auditory hair cells
<ol>
	<li>Mount the chamber with a freshly isolated organ of Corti on the X-Y piezo stage using double-sided tape and make sure that it is firmly secured to minimize chamber drift in X and Y axes (Figure 1B).</li>
	<li>Follow steps in Section 1 to place a new nanopipette and check for the correct pipette resistance.</li>
	<li>Using patch clamp micromanipulator, position nanopipette over the hair cell region, while observing the organ of Corti explant in an inverted microscope.</li>
	<li>Check if the system is stable with a setpoint of 0.5% or lower by recording the real-time current and Z positioning signal on the oscilloscope (as in Figure 1C). If Z signal is not stable, try to decrease the cutoff frequency of the low-pass filter of the patch clamp amplifier. However, it cannot be lower than the response time of Z piezo actuator (to avoid pipette collision with the sample due to delayed current readings). 
	NOTE: In practice, 5 kHz setting of this filter is found to be optimal. It is better to replace the nanopipette, if Z-signal is still unstable.</li>
	<li>Once a stable recording is achieved, determine the optimal setpoint and approach the sample with HPICM pipette as described in the steps 3.6-3.7 above.</li>
	<li>First, perform low resolution imaging (see&#160;Table 1), using a hop amplitude of at least 6 to 8 &#181;m. To image tall structures such as the hair cell stereocilia bundles, make sure that the hop amplitude is enough to avoid collision with these structures. 
	NOTE: If the hop amplitude is not enough, the pipette will not be able to jump over a stereocilium and there will be an imminent collision. The collision of the HPICM probe with a stereocilium may damage the hair bundle. Therefore, in cases when the height of the stereocilia bundle is uncertain, use a bigger hop amplitude.</li>
	<li>Get familiar with the topography of the organ of Corti by first performing and/or studying images obtained with scanning electron microscopy (Figure 5). 
	NOTE: If the HPICM image is uniform with the heights smaller than 1 &#181;m in every imaging point, the pipette is likely scanning the glass bottom and not the tissue. Alternatively, the pipette may &#34;land&#34; on a different region of the cochlear explant, away from the hair cells.</li>
	<li>If the pipette needs to be moved to a new X-Y location, retract it about 500 nm to avoid collisions with any tall features within the tissue. Repeat low-resolution HPICM imaging until the region of interest with the hair cells is found.</li>
	<li>After the region of interest is found, start imaging at a higher resolution (see Table 1). Try to spend less than 15 min when imaging a whole hair bundle. 
	NOTE: The hair cell bundles in the live tissue are not still but may change their orientation, for example, due to shape changes in the underlying supporting cells. Therefore, the images may exhibit movement artefacts if the image acquisition is too slow.</li>
	<li>Once again, determine the tallest features in the low-resolution images before the decreasing the hop amplitude for high-resolution imaging. For a region of interest covering entire hair cell bundle, reduce the hop amplitude to 4-5 &#181;m, while for a relatively small and &#34;flat&#34; region within the bundle (e.g., 2 x 2 &#181;m) reduce the hop amplitude even further, down to less than 1 &#181;m, thereby increasing the speed and resolution of imaging.</li>
</ol>
7.&#160;Image processing
NOTE: Imaging artefacts are common in HPICM imaging. Some of them can be corrected by image acquisition parameters, while others require post-processing either with a specialized SICM viewer or with more general data-processing programs like ImageJ or MatLab. Here we describe the most common artefacts and how we fix them with SICM viewer.
<ol>
	<li>Perform slope correction 
	&#8203;NOTE: It is not obvious for a beginner, but human eye cannot resolve sub-micrometer size features at the surface of a cell, if the imaging area has an overall slope of equal or larger size (Figure 3A,B, left). Therefore, it is necessary to determine the average slope of an imaged area (by fitting HPICM 3D image data to a single plane) and subtract it from the HPICM image (Figure 3A,B, middle).
	<ol>
		<li>Click Open to open an image with SICM viewer.</li>
		<li>Select the Image Correction tab.</li>
		<li>Select the Correct Slope tab.</li>
		<li>Press the Correct Slope button for an automated slope correction.</li>
	</ol>
	</li>
	<li>Perform line alignment 
	&#8203;NOTE: As mentioned before, mechanical and/or thermal drifts as well as cell movement artefacts represent a significant problem in HPICM imaging. A small drift with a speed of less than a micrometer per minute is usually not noticeable in a regular patch clamp setup. Yet, it could produce artefacts of several tens of nanometers in HPICM imaging, which is significantly larger than the resolution of HPICM. Therefore, it is not uncommon to encounter sudden jumps in Z axis between two neighboring HPICM scan lines during imaging. This could be corrected by analyzing differences between starting (and/or ending) Z-values in these neighboring scan lines.
	<ol>
		<li>Click Open to open an image with SICM viewer.</li>
		<li>Select the Image Correction tab.</li>
		<li>Select the Correct Slope tab.</li>
		<li>Choose the width of lines to be aligned. Press on the button ButtonDestripeLineFit&#160;for an automated line alignment correction.</li>
	</ol>
	</li>
	<li>Perform noise reduction 
	&#8203;NOTE: While obtaining images with HPICM, small fluctuations in the nanopipette current can lead to the nanopipette stopping far from the surface of the sample, especially with low setpoints. It results in the appearance of small white dots in the image. In order to correct this imaging artefact, it is necessary to identify the imaging points with the Z-value significantly larger than that of the neighbors and replace this value with an average of the neighbors. This is be done by an adjustable median filter.
	<ol>
		<li>Click Open to open an image with SICM viewer.</li>
		<li>Select the Image Processing tab.</li>
		<li>Select the Noise reduction tab.</li>
		<li>Set the Threshold filter (&#181;m) for the pixels to be removed.</li>
	</ol>
	</li>
</ol>

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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+scanning+ion-conductance+microscope.">The scanning ion-conductance microscope.</a> Science. 243 (4891), 641-643 (1989).</li><li>Korchev, Y. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specialized+scanning+ion-conductance+microscope+for+imaging+of+living+cells.">Specialized scanning ion-conductance microscope for imaging of living cells.</a> Journal of Microscopy. 188 (Pt 1), 17-23 (1997).</li><li>Shevchuk, A. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+proteins+in+membranes+of+living+cells+by+high-resolution+scanning+ion+conductance+microscopy.">Imaging proteins in membranes of living cells by high-resolution scanning ion conductance microscopy.</a> Angewandte Chemie (International ed in English. 45 (14), 2212-2216 (2006).</li><li>Novak, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoscale+live-cell+imaging+using+hopping+probe+ion+conductance+microscopy.">Nanoscale live-cell imaging using hopping probe ion conductance microscopy.</a> Nature Methods. 6 (4), 279-281 (2009).</li><li>V&#233;lez-Ortega, A. C., Frolenkov, G. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+live+cochlear+stereocilia+at+a+nanoscale+resolution+using+hopping+probe+ion+conductance+microscopy.">Visualization of live cochlear stereocilia at a nanoscale resolution using hopping probe ion conductance microscopy.</a> Methods in Molecular Biology. 1427, 203-221 (2016).</li><li>Gu, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+scanning+patch-clamp:+new+insights+into+cell+function.">High-resolution scanning patch-clamp: new insights into cell function.</a> FASEB Journal Official Publication of the Federation of American Societies for Experimental Biology. 16 (7), 748-750 (2002).</li><li>Frolenkov, G. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-channel+recordings+from+the+apical+surface+of+outer+hair+cells+with+a+scanning+ion+conductance+probe.">Single-channel recordings from the apical surface of outer hair cells with a scanning ion conductance probe.</a> Association for Research in Otolaryngology. Abs. 444, (2004).</li><li>S&#225;nchez, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Noncontact+measurement+of+the+local+mechanical+properties+of+living+cells+using+pressure+applied+via+a+pipette.">Noncontact measurement of the local mechanical properties of living cells using pressure applied via a pipette.</a> Biophysical Journal. 95 (6), 3017-3027 (2008).</li><li>Korchev, Y. E., Negulyaev, Y. A., Edwards, C. R., Vodyanoy, I., Lab, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+localization+of+single+active+ion+channels+on+the+surface+of+a+living+cell.">Functional localization of single active ion channels on the surface of a living cell.</a> Nature Cell Biology. 2 (9), 616-619 (2000).</li><li>Shevchuk, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Angular+approach+scanning+ion+conductance+microscopy.">Angular approach scanning ion conductance microscopy.</a> Biophysical Journal. 110 (10), 2252-2265 (2016).</li><li>Furness, D. N., Katori, Y., Nirmal Kumar, B., Hackney, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+dimensions+and+structural+attachments+of+tip+links+in+mammalian+cochlear+hair+cells+and+the+effects+of+exposure+to+different+levels+of+extracellular+calcium.">The dimensions and structural attachments of tip links in mammalian cochlear hair cells and the effects of exposure to different levels of extracellular calcium.</a> Neuroscience. 154 (1), 10-21 (2008).</li></ol>

The authors have no competing interests.

To obtain successful HPICM images, users need to establish a low noise and low vibration system and manufacture appropriate pipettes. We strongly recommend the use of AFM calibration standards to test the stability of the system before attempting to perform any live cell imaging. Once the resolution of the system is tested, users can consider imaging fixed organ of Corti samples to get familiar with the imaging settings before attempting any live cell imaging.
The optimal setpoint for imaging ...

Despite the fact that stereocilia bundles in the auditory hair cells are big enough to be visualized by optical microscopy and deflected in live cells in a patch clamp experiment, the essential structural components of the transduction machinery such as tip links could be imaged only with the electron microscopy in dead cells. In the mammalian auditory hair cells, the transduction machinery is located at the lower ends of the tip links, i.e., at the tips of the shorter row stereocilia1 and regulated locally through the signaling at the tips of stereocilia2,3. Yet, label-free imaging of the surface structures at this location in live hair cells is not possible due to the small sizes of stereocilia.
The mammalian cochlea has two types of auditory sensory cells: inner and outer hair cells. In the inner hair cells, stereocilia are longer and thicker compared to those in the outer hair cells4. The first and second row of stereocilia have a diameter of 300-500 nm in mouse or rat inner hair cells. Due to the diffraction of light, the maximum resolution achievable with a label-free optical microscopy is approximately 200 nm. Hence, visualization of individual stereocilia within first and second rows of the inner hair cell bundle is relatively easy&#160;with optical microscopy. In contrast, shorter row stereocilia in the inner hair cells and all stereocilia of the outer hair cells have diameters around 100-200 nm and cannot be visualized with optical microscopy5. Despite recent progress in super-resolution imaging, this fundamental limitation persists in any optical label-free imaging. All current commercially available super-resolution techniques do require some sort of fluorescent molecules6, which limits their applications. In addition to limitations due to the need for specific fluorescently tagged molecules, exposure to intense light irradiation has been shown to induce cellular damage and might influence cellular processes, which is a great disadvantage when studying live cells7.
Our current knowledge of the ultrastructural details of hair cell stereocilia bundles has been obtained mostly with various electron microscopy (EM) techniques, such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), freeze-fracture EM, and recently with 3D techniques such as serial sectioning with focused ion beam or cryo-EM tomography8,9,10,11,12,13,14,15,16. Unfortunately, all these EM techniques require chemical or cryofixation of the sample. Depending on the time scale of the phenomena, this requirement makes a study of the dynamic processes at the tips of stereocilia either impossible or very labor intensive.
Limited efforts have been made to image hair bundles of live hair cells with atomic force microscopy (AFM)17,18. Since AFM operates in physiological solutions, it could, in theory, visualize dynamic changes in the stereocilia bundles of live hair cells over time. The problem lies in the principles of high-resolution AFM, which implies certain physical contact between the AFM probe and the sample, even in the least damaging &#34;tapping&#34; mode19. When the AFM probe encounters a stereocilium, it usually crashes against it, damaging the structure of the hair bundle. As a result, this technique is not suitable for visualizing live, or even fixed, hair cells bundles17,18. The problem may be partially alleviated by using a large ball-shaped AFM probe that imposes only hydrodynamic forces to the surface of the sample20. However, even though such a probe is ideally suited to test mechanical properties of the sample21, it provides only a sub-micrometer resolution when imaging the organ of Corti22 and still applies to the sample a force that may be substantial for the highly sensitive stereocilia bundles.
Scanning ion conductance microscopy (SICM) is a version of scanning probe microscopy that uses a glass pipette probe filled with a conductive solution23. SICM detects the surface when the pipette approaches the cell and the electric current through the pipette decreases. Since this is happening well before touching the cell, the SICM is ideally suited for non-contact imaging of live cells in physiological solution24. The best resolution of SICM is on the order of single nanometers, which allows resolving individual protein complexes at the plasma membrane of a living cell25. However, similar to other scanning probe techniques, SICM is able to image only relatively flat surfaces. We overcame this limitation by inventing hopping probe ion conductance microscope (HPICM)26, in which the nanopipette approaches the sample at each imaging point (Figure 1A). Using HPICM, we were able to image stereocilia bundles in live auditory hair cells with nanoscale resolution27.
Another fundamental advantage of this technique is that HPICM is not only an imaging tool. In contrast to other scanning probe techniques, the HPICM/SICM probe is an electrode widely used in cell physiology for electrical recordings and local delivery of various stimuli. Ion channel activity does not usually interfere with HPICM imaging, because the total current through the HPICM probe is several orders of magnitude larger than the extracellular current generated by the largest ion channels25. However, HPICM allows precise positioning of the nanopipette over a structure of interest and subsequent single-channel patch-clamp recording from this structure28. This is how we obtained the first preliminary recordings of single channel activity at the tips of the outer hair cell stereocilia29. It is worth mentioning that even a large current through the nanopipette cannot produce significant changes of the potential across the plasma membrane due to enormous electrical shunt of the extracellular medium. However, individual ion channels can be activated mechanically by flow of liquid through the nanopipette30 or chemically by local application of an agonist31.
In HPICM, the image is generated when a nanopipette sequentially approaches the sample at one point, retracts, and then moves in lateral direction to repeat the approach (Figure 1A). A patch clamp amplifier constantly applies voltage to an AgCl wire in the pipette (Figure 1B) to generate a current of ~1 nA in the bath solution. The value of this current when the pipette is away from the surface of the cell is determined as a reference current (Iref, Figure 1C). Then, the pipette moves in the Z axis to approach the sample until the current is reduced by an amount predefined by the user (setpoint), usually 0.2%-1% of the Iref (Figure 1C, top trace). The system then saves Z value at this moment as the height of the sample, together with X and Y coordinates of this imaging point. Then, the pipette is retracted away from the surface (Figure 1C, bottom trace) at a speed defined by the user, usually 700-900 nm/ms. After retraction, the pipette (or, in our case, the sample - see Figure 1B) is moved laterally to the next imaging point, a new reference current value is obtained, and the pipette once again approaches the sample, repeating the process. The X-Y movement of the pipette is preferred in an upright microscope setup that is typically used for recordings of the hair cell mechanotransduction currents. In this setting, the HPICM probe approaches the hair cell bundles not from the top but at an angle32. However, the best resolution of HPICM imaging is achieved in an inverted microscope setup (Figure 1A,B), where the movement of the sample in X-Y directions is de-coupled from Z-movement of the nanopipette, thereby eliminating potential mechanical artefacts.
Using HPICM, we obtained topographic images of mouse and rat inner and outer hair cell stereocilia bundles, and even visualized the links between the stereocilia that are about 5 nm in diameter26,27. The success of hair cell bundle imaging with this technique relies on several factors. First, the noise (variance) of the nanopipette current should be as small as possible to allow the lowest possible setpoint for HPICM imaging. A low setpoint allows HPICM probe to &#8220;sense&#8221; stereocilia surface at a larger distance and at any angle to the probe approach and, surprisingly, improves X-Y resolution of HPICM imaging (see Discussion). Second, the vibrations and drifts in the system should be decreased to less than 10 nm, since they contribute directly to the imaging artefacts. Finally, even though the HPICM probe and the specimen stage are moved in Z and X-Y axes by the calibrated feedback-controlled piezo actuators that have an accuracy of a single nanometer or better, the diameter of the nanopipette tip determines the spread of the current (sensing volume) and hence the resolution (Figure 1A). Therefore, before imaging live hair cells, it is vital to pull the adequate pipettes, reach the desired resolution with calibration samples, and achieve low noise in the recording system.
For at least a couple of decades, the SICM technique has not been commercially available and it has been developing by only few labs in the world with the leading lab of Prof. Korchev in the Imperial College (UK). Recently, several SICM systems became commercially available (see Table of Materials), all of which are based on the original HPICM principles. However, imaging stereocilia bundles in the hair cells requires several custom modifications that are technically challenging (or even impossible) in the closed &#8220;ready-to-go&#8221; systems. Therefore, some component integration is needed. Since HPICM setup represents a patch clamp rig with more stringent vibration and drift requirements and a piezo-driven movement of the HPICM probe and the sample (Figure 1D), this integration is relatively easy for any researcher, who is proficient in patch clamping. However, a scientist without proper background would definitely need some training in electrophysiology first. Despite remaining challenges such as increasing the speed of imaging (see Discussion), we have been able to image stereocilia bundles in live hair cells with nanoscale resolution without damaging them.&#160;
This paper presents a detailed protocol to perform successful HPICM imaging of the live auditory hair cell bundles in young postnatal rat or mouse cochlear explants using our custom system. The integrated components are listed in the Table of Materials. The paper also describes common problems that can be encountered and how to troubleshoot them.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Analog oscilloscope</td>
			<td>B&#38;K Precision</td>
			<td>2160C</td>
			<td>Analog oscilloscope for real-time monitoring of nanopipette current and Z-axis approach</td>
		</tr>
		<tr>
			<td>AFM calibration standards</td>
			<td>TED PELLA Inc</td>
			<td>HS-100MG; HS-20MG</td>
			<td>These 100 and 20 nm calibration standards are used to test the performance of HPICM system</td>
		</tr>
		<tr>
			<td>Benchtop vibration Isolator</td>
			<td>AMETEK/TMC</td>
			<td>Everstill K-400</td>
			<td>Active vibration isolation</td>
		</tr>
		<tr>
			<td>Borosilicate glass capillaries</td>
			<td>World Precision Instruments (WPI)</td>
			<td>1B100F-4</td>
			<td>Borosilicate glass capillaries for the nanopipettes</td>
		</tr>
		<tr>
			<td>D-(+)-Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G8270</td>
			<td>To be added to the bath solution to adjust osmolarity</td>
		</tr>
		<tr>
			<td>Digitizer</td>
			<td>National Instruments Corporation</td>
			<td>PCI-6221</td>
			<td>Multi-channel input/output digitizer</td>
		</tr>
		<tr>
			<td>Fast analog Proportional-Integral-Derivative (PID) control for Z movement</td>
			<td>Standford Research Systems</td>
			<td>SIM900, SIM960, SIM980</td>
			<td>Instrumentation modules integrated in an external PID controller for Z movement. It requires a fast response that is usually not implemented in commercial piezo amplifiers.</td>
		</tr>
		<tr>
			<td>Faraday cage</td>
			<td>AMETEK/TMC</td>
			<td>Type II</td>
			<td>Required to shield electromagnetic interference</td>
		</tr>
		<tr>
			<td>Glass bottom dish</td>
			<td>World Precision Instruments (WPI)</td>
			<td>FD5040-100</td>
			<td>Used as the dish for the chamber for the tissue</td>
		</tr>
		<tr>
			<td>Hanks&#39; Balanced Salt Solution (HBSS)</td>
			<td>Gibco, Thermo Fisher Scientific</td>
			<td>14025092</td>
			<td>Extracellular (bath) solution</td>
		</tr>
		<tr>
			<td>Instrumentation amplifier</td>
			<td>Brownlee Precision</td>
			<td>Model 440</td>
			<td>Instrumentation amplifier provides required offsets, filtering, and secondary magnification or attenuation</td>
		</tr>
		<tr>
			<td>Laser-based micropipette puller</td>
			<td>Sutter Instrument</td>
			<td>P-2000/G</td>
			<td>Micropipette puller to fabricate the nanopipettes. Laser is needed for sharp quartz pipettes.</td>
		</tr>
		<tr>
			<td>Lebovitz&#39;s L-15, without phenol red</td>
			<td>Gibco, Thermo Fisher Scientific</td>
			<td>21083027</td>
			<td>Extracellular (bath) solution</td>
		</tr>
		<tr>
			<td>Micromanipulator</td>
			<td>Scientifica</td>
			<td>PatchStar</td>
			<td>Used for &#34;course&#34; positioning of the Z piezo actuator</td>
		</tr>
		<tr>
			<td>Microscope</td>
			<td>Nikon</td>
			<td>Eclipse TS100</td>
			<td>Inverted optical microscope</td>
		</tr>
		<tr>
			<td>Patch amplifier</td>
			<td>Molecular Devices</td>
			<td>Axopatch 200B</td>
			<td>The patch clamp amplifier measures the current through the nanopipette</td>
		</tr>
		<tr>
			<td>Piezo amplifier (XY axes)</td>
			<td>Physik Instrumente (PI)</td>
			<td>E-500.00, E-505.00, E-509.C2A</td>
			<td>Amplification and PID control for XY piezo translation stage</td>
		</tr>
		<tr>
			<td>Piezo amplifier (Z axis)</td>
			<td>Piezosystem jena</td>
			<td>ENT 400 &#38; 800</td>
			<td>Custom amplifier consisting of ENT 400 power supply and two ENT 800 amplifiers in parallel to achieve max current of 1.6 nA</td>
		</tr>
		<tr>
			<td>Plastic Coverslips</td>
			<td>TED PELLA Inc</td>
			<td>26028</td>
			<td>Used in the fabrication of the chambers for the tissue&#160;</td>
		</tr>
		<tr>
			<td>SICM controller &#38; software*</td>
			<td>Ionscope, UK (ionscope.com)</td>
			<td>N/A</td>
			<td>Custom controller based on SBC6711 digital signal processing board from Innovative Integration Ltd</td>
		</tr>
		<tr>
			<td>Silicone elastomer (Sylgard)</td>
			<td>World Precision Instruments (WPI)</td>
			<td>SYLG184</td>
			<td>Used to attach the flexible glass fibers to the chamber for the tissue</td>
		</tr>
		<tr>
			<td>Silicon glue</td>
			<td>The Dow Chemical Company</td>
			<td>734</td>
			<td>Used to glue the different parts of the chamber for the tissue</td>
		</tr>
		<tr>
			<td>Tungsten rod</td>
			<td>A-M Systems</td>
			<td>717500</td>
			<td>Used for holding the dental floss strands in the chamber for the tissue</td>
		</tr>
		<tr>
			<td>XY piezo nanopositioner</td>
			<td>Physik Instrumente (PI)</td>
			<td>P-733.2DD</td>
			<td>XY translation stage with capacitive sensors</td>
		</tr>
		<tr>
			<td>Z piezo nanopositioner</td>
			<td>Piezosystem jena</td>
			<td>RA 12/24 SG</td>
			<td>Ring piezoactuator with a strain gage sensor</td>
		</tr>
		<tr>
			<td colspan="4">*Ionscope does not sell separate SICM controllers anymore. There are few other commercial systems:&#160; NX12-Bio and NX10 SICM,&#160;</td>
		</tr>
		<tr>
			<td colspan="4">Park Systems, Korea and SICM modules from ICAPPIC Limited, UK (icappic.com). All these systems are based on the original&#160;</td>
		</tr>
		<tr>
			<td colspan="4">HPICM principles. However, imaging stereocilia bundles in the hair cells requires several custom modifications that are technically&#160;</td>
		</tr>
		<tr>
			<td colspan="4">challenging (or even impossible) in the closed &#8220;ready-to-go&#8221; systems such as Ionscope or NX12-Bio/NX10. Currently, there is only one&#160;</td>
		</tr>
		<tr>
			<td colspan="4">modular system (ICAPPIC) that has the flexibility to suit any SICM/HPICM experiment but requires some component integration.&#160;</td>
		</tr>
	</tbody>
</table>

stereocilia bundle imaging with nanoscale resolution in live mammalian auditory hair cells

Inner ear hair cells detect sound-induced displacements and transduce these stimuli into electrical signals in a hair bundle that consists of stereocilia that are arranged in rows of increasing height. When stereocilia are deflected, they tug on tiny (~5 nm in diameter) extracellular tip links interconnecting stereocilia, which convey forces to the mechanosensitive transduction channels. Although mechanotransduction has been studied in live hair cells for decades, the functionally important ultrastructural details of the mechanotransduction machinery at the tips of stereocilia (such as tip link dynamics or transduction-dependent stereocilia remodeling) can still be studied only in dead cells with electron microscopy. Theoretically, scanning probe techniques, such as atomic force microscopy, have enough resolution to visualize the surface of stereocilia. However, independent of imaging mode, even the slightest contact of the atomic force microscopy probe with the stereocilia bundle usually damages the bundle. Here we present a detailed protocol for the hopping probe ion conductance microscopy (HPICM) imaging of live rodent auditory hair cells. This non-contact scanning probe technique allows time lapse imaging of the surface of live cells with a complex topography, like hair cells, with single nanometers resolution and without making physical contact with the sample. The HPICM uses an electrical current passing through the glass nanopipette to detect the cell surface in close vicinity to the pipette, while a 3D-positioning piezoelectric system scans the surface and generates its image. With HPICM, we were able to image stereocilia bundles and the links interconnecting stereocilia in live auditory hair cells for several hours without noticeable damage. We anticipate that the use of HPICM will allow direct exploration of ultrastructural changes in the stereocilia of live hair cells for better understanding of their function.

The protocol presented in this paper can be used to visualize any live cells with complex topography. Following these steps, we routinely obtain images of live rat auditory hair cell bundles (Figure 6B,D). In spite of having lower X-Y resolution when compared to SEM images, our HPICM images can successfully resolve the different rows of stereocilia, the shape of the stereocilia tips, and even the small links (~5 nm in diameter) connecting adjacent stereocilia (<strong class=...

Watch this Scientific Journal Video about Stereocilia Bundle Imaging with Nanoscale Resolution in Live Mammalian Auditory Hair Cells at JoVE.com

Stereocilia Bundle Imaging with Nanoscale Resolution in Live Mammalian Auditory Hair Cells

Here we present a protocol for the Hopping Probe Ion Conductance Microscopy (HPICM), a non-contact scanning probe technique that allows nanoscale imaging of stereocilia bundles in live auditory hair cells.

Inner ear hair cells detect sound-induced displacements and transduce these stimuli into electrical signals in a hair bundle that consists of stereocilia ...

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3.0K Views.  University of Kentucky. Here we present a protocol for the Hopping Probe Ion Conductance Microscopy (HPICM), a non-contact scanning probe technique that allows nanoscale imaging of stereocilia bundles in live auditory hair cells.

Video: Stereocilia Bundle Imaging with Nanoscale Resolution in Live Mammalian Auditory Hair Cells

Live-imaging of PKC Translocation in Sf9 Cells and in Aplysia Sensory Neurons

Protein kinase Cs (PKCs) are serine threonine kinases that play a central role in regulating a wide variety of cellular processes such as cell growth and learning and memory. There are four known families of PKC isoforms in vertebrates: classical PKCs (&alpha;, &beta;I, &beta;II and &gamma;), novel type I PKCs (&#949; and &eta;), novel type II PKCs (&delta; and &theta;), and atypical PKCs (&zeta; and &iota;). The classical PKCs are activated by Ca2+ and diacylclycerol (DAG), while the novel PKCs are activated by DAG, but are Ca2+-independent. The atypical PKCs are activated by neither Ca2+ nor DAG. In Aplysia californica, our model system to study memory formation, there are three nervous system specific PKC isoforms one from each major class, namely the conventional PKC Apl I, the novel type I PKC Apl II and the atypical PKC Apl III. PKCs are lipid-activated kinases and thus activation of classical and novel PKCs in response to extracellular signals has been frequently correlated with PKC translocation from the cytoplasm to the plasma membrane. Therefore, visualizing PKC translocation in real time in live cells has become an invaluable tool for elucidating the signal transduction pathways that lead to PKC activation. For instance, this technique has allowed for us to establish that different isoforms of PKC translocate under different conditions to mediate distinct types of synaptic plasticity and that serotonin (5HT) activation of PKC Apl II requires production of both DAG and phosphatidic acid (PA) for translocation 1-2. Importantly, the ability to visualize the same neuron repeatedly has allowed us, for example, to measure desensitization of the PKC response in exquisite detail 3. In this video, we demonstrate each step of preparing Sf9 cell cultures, cultures of Aplysia sensory neurons have been described in another video article 4, expressing fluorescently tagged PKCs in Sf9 cells and in Aplysia sensory neurons and live-imaging of PKC translocation in response to different activators using laser-scanning microscopy.

In this video, we demonstrate visualization of PKC translocation in living cells using fluorescently tagged PKCs.

Protein kinase Cs (PKCs) are serine threonine kinases that play a central role in regulating a wide variety of cellular processes such as cell growth and ...

Time-lapse Live Imaging of Clonally Related Neural Progenitor Cells in the Developing Zebrafish Forebrain

Precise patterns of division, migration and differentiation of neural progenitor cells are crucial for proper brain development and function1,2. To understand the behavior of neural progenitor cells in the complex in vivo environment, time-lapse live imaging of neural progenitor cells in an intact brain is critically required. In this video, we exploit the unique features of zebrafish embryos to visualize the development of forebrain neural progenitor cells in vivo. We use electroporation to genetically and sparsely label individual neural progenitor cells. Briefly, DNA constructs coding for fluorescent markers were injected into the forebrain ventricle of 22 hours post fertilization (hpf) zebrafish embryos and electric pulses were delivered immediately. Six hours later, the electroporated zebrafish embryos were mounted with low melting point agarose in glass bottom culture dishes. Fluorescently labeled neural progenitor cells were then imaged for 36hours with fixed intervals under a confocal microscope using water dipping objective lens. The present method provides a way to gain insights into the in vivo development of forebrain neural progenitor cells and can be applied to other parts of the central nervous system of the zebrafish embryo.

The present video demonstrates a method which takes advantage of the combination of electroporation and confocal microscopy to perform live imaging on individual neural progenitor cells in the developing zebrafish forebrain. In vivo analysis of the development of forebrain neural progenitor cells at a clonal level can be achieved in this way.

Precise patterns of division, migration and differentiation of neural progenitor cells are crucial for proper brain development and function1,2. To ...

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding fundamental biological mechanisms. Striking progress has been particularly evident in Drosophila, whose extensive toolkit of mutants and transgenic lines provides a convenient model to study evolutionarily-conserved developmental and cell biological mechanisms. We are interested in understanding the mechanisms that control cell fate specification in the adult peripheral nervous system (PNS) in Drosophila. Bristles that cover the head, thorax, abdomen, legs and wings of the adult fly are individual mechanosensory organs, and have been studied as a model system for understanding mechanisms of Notch-dependent cell fate decisions. Sensory organ precursor (SOP) cells of the microchaetes (or small bristles), are distributed throughout the epithelium of the pupal thorax, and are specified during the first 12 hours after the onset of pupariation. After specification, the SOP cells begin to divide, segregating the cell fate determinant Numb to one daughter cell during mitosis. Numb functions as a cell-autonomous inhibitor of the Notch signaling pathway.
Here, we show a method to follow protein dynamics in SOP cell and its progeny within the intact pupal thorax using a combination of tissue-specific Gal4 drivers and GFP-tagged fusion proteins 1,2.This technique has the advantage over fixed tissue or cultured explants because it allows us to follow the entire development of an organ from specification of the neural precursor to growth and terminal differentiation of the organ. We can therefore directly correlate changes in cell behavior to changes in terminal differentiation. Moreover, we can combine the live imaging technique with mosaic analysis with a repressible cell marker (MARCM) system to assess the dynamics of tagged proteins in mitotic SOPs under mutant or wildtype conditions. Using this technique, we and others have revealed novel insights into regulation of asymmetric cell division and the control of Notch signaling activation in SOP cells (examples include references 1-6,7 ,8).

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

In this video, we describe a method for live cell imaging of asymmetrically dividing sensory organ progenitor cells and epidermal cells in intact Drosophila pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding ...

High-resolution Live Imaging of Cell Behavior in the Developing Neuroepithelium

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central nervous system (CNS). Although much is known about the molecular mechanisms that pattern the spinal cord and elicit neuronal differentiation1, 2, we lack a deep understanding of these early events at the level of cell behavior. It is thus critical to study the behavior of neural progenitors in real time as they undergo neurogenesis.
In the past, real-time imaging of early embryonic tissue has been limited by cell/tissue viability in culture as well as the phototoxic effects of fluorescent imaging. Here we present a novel assay for imaging such tissue for long periods of time, utilizing a novel ex vivo slice culture protocol and wide-field fluorescence microscopy (Fig. 1). This approach achieves long-term time-lapse monitoring of chick embryonic spinal cord progenitor cells with high spatial and temporal resolution.
This assay may be modified to image a range of embryonic tissues3, 4 In addition to the observation of cellular and sub-cellular behaviors, the development of novel and highly sensitive reporters for gene activity (for example, Notch signaling5) makes this assay a powerful tool with which to understand how signaling regulates cell behavior during embryonic development.

Imaging embryonic tissue in real-time is challenging over long periods of time. Here we present an assay for monitoring cellular and sub-cellular changes in chick spinal cord for long periods with high spatial and temporal resolution. This technique can be adapted for other regions of the nervous system and developing embryo.

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central ...

Patch Clamp Recordings in Inner Ear Hair Cells Isolated from Zebrafish

Patch clamp analyses of the voltage-gated channels in sensory hair cells isolated from a variety of species have been described previously1-4 but this video represents the first application of those techniques to hair cells from zebrafish. Here we demonstrate a method to isolate healthy, intact hair cells from all of the inner ear end-organs: saccule, lagena, utricle and semicircular canals. Further, we demonstrate the diversity in hair cell size and morphology and give an example of the kinds of patch clamp recordings that can be obtained. The advantage of the use of this zebrafish model system over others stems from the availability of zebrafish mutants that affect both hearing and balance. In combination with the use of transgenic lines and other techniques that utilize genetic analysis and manipulation, the cell isolation and electrophysiological methods introduced here should facilitate greater insight into the roles hair cells play in mediating these sensory modalities.

The purpose of this video is to demonstrate procedures for obtaining healthy, intact hair cells from the inner ear organs of adult zebrafish and then using them for patch clamp studies aimed at characterizing the biophysical properties of their voltage-gated channels.

Patch  clamp analyses of the voltage-gated channels in sensory hair cells isolated  from a variety of species have been described previously1-4 but this  ...

Functional Imaging of Auditory Cortex in Adult Cats using High-field fMRI

Current knowledge of sensory processing in the mammalian auditory system is mainly derived from electrophysiological studies in a variety of animal models, including monkeys, ferrets, bats, rodents, and cats. In order to draw suitable parallels between human and animal models of auditory function, it is important to establish a bridge between human functional imaging studies and animal electrophysiological studies. Functional magnetic resonance imaging (fMRI) is an established, minimally invasive method of measuring broad patterns of hemodynamic activity across different regions of the cerebral cortex. This technique is widely used to probe sensory function in the human brain, is a useful tool in linking studies of auditory processing in both humans and animals and has been successfully used to investigate auditory function in monkeys and rodents. The following protocol describes an experimental procedure for investigating auditory function in anesthetized adult cats by measuring stimulus-evoked hemodynamic changes in auditory cortex using fMRI. This method facilitates comparison of the hemodynamic responses across different models of auditory function thus leading to a better understanding of species-independent features of the mammalian auditory cortex.

Functional studies of the auditory system in mammals have traditionally been conducted using spatially-focused techniques such as electrophysiological recordings. The following protocol describes a method of visualizing large-scale patterns of evoked hemodynamic activity in the cat auditory cortex using functional magnetic resonance imaging.

Current knowledge of sensory processing in the mammalian auditory system is mainly derived from electrophysiological studies in a variety of animal ...

Super-resolution Imaging of Neuronal Dense-core Vesicles

Detection of fluorescence provides the foundation for many widely utilized and rapidly advancing microscopy techniques employed in modern biological and medical applications. Strengths of fluorescence include its sensitivity, specificity, and compatibility with live imaging. Unfortunately, conventional forms of fluorescence microscopy suffer from one major weakness, diffraction-limited resolution in the imaging plane, which hampers studies of structures with dimensions smaller than ~250 nm. Recently, this limitation has been overcome with the introduction of super-resolution fluorescence microscopy techniques, such as photoactivated localization microscopy (PALM). Unlike its conventional counterparts, PALM can produce images with a lateral resolution of tens of nanometers. It is thus now possible to use fluorescence, with its myriad strengths, to elucidate a spectrum of previously inaccessible attributes of cellular structure and organization.
Unfortunately, PALM is not trivial to implement, and successful strategies often must be tailored to the type of system under study. In this article, we show how to implement single-color PALM studies of vesicular structures in fixed, cultured neurons. PALM is ideally suited to the study of vesicles, which have dimensions that typically range from ~50-250 nm. Key steps in our approach include labeling neurons with photoconvertible (green to red) chimeras of vesicle cargo, collecting sparsely sampled raw images with a super-resolution microscopy system, and processing the raw images to produce a high-resolution PALM image. We also demonstrate the efficacy of our approach by presenting exceptionally well-resolved images of dense-core vesicles (DCVs) in cultured hippocampal neurons, which refute the hypothesis that extrasynaptic trafficking of DCVs is mediated largely by DCV clusters.

We describe how to implement photoactivated localization microscopy (PALM)-based studies of vesicles in fixed, cultured neurons. Key components of our protocol include labeling vesicles with photoconvertible chimeras, collecting sparsely sampled raw images with a super-resolution microscopy system, and processing the raw images to produce a super-resolution image.

Detection of fluorescence provides the foundation for many widely utilized and rapidly advancing microscopy techniques employed in modern biological and ...

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (&#62;3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice&#39;s kappa metric. Mean Dice&#39;s kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has ...

Optogenetic Stimulation of the Auditory Nerve

Direct electrical stimulation of spiral ganglion neurons (SGNs) by cochlear implants (CIs) enables open speech comprehension in the majority of implanted deaf subjects1-6. Nonetheless, sound coding with current CIs has poor frequency and intensity resolution due to broad current spread from each electrode contact activating a large number of SGNs along the tonotopic axis of the cochlea7-9. Optical stimulation is proposed as an alternative to electrical stimulation that promises spatially more confined activation of SGNs and, hence, higher frequency resolution of coding. In recent years, direct infrared illumination of&#160;the cochlea has been used to evoke responses in the auditory nerve10. Nevertheless it requires higher energies than electrical stimulation10,11 and uncertainty remains as to the underlying mechanism12. Here we describe a method based on optogenetics to stimulate SGNs with low intensity blue light, using transgenic mice with neuronal expression of channelrhodopsin 2 (ChR2)13 or virus-mediated expression of the ChR2-variant CatCh14. We used micro-light emitting diodes (&#181;LEDs) and fiber-coupled lasers to stimulate ChR2-expressing SGNs through a small artificial opening (cochleostomy) or the round window. We assayed the responses by scalp recordings of light-evoked potentials (optogenetic auditory brainstem response: oABR) or by microelectrode recordings from the auditory pathway and compared them with acoustic and electrical stimulation.

Cochlear implants (CIs) enable hearing by direct electrical stimulation of the auditory nerve. However, poor frequency and intensity resolution limits the quality of hearing with CIs. Here we describe optogenetic stimulation of the auditory nerve in mice as an alternative strategy for auditory research and developing future CIs.

Direct electrical stimulation of spiral ganglion neurons (SGNs) by cochlear implants (CIs) enables open speech comprehension in the majority of implanted ...

High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning

The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory discrimination learning in mice is described. In this learning paradigm, mice are trained in a shuttle box Go/NoGo-task to discriminate between rising and falling frequency-modulated tones in order to avoid a mild electric foot-shock. The protocol involves the enrichment of synaptosomes from four brain areas, namely the auditory cortex, frontal cortex, hippocampus, and striatum, at different stages of training. Synaptic protein expression patterns obtained from trained mice are compared to na&#239;ve controls using a proteomic approach. To achieve sufficient analytical depth, samples are fractionated in three different ways prior to mass spectrometry, namely 1D SDS-PAGE/in-gel digestion, in-solution digestion and phospho-peptide enrichment. 
High-resolution proteomic analysis on a mass spectrometer and label-free quantification are used to examine synaptic protein profiles in phospho-peptide-depleted and phospho-peptide-enriched fractions of synaptosomal protein samples. A commercial software package is utilized to reveal proteins and phospho-peptides with significantly regulated relative synaptic abundance levels (trained/na&#239;ve controls). Common and differential regulation modes for the synaptic proteome in the investigated brain regions of mice after training were observed. Subsequently, meta-analyses utilizing several databases are employed to identify underlying cellular functions and biological pathways.

The identification of molecules and pathways controlling synaptic plasticity and memory is still a major challenge in neuroscience. Here, a workflow is described addressing the relative quantification of synaptic proteins supposedly involved in the molecular reorganization of synapses during learning and memory consolidation in an auditory learning paradigm.

The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory ...