We would like to thank Ms. Christine A. Winters for excellent technical assistance. This work was supported by the Basic Neuroscience Program of the NINDS Intramural Research Program, NIH (Z01 NS002610).

The approach described here was developed using specific instruments, tools and software. Because labs will not be using the same experimental setup the approach is generalized where possible.
1. Rapid Freezing
The analytical method to be described is absolutely dependent on cryogenic approaches for: 1) the &#34;cryofixation&#34; of cells or tissues in a manner that quantitatively preserves the distribution of diffusible tissue components and chemical elements as they were in live cells at the instant of freezing; and 2) the preparation of ultrathin cryosections suitable for imaging and analysis in a TEM. These techniques are briefly described here, but details necessary to reproduce these procedures in other laboratories are beyond the scope of this article. Interested readers are referred to excellent recent articles9,14.
Caution: This section describes the use of liquefied ethane, which is highly flammable and potentially explosive; appropriate precautions should be taken. Operator must also be familiar with liquid nitrogen (LN2) safety precautions, including protective lab coat, glasses, and cryoresistant gloves. Note: Here and throughout, all tools (forceps, etc.) used to handle frozen specimens must be precooled in LN2 before use to avoid accidental thawing.
Cultured cells on coverslips
<ol>
	<li>Prepare a plunge freezing device by condensing gaseous ethane at -160 &#176;C in the LN2-cooled central well. Fill to the mark and cover the well with the pivoting aluminum lid when not in use.</li>
	<li>Using filter paper wedges, blot plastic coverslips of cultured cells under experimentally appropriate conditions to a thin aqueous film. Blot from the edge so as to avoid touching the tissue; the ideal residual film, determined by trial-and-error, is as thin as possible but not so thin as to evaporate and allow drying of the tissue surface.</li>
	<li>Holding the coverslip by the edge with clamping forceps, quickly immerse in liquid ethane, either manually or using the gravity-powered plunger.</li>
	<li>Place the frozen coverslip in a nearby styrofoam bowl of LN2, large enough to manipulate the desired number of coverslips into long-term storage containers. Aluminum screw cap cans that don&#39;t seize under LN2 are recommended.</li>
</ol>
Rapid freezing of cultured brain slices
<ol start="5">
	<li>Under a dissecting microscope, view and orient an organotypic hippocampal slice, undisturbed and still attached to the culture membrane insert. Place fiducial marks on the membrane near the edge of the slice with a black Sharpie-type pen and photograph.</li>
	<li>Still under the microscope, cut out approx. 5 x 5 mm membrane squares with individual slices centered on the squares. Avoid touching the slice or bending the membrane.</li>
	<li>Mount a membrane-supported slice, cushioned by a &#188; in&#160;diameter agar pad, on a custom&#160;designed aluminum disk made to fit a cryoultramicrotome (described below). Rapidly freeze the slice by pneumatically propelling it against an LN2-cooled sapphire block by means of a customized &#34;slam freezing&#34; device.</li>
	<li>Move to storage as described for cultured cells.</li>
</ol>
2. Cryosectioning
CAVEAT: Successfully producing dry-cut ribbons of ultrathin sections, while straightforward and logical, requires training, patience and considerable practice.
<ol>
	<li>Bake out a cryoultramicrotome equipped with a cryoattachment and cool to&#160;-135 &#176;C.</li>
	<li>Cut frozen coverslips into approx. 3 x 3 mm squares using a sharp, precooled scalpel. Embed pieces with cultures facing up in a viscous liquid &#34;cryoglue&#34; (a 1:6 mixture of ethanol and 2-propanol&#160;11), on standard 3&#160;mm diameter aluminum pins designed to fit the microtome specimen chuck. Avoid leaking cryoglue onto culture surface. Solidify cryoglue by lowering the cryobox temperature to &#8804;&#160;-160 &#176;C.
	<ul class="lalpha">
		<li>For frozen brain slices, securely attach discs directly to a custom-made specimen chuck by means of a screw collar.</li>
	</ul>
	</li>
	<li>Trim selected areas of the frozen specimens - e.g.&#160;cell-rich areas of coverslip pieces or identified areas of slices - to an approx. 250 x 250 &#956;m block face and ~100 &#956;m depth using a diamond trimming tool.</li>
	<li>Dry-cut ribbons of thin sections at ca. -160 &#176;C using a 35&#176; diamond cryoknife, essentially as described in referencs4,9. Cutting speed and knife clearance angle are determined empirically; a good starting point is 0.4-0.6 mm/sec at 9&#176;. The nominal thickness, i.e.&#160;specimen advance, of hydrated sections is typically 80 nm, although sections are actually 1.5-2.0x thicker, mainly due to compression. For satisfactory sectioning, an antistatic device is essential. Place the ionizing tip of the device 0.5-1 cm from the knife edge and adjust output power until satisfactory ribbons of sections are produced.</li>
	<li>Prepare eyelash probes by gluing (with epoxy) eyelashes to wood applicator sticks. Using such a probe, pick up and transfer sections from the back of the knife onto glow-discharged, carbon-coated pioloform support films cast over 100-mesh folding copper grids and resting on a half-folded indium foil envelope on a working shelf behind the knife. Fold over the top half of the grid and envelope, press with a cold pressing tool.</li>
	<li>Transfer wrapped grids to a convenient grid box and store in an aluminum can as described in step 1.4.</li>
</ol>
3. Cryotransfer of Specimens to the Electron Microscope
The core instrument for EPMA in this laboratory is an analytical electron microscope operated at 120 kV and equipped for cryomicroscopy, that is, designed with a clean vacuum, specimen-area anticontaminator, a 2k x 2k high-sensitivity digital camera and cryotransfer specimen holder. Check beforehand microscope alignment and operating conditions in both low- and high-magnification modes and confirm a satisfactory column vacuum, ideally &#8804;10-7 Torr. Tune up as necessary.
<ol>
	<li>Confirm that the vacuum insulation of the Dewar component of the cryoholder is satisfactory. Pump as necessary.</li>
	<li>Cool the cryoholder to its minimum temperature, at least -160 &#176;C, while under high vacuum within the microscope stage; detach the cable connecting the holder to its control box. Tilt the goniometer 45&#176; clockwise before removing the holder to minimize LN2 spilling onto operator and microscope surfaces.</li>
	<li>Prepare the benchtop cryoworkstation by cooling the integral insulated cup to &#8804;160 &#176;C.</li>
	<li>Transfer (quickly!) the cooled cryoholder from microscope to cryo workstation. Retract the holder&#39;s frost shield.</li>
	<li>Retrieve under LN2 a grid sandwich from storage and place on the working table of the cryoworkstation. A retaining ring for the holder&#39;s specimen well is also placed on the table.</li>
	<li>Open the indium envelope and move the enclosed folding grid to the specimen well of the cryoholder. Secure the grid with retaining ring using the spanner tool provided and close the frost shield.</li>
	<li>Quickly remove the cryoholder from the cryoworkstation and insert into the airlock of the microscope and go through the pumping sequence as quickly as possible. On insertion, there should be minimal disruption of the column vacuum.</li>
	<li>Return goniometer to 0&#176; tilt. Reconnect and reenergize the control box and confirm that the specimen temperature is &#8804;150&#160;&#176;C.</li>
	<li>Refill the Dewar of the specimen holder and allow vacuum and temperature to fully recover.</li>
</ol>
4. Visual Survey of Sections
<ol>
	<li>Retract the frost shield of the holder to expose specimen and turn on the electron beam.</li>
	<li>Visually evaluate the specimen at low magnification, typically 250X, and low illumination. As illustrated in Figure 1, sections should be thin and smooth, not folded or overlapping, flat and well attached to the support film, and generally not obscured by grid bars.</li>
	<li>Optionally photograph selected sections. (NOTE: Minimize beam exposure, since frozen-hydrated sections are very susceptible to beam-induced damage.) Use the automated digital goniometer stage to store coordinates of selected sections.</li>
</ol>
5. Freeze-drying of Sections
<ol>
	<li>Freeze-dry sections by increasing holder temperature to ca. -100 &#176;C for ~30 min.</li>
	<li>Recool holder to -160 &#176;C or below.</li>
	<li>Before imaging, turn off cryoholder control unit and physically disconnect controller cable to avoid image drift due to thermal cycling and/or vibration pickup.</li>
</ol>
6. Imaging of Cells and Organelles
Structural images of freeze-dried sections are obtained at ca. -160 &#176;C as low-dose, zero-loss images recorded digitally using a 2k x 2k slow-scan CCD camera controlled by appropriate software.
<ol>
	<li>Activate the EM in hi-mag mode.</li>
	<li>Choose and image at ~2,000X (as TIFFs, see Figure 2) selected cells and subcellular areas of interest in high-quality sections whose locations were previously recorded and stored. (NOTE: The dried sections are now substantially less fragile and less susceptible to electron beam damage.</li>
	<li>Evaluate images in order to select regions of interest (ROIs) for X-ray analysis. This step can optionally be performed off-line, in which case the EM can be turned off and the specimen allowed to warm to room temperature.</li>
</ol>
7. Acquisition of X-ray Spectra
X-ray spectra can be recorded using any of several commercial or custom-designed X-ray analysis systems minimally consisting of an energy-dispersive X-ray (EDX) detector, associated pulse-processor electronics and compatible acquisition and display software. (The system used in this lab is described in Table 1.)
<ol>
	<li>Configure the EM for the X-ray acquisition by inserting the EDX detector into the column (if necessary), withdrawing the objective aperture, and inserting and centering any stray radiation apertures. Adjust the cryoholder to the lowest temperature at which frost contamination of the specimen is avoided, but at least below -100 &#176;C.</li>
	<li>Tilt the holder 20&#176; toward the detector.</li>
	<li>Under wide-field imaging conditions, and assuming one intends to analyze the matrix of an individual mitochondria, choose a mitochondrion for analysis, move it to the center of the field and focus.</li>
	<li>Go to spot mode (on some microscopes just converge the beam using second condenser focus) and increase the beam current to ca. 3 nA (as measured with a Faraday cup or similar) into a 100 nm spot.</li>
	<li>Launch the spectrum acquisition software and begin 100 sec acquisitions, which can be viewed live time on the display monitor. Save recorded spectrum (Figure 2). The industry standard EMSA format is preferred.</li>
	<li>Shut down the EM and transfer the multiple-spectra file(s) to an (offline) analysis workstation.</li>
</ol>
8. Analysis of X-ray Spectra
Qualitative analysis
An EDX spectrum (Figure 2, inset) is essentially an x-y plot of the X-ray intensity vs. energy. Spectra contain qualitative and quantitative information about the elemental composition of the analyzed volume, in that the &#34;characteristic&#34; energy of a peak identifies the element giving rise to that peak while the intensity reflects the amount of that element. The characteristic peaks ride on top of a slowly varying background, the &#34;continuum&#34;. (The legend to Figure 2 further discusses salient details of EDX spectra.) The energy of the peak manifolds for the entire periodic table are defined by the well known electronic structure of elements, thus all EDX software links to a database that automatically identifies components of an analyte. In a physiological context, elements of general interest that are well suited to EDX analysis include Na (K&#945; at 1.04 keV), P (2.01 keV), K (3.31 keV), and Ca (3.69 keV).
<ol>
	<li>Take advantage of available software database and peak matching routines to identify major elements in the spectra. In a biological specimen expect to find peaks for Na, Mg, P, S, Cl, K,&#160;and Ca. (CAUTION: The last two elements overlap!)</li>
</ol>
Quantitative analysis
Quantitative analysis of EDX spectra consists of extracting the integrated area of identified peaks and converting this value to a concentration. For biological analysis, the established approach is the Hall peak/continuum method4,7,10, which takes advantage of the fact that the intensity of the continuum (defined above and in Figure 2) is proportional to the dry mass of the analyzed volume. Thus, the ratio of peak area/continuum area, when compared to the same ratio in spectra of standards of known composition, specifies the concentration in the targeted cellular compartment. Note that this approach provides concentrations in units of moles per weight, typically expressed as mmol/kg dry weight. This unit is unusual and for interpretation may require additional conversion to, for example, mmol/L&#160;wet weight or mmol/mg protein, as described elsewhere4,10.
<ol start="2">
	<li>Extract peak areas (and error estimates) of biological elements between Z = 10-20 (0.5-4.0 keV), i.e.&#160;Na, Mg, P, S, Cl, K, and Ca, using one of the fitting routines built into analysis software (see Table 1, especially footnote 4). This lab uses Simplex or multiple-least squares fitting. Note that this fitting requires careful attention to resolving the overlap between K and Ca peaks (see Figure 2).</li>
	<li>Integrate the continuum between 1.45-1.61 keV. Alternative interference-free regions can be used.</li>
	<li>Calculate peak/continuum ratios and then concentrations by comparison to standards. Propagate errors throughout the analysis.</li>
	<li>Use standard statistical software and formulas to estimate averages that reflect biological variability.</li>
</ol>

<ol>
	<li>Aronova, M. A., Kim, Y. C., Pivovarova, N. B., Andrews, S. B., Leapman, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+EFTEM+mapping+of+near+physiological+calcium+concentrations+in+biological+specimens.">Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens.</a> Ultramicroscopy. 109, 201-212 (2009).</li><li>Aronova, M. A., Leapman, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elemental+mapping+by+electron+energy+loss+spectroscopy+in+biology.">Elemental mapping by electron energy loss spectroscopy in biology.</a> Methods Mol. Biol. 950, 209-226 (2013).</li><li>Bezprozvanny, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calcium+signaling+and+neurodegenerative+diseases.">Calcium signaling and neurodegenerative diseases.</a> Trends Mol. Med. 15, 89-100 (2009).</li><li>Fernandez-Segura, E., Warley, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron+probe+X-ray+microanalysis+for+the+study+of+cell+physiology.">Electron probe X-ray microanalysis for the study of cell physiology.</a> Methods Cell Biol. 88, 19-43 (2008).</li><li>Gibson, G. E., Starkov, A., Blass, J. P., Ratan, R. R., Beal, M. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cause+and+consequence:+Mitochondrial+dysfunction+initiates+and+propagates+neuronal+dysfunction,+neuronal+death+and+behavioral+abnormalities+in+age-associated+neurodegenerative+diseases.">Cause and consequence: Mitochondrial dysfunction initiates and propagates neuronal dysfunction, neuronal death and behavioral abnormalities in age-associated neurodegenerative diseases.</a> Biochim. Biophys. Acta. 1802, 122-134 (2010).</li><li>Leapman, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+techniques+in+electron+microscopy.">Novel techniques in electron microscopy.</a> Curr. Opin. Neurobiol. 14, 591-598 (2004).</li><li>LeFurgey, A., Bond, M., Ingram, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frontiers+in+electron+probe+microanalysis:+application+to+cell+physiology.">Frontiers in electron probe microanalysis: application to cell physiology.</a> Ultramicroscopy. 24, 185-219 (1988).</li><li>Newbury, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+new+X-ray+mapping:+X-ray+spectrum+imaging+above+100+kHz+output+count+rate+with+the+silicon+drift+detector.">The new X-ray mapping: X-ray spectrum imaging above 100 kHz output count rate with the silicon drift detector.</a> Microsc. Microanal. 12, 26-35 (2006).</li><li>Pierson, J., Vos, M., McIntosh, J. R., Peters, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Perspectives+on+electron+cryotomography+of+vitreous+cryo-sections.">Perspectives on electron cryotomography of vitreous cryo-sections.</a> J. Electron Microsc. 60, S93-S100 (2011).</li><li>Pivovarova, N. B., Hongpaisan, J., Andrews, S. B., Friel, D. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Depolarization-induced+mitochondrial+Ca+accumulation+in+sympathetic+neurons:+spatial+and+temporal+characteristics.">Depolarization-induced mitochondrial Ca accumulation in sympathetic neurons: spatial and temporal characteristics.</a> J. Neurosci. 19, 6372-6384 (1999).</li><li>Pivovarova, N. B., Nguyen, H. V., Winters, C. A., Brantner, C. A., Smith, C. L., Andrews, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Excitotoxic+calcium+overload+in+a+subpopulation+of+mitochondria+triggers+delayed+death+in+hippocampal+neurons.">Excitotoxic calcium overload in a subpopulation of mitochondria triggers delayed death in hippocampal neurons.</a> J. Neurosci. 24, 5611-5622 (2004).</li><li>Ritchie, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectrum+simulation+in+DTSA-II.">Spectrum simulation in DTSA-II.</a> Microsc. Microanal. 15, 454-468 (2009).</li><li>Stanika, R. I., Winters, C. A., Pivovarova, N. B., Andrews, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+NMDA+receptor-dependent+calcium+loading+and+mitochondrial+dysfunction+in+CA1+vs.+CA3+hippocampal+neurons.">Differential NMDA receptor-dependent calcium loading and mitochondrial dysfunction in CA1 vs. CA3 hippocampal neurons.</a> Neurobiol. Dis. 37, 403-411 (2010).</li><li>Zhang, 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=Direct+visualization+of+receptor+arrays+in+frozen-hydrated+sections+and+plunge-frozen+specimens+of+E.+coli+engineered+to+overproduce+the+hemotaxis+receptor+Tsr.">Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the hemotaxis receptor Tsr.</a> J. Microsc. 216, 76-83 (2004).</li></ol>

The authors report no conflicts of interest.

The electron microscope-based analytical method presented here allows for the detection, identification, and quantitation of several elements of biological interest, including Na, K, P, and especially Ca. These analyses can be carried out at subcellular, i.e., intra-organelle, resolution owing to the ability to locate and identify structures of interest in high-quality images of cryosections prepared from rapidly frozen specimens. Note that no staining is required to record electron images comparable in structur...

Calcium ions are arguably the most important and versatile cell signaling entity in biology, playing an essential role in normal processes as diverse as synaptic transmission and gene expression. On the other hand, calcium is equally important in cell death. In particular, calcium deregulation is a key factor in neuronal injury in stroke, Parkinson&#39;s, Alzheimer&#39;s and other neurodegenerative diseases3,5. Thus, it is critically important to understand quantitatively how calcium is distributed within cells, and how this changes following physiological or pathophysiological stimuli. This goal is complicated by the fact that calcium is dynamically distributed between two physical states - free in solution or bound to a substrate - and that cellular calcium concentrations change over several orders of magnitude as a consequence of stimulation.
While there are several advanced methodologies available for the analysis of free intracellular calcium, the determination of total calcium concentrations in defined intracellular compartments is realistically limited to one approach, namely, electron probe microanalysis (EPMA). EPMA is a technique that couples an X-ray spectrometer to a transmission electron microscope (TEM). The TEM electron gun focuses a stationary, submicron electron probe on a subcellular region of interest and the element-specific X-rays emitted as a result of electron bombardment are collected and analyzed (see references7,4 for detailed technical reviews). Advantages of EPMA include single organelle-level resolution and submillimolar sensitivity. In practice, however, EPMA requires specialized cryotechniques and instrumentation for specimen preparation and analysis. Here, the tools, techniques and instruments appropriate for measurements of intracellular calcium using EPMA are described. Intramitochondrial calcium is of special interest on account of the critical role that mitochondrial calcium overload plays in neurodegenerative diseases.

<table border="1">
	<tbody>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>REAGENTS/MATERIALS</td>
		</tr>
		<tr>
			<td>Thermanox plastic coverslips</td>
			<td>Thermo Fischer Scientific</td>
			<td>72280</td>
			<td></td>
		</tr>
		<tr>
			<td>Culture inserts</td>
			<td>BD Falcon</td>
			<td>353090</td>
			<td>For 6-well plates</td>
		</tr>
		<tr>
			<td>Cryopins</td>
			<td>Leica Microsystems</td>
			<td>16701952</td>
			<td>Grooved</td>
		</tr>
		<tr>
			<td>Wood applicators</td>
			<td>EM Sciences</td>
			<td>72300</td>
			<td></td>
		</tr>
		<tr>
			<td>Folding EM grids</td>
			<td>Ted Pella</td>
			<td>4GC100/100</td>
			<td>100 mesh</td>
		</tr>
		<tr>
			<td>Indium foil</td>
			<td>Alfa Aesar</td>
			<td>13982</td>
			<td>0.25 mm thick</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>EQUIPMENT</td>
		</tr>
		<tr>
			<td>Plunge freezing device</td>
			<td>Leica Microsystems</td>
			<td>KF-80</td>
			<td></td>
		</tr>
		<tr>
			<td>Slam freezing device</td>
			<td>LifeCell</td>
			<td>CF-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultramicrotome</td>
			<td>Leica Microsystems</td>
			<td>UC6</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryoattachment for microtome</td>
			<td>Leica Microsystems</td>
			<td>FC6</td>
			<td></td>
		</tr>
		<tr>
			<td>Diamond cryotrimming tool</td>
			<td>Diatome</td>
			<td>Cryotrim 45</td>
			<td></td>
		</tr>
		<tr>
			<td>Diamond cryoknife</td>
			<td>Diatome</td>
			<td>Cryo 35</td>
			<td></td>
		</tr>
		<tr>
			<td>Antistatic device</td>
			<td>Diatome</td>
			<td>Hauf Static Line</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryo electron microscope</td>
			<td>Carl Zeiss Microscopy</td>
			<td>EM912 Omega</td>
			<td></td>
		</tr>
		<tr>
			<td>EM cryo specimen holder</td>
			<td>Gatan</td>
			<td>CT3500</td>
			<td></td>
		</tr>
		<tr>
			<td>Slow-scan CCD camera, 2k x 2k</td>
			<td>Troendle (TRS)</td>
			<td>Sharpeye</td>
			<td></td>
		</tr>
		<tr>
			<td>Image acquisition software</td>
			<td>Olympus SIS</td>
			<td>iTEM suite</td>
			<td></td>
		</tr>
		<tr>
			<td>ED x-ray detector</td>
			<td>Oxford Instruments</td>
			<td>Linksystem Pentafet</td>
			<td></td>
		</tr>
		<tr>
			<td>Pulse Processor</td>
			<td>Oxford Instruments</td>
			<td>XP-3</td>
			<td></td>
		</tr>
		<tr>
			<td>PCI backplane card</td>
			<td>4pi Systems</td>
			<td>Spectral Engine II</td>
			<td></td>
		</tr>
		<tr>
			<td>Desktop computer</td>
			<td>Apple</td>
			<td>Any OS9-compatible model</td>
			<td></td>
		</tr>
		<tr>
			<td>X-ray analysis software</td>
			<td>NIST</td>
			<td>DTSA, DTSA II</td>
			<td></td>
		</tr>
		<tr>
			<td>Spreadsheet software</td>
			<td>Microsoft</td>
			<td>Excel</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>
			<ol>
				<li>The CF100 is no longer sold commercially, although the machine is available at many academic facilities, and complete machines or parts can be found on-line.</li>
				<li>A video tutorial for the CT3500 cryotransfer holder is available at <a href="http://www.gatan.com/files/Movies/CT3500_Cryo_transfer_holder.mp4" target="_blank">http://www.gatan.com/files/Movies/CT3500_Cryo_transfer_holder.mp4</a>.</li>
				<li>The SEII is obsolete; the Universal Spectral Engine Is a later, PC-compatible product with comparable functionality. 4pi has ceased manufacturing and sales but still provides technical customer support. Used systems are often found online.</li>
				<li>The original DTSA is now obsolete. NIST offers in the public domain an updated successor, DTSA II 12 (<a href="http://www.nist.gov/mml/mmsd/software.cfm" target="_blank">http://www.nist.gov/mml/mmsd/software.cfm</a>)</li>
			</ol>
			</td>
		</tr>
	</tbody>
</table>

measurement of total calcium in neurons by electron probe x-ray microanalysis

In this article the tools, techniques, and instruments appropriate for quantitative measurements of intracellular elemental content using the technique known as electron probe microanalysis (EPMA) are described. Intramitochondrial calcium is a particular focus because of the critical role that mitochondrial calcium overload plays in neurodegenerative diseases. The method is based on the analysis of X-rays generated in an electron microscope (EM) by interaction of an electron beam with the specimen. In order to maintain the native distribution of diffusible elements in electron microscopy specimens, EPMA requires &#34;cryofixation&#34; of tissue followed by the preparation of ultrathin cryosections. Rapid freezing of cultured cells or organotypic slice cultures is carried out by plunge freezing in liquid ethane or by slam freezing against a cold metal block, respectively. Cryosections nominally 80 nm thick are cut dry with a diamond knife at ca. -160 &#176;C, mounted on carbon/pioloform-coated copper grids, and cryotransferred into a cryo-EM using a specialized cryospecimen holder. After visual survey and location mapping at &#8804;-160 &#176;C and low electron dose, frozen-hydrated cryosections are freeze-dried at -100 &#176;C for ~30 min. Organelle-level images of dried cryosections are recorded, also at low dose, by means of a slow-scan CCD camera and subcellular regions of interest selected for analysis. X-rays emitted from ROIs by a stationary, focused, high-intensity electron probe are collected by an energy-dispersive X-ray (EDX) spectrometer, processed by associated electronics, and presented as an X-ray spectrum, that is, a plot of X-ray intensity vs. energy. Additional software facilitates: 1) identification of elemental components by their &#34;characteristic&#34; peak energies and fingerprint; and 2) quantitative analysis by extraction of peak areas/background. This paper concludes with two examples that illustrate typical EPMA applications, one in which mitochondrial calcium analysis provided critical insight into mechanisms of excitotoxic injury and another that revealed the basis of ischemia resistance.

Brain cells typically sustain excitotoxic injury as a result of the pathological neurotransmitter release that occurs under ischemic conditions. EPMA was critical to discovering how the ability of neuronal mitochondria to sequester massive amounts of calcium underlies the mechanism of injury. The electron micrograph in Figure 3 illustrates the appearance of mitochondria in freeze-dried cryosections of cultured hippocampal neurons rapidly frozen after 30 min exposure to an excitotoxic stimulus (100 &#956;...

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Measurement of Total Calcium in Neurons by Electron Probe X-ray Microanalysis

This paper describes the application of cryoanalytical electron microscopy to the quantitative measurement of total calcium content and distribution at subcellular resolution in physiologically defined biological specimens.

In this article the tools, techniques, and instruments appropriate for quantitative measurements of intracellular elemental content using the technique ...

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JoVE Journal

Neuroscience

12.0K Views.  National Institutes of Health. This paper describes the application of cryoanalytical electron microscopy to the quantitative measurement of total calcium content and distribution at subcellular resolution in physiologically defined biological specimens.

Video: Measurement of Total Calcium in Neurons by Electron Probe X-ray Microanalysis

Dissection and Culture of Commissural Neurons from Embryonic Spinal Cord

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies of these neurons are located in the dorsal spinal cord and their axons follow stereotyped trajectories during embryonic development. Commissural axons initially project ventrally towards the floorplate. After crossing the midline, these axons turn anteriorly and project towards the brain. Each of these steps is regulated by the action of several guidance cues. Cultures highly enriched in commissural neurons are ideally suited for many experiments addressing the mechanisms of axon pathfinding, including turning assays, immunochemistry and biochemistry. Here, we describe a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. First, the spinal cord is isolated and dorsal strips are dissected out. The dorsal tissue is then dissociated into a cell suspension by trypsinization and mechanical disruption. Neurons are plated onto poly-L-lysine-coated glass coverslips or tissue-culture dishes. After 30 hours in vitro, most neurons have extended an axon. The purity of the culture (Yam et al. 2009), typically over 90%, can be assessed by immunolabeling with the commissural neuron markers DCC, LH2 and TAG1 (Helms and Johnson, 1998). This neuronal preparation is a useful tool for in vitro studies of the cellular and molecular mechanisms of commissural axon growth and guidance during spinal cord development.

This video demonstrates a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. Dissociated commissural neurons are useful to study the cellular and molecular mechanisms of axon growth and guidance.

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies ...

Large-scale Recording of Neurons by Movable Silicon Probes in Behaving Rodents

A major challenge in neuroscience is linking behavior to the collective activity of neural assemblies. Understanding of input-output relationships of neurons and circuits requires methods with the spatial selectivity and temporal resolution appropriate for mechanistic analysis of neural ensembles in the behaving animal, i.e. recording of representatively large samples of isolated single neurons. Ensemble monitoring of neuronal activity has progressed remarkably in the past decade in both small and large-brained animals, including human subjects1-11. Multiple-site recording with silicon-based devices are particularly effective because of their scalability, small volume and geometric design.
Here, we describe methods for recording multiple single neurons and local field potential in behaving rodents, using commercially available micro-machined silicon probes with custom-made accessory components. There are two basic options for interfacing silicon probes to preamplifiers: printed circuit boards and flexible cables. Probe supplying companies (<a href="http://www.neuronexustech.com/" >http://www.neuronexustech.com/</a>; <a href="http://www.sbmicrosystems.com/">http://www.sbmicrosystems.com/</a>; <a href="http://www.acreo.se/">http://www.acreo.se/</a>) usually provide the bonding service and deliver probes bonded to printed circuit boards or flexible cables. Here, we describe the implantation of a 4-shank, 32-site probe attached to flexible polyimide cable, and mounted on a movable microdrive. Each step of the probe preparation, microdrive construction and surgery is illustrated so that the end user can easily replicate the process.

We describe methods for large-scale recording of multiple single units and local field potential in behaving rodents with silicon probes. Drive fabrication, probe attachment to the drive and probe implantation processes are illustrated in sufficient details for easy replication.

A major challenge in neuroscience is linking behavior to the collective activity of neural assemblies. Understanding of input-output relationships of ...

Simultaneous Recording of Calcium Signals from Identified Neurons and Feeding Behavior of Drosophila melanogaster

To study neuronal networks in terms of their function in behavior, we must analyze how neurons operate when each behavioral pattern is generated. Thus, simultaneous recordings of neuronal activity and behavior are essential to correlate brain activity to behavior. For such behavioral analyses, the fruit fly, Drosophila melanogaster, allows us to incorporate genetically encoded calcium indicators such as GCaMP1, to monitor neuronal activity, and to use sophisticated genetic manipulations for optogenetic or thermogenetic techniques to specifically activate identified neurons2-5. Use of a thermogenetic technique has led us to find critical neurons for feeding behavior (Flood et al., under revision). As a main part of feeding behavior, a Drosophila adult extends its proboscis for feeding6 (proboscis extension response; PER), responding to a sweet stimulus from sensory cells on its proboscis or tarsi. Combining the protocol for PER7 with a calcium imaging technique8 using GCaMP3.01, 9, I have established an experimental system, where we can monitor activity of neurons in the feeding center &#x2013; the suboesophageal ganglion (SOG), simultaneously with behavioral observation of the proboscis. I have designed an apparatus ("Fly brain Live Imaging and Electrophysiology Stage": "FLIES") to accommodate a Drosophila adult, allowing its proboscis to freely move while its brain is exposed to the bath for Ca2+ imaging through a water immersion lens. The FLIES is also appropriate for many types of live experiments on fly brains such as electrophysiological recording or time lapse imaging of synaptic morphology. Because the results from live imaging can be directly correlated with the simultaneous PER behavior, this methodology can provide an excellent experimental system to study information processing of neuronal networks, and how this cellular activity is coupled to plastic processes and memory.

Simultaneous Recording of Calcium Signals from Identified Neurons and Feeding Behavior of Drosophila melanogaster

The fruit fly, Drosophila melanogaster, extends its proboscis for feeding, responding to a sugar stimulus from its proboscis or tarsus. I have combined observations of the proboscis extension response (PER) with a calcium imaging technique, allowing us to monitor the activity of neurons in the brain, simultaneously with behavioral observation.

To study neuronal networks in terms of their function in behavior, we must analyze how neurons operate when each behavioral pattern is generated.  Thus, ...

Imaging Calcium Responses in GFP-tagged Neurons of Hypothalamic Mouse Brain Slices

Despite an enormous increase in our knowledge about the mechanisms underlying the encoding of information in the brain, a central question concerning the precise molecular steps as well as the activity of specific neurons in multi-functional nuclei of brain areas such as the hypothalamus remain. This problem includes identification of the molecular components involved in the regulation of various neurohormone signal transduction cascades. Elevations of intracellular Ca2+ play an important role in regulating the sensitivity of neurons, both at the level of signal transduction and at synaptic sites.
New tools have emerged to help identify neurons in the myriad of brain neurons by expressing green fluorescent protein (GFP) under the control of a particular promoter. To monitor both spatially and temporally stimulus-induced Ca2+ responses in GFP-tagged neurons, a non-green fluorescent Ca2+ indicator dye needs to be used. In addition, confocal microscopy is a favorite method of imaging individual neurons in tissue slices due to its ability to visualize neurons in distinct planes of depth within the tissue and to limit out-of-focus fluorescence. The ratiometric Ca2+ indicator fura-2 has been used in combination with GFP-tagged neurons1. However, the dye is excited by ultraviolet (UV) light. The cost of the laser and the limited optical penetration depth of UV light hindered its use in many laboratories. Moreover, GFP fluorescence may interfere with the fura-2 signals2. Therefore, we decided to use a red fluorescent Ca2+ indicator dye. The huge Stokes shift of fura-red permits multicolor analysis of the red fluorescence in combination with GFP using a single excitation wavelength. We had previously good results using fura-red in combination with GFP-tagged olfactory neurons3. The protocols for olfactory tissue slices seemed to work equally well in hypothalamic neurons4. Fura-red based Ca2+ imaging was also successfully combined with GFP-tagged pancreatic &beta;-cells and GFP-tagged receptors expressed in HEK cells5,6. A little quirk of fura-red is that its fluorescence intensity at 650 nm decreases once the indicator binds calcium7. Therefore, the fluorescence of resting neurons with low Ca2+ concentration has relatively high intensity. It should be noted, that other red Ca2+-indicator dyes exist or are currently being developed, that might give better or improved results in different neurons and brain areas.

In this protocol, we update recent progress in imaging Ca2+ signals of GFP-tagged neurons in brain tissue slices using a red fluorescent Ca2+ indicator dye.

Despite an enormous increase in our knowledge about the mechanisms underlying the encoding of information in the brain, a central question concerning the ...

Preparation of Primary Neurons for Visualizing Neurites in a Frozen-hydrated State Using Cryo-Electron Tomography

Neurites, both dendrites and axons, are neuronal cellular processes that enable the conduction of electrical impulses between neurons. Defining the structure of neurites is critical to understanding how these processes move materials and signals that support synaptic communication. Electron microscopy (EM) has been traditionally used to assess the ultrastructural features within neurites; however, the exposure to organic solvent during dehydration and resin embedding can distort structures. An important unmet goal is the formulation of procedures that allow for structural evaluations not impacted by such artifacts.
Here, we have established a detailed and reproducible protocol for growing and flash-freezing whole neurites of different primary neurons on electron microscopy grids followed by their examination with cryo-electron tomography (cryo-ET). This technique allows for 3-D visualization of frozen, hydrated neurites at nanometer resolution, facilitating assessment of their morphological differences. Our protocol yields an unprecedented view of dorsal root ganglion (DRG) neurites, and a visualization of hippocampal neurites in their near-native state. As such, these methods create a foundation for future studies on neurites of both normal neurons and those impacted by neurological disorders.

To preserve neuronal processes for ultrastructural analysis, we describe a protocol for plating of primary neurons on electron microscopy grids followed by flash freezing, yielding samples suspended in a layer of vitreous ice. These samples can be examined with a cryo-electron microscope to visualize structures at the nanometer scale.

Neurites, both dendrites and axons, are neuronal cellular processes that enable the conduction of electrical impulses between neurons. Defining the ...

Simultaneous Electrophysiological Recording and Calcium Imaging of Suprachiasmatic Nucleus Neurons

Simultaneous electrophysiological and fluorescent imaging recording methods were used to study the role of changes of membrane potential or current in regulating the intracellular calcium concentration. Changing environmental conditions, such as the light-dark cycle, can modify neuronal and neural network activity and the expression of a family of circadian clock genes within the suprachiasmatic nucleus (SCN), the location of the master circadian clock in the mammalian brain. Excitatory synaptic transmission leads to an increase in the postsynaptic Ca2+ concentration that is believed to activate the signaling pathways that shifts the rhythmic expression of circadian clock genes. Hypothalamic slices containing the SCN were patch clamped using microelectrodes filled with an internal solution containing the calcium indicator bis-fura-2. After a seal was formed between the microelectrode and the SCN neuronal membrane, the membrane was ruptured using gentle suction and the calcium probe diffused into the neuron filling both the soma and dendrites. Quantitative ratiometric measurements of the intracellular calcium concentration were recorded simultaneously with membrane potential or current. Using these methods it is possible to study the role of changes of the intracellular calcium concentration produced by synaptic activity and action potential firing of individual neurons. In this presentation we demonstrate the methods to simultaneously record electrophysiological activity along with intracellular calcium from individual SCN neurons maintained in brain slices.

Procedures are described to perform simultaneous recordings of membrane potential or current and changes of intracellular calcium concentration. Suprachiasmatic nucleus neurons are filled with the calcium indicator bis-fura-2 using a patch clamp electrode in the whole cell patch clamp configuration.

Simultaneous electrophysiological and fluorescent imaging recording methods were used to study the role of changes of membrane potential or current in ...

Calcium Phosphate Transfection of Primary Hippocampal Neurons

Calcium phosphate precipitation is a convenient and economical method for transfection of cultured cells. With optimization, it is possible to use this method on hard-to-transfect cells like primary neurons. Here we describe our detailed protocol for calcium phosphate transfection of hippocampal neurons cocultured with astroglial cells.

Calcium phosphate precipitation is a convenient and economical method for transfection of cultured cells. With optimization, it is possible to use this ...

Ratiometric Calcium Imaging of Individual Neurons in Behaving Caenorhabditis Elegans

It has become increasingly clear that neural circuit activity in behaving animals differs substantially from that seen in anesthetized or immobilized animals. Highly sensitive, genetically encoded fluorescent reporters of Ca2+ have revolutionized the recording of cell and synaptic activity using non-invasive optical approaches in behaving animals. When combined with genetic and optogenetic techniques, the molecular mechanisms that modulate cell and circuit activity during different behavior states can be identified.
Here we describe methods for ratiometric Ca2+ imaging of single neurons in freely behaving Caenorhabditis elegans worms. We demonstrate a simple mounting technique that gently overlays worms growing on a standard Nematode Growth Media (NGM) agar block with a glass coverslip, permitting animals to be recorded at high-resolution during unrestricted movement and behavior. With this technique, we use the sensitive Ca2+ reporter GCaMP5 to record changes in intracellular Ca2+ in the serotonergic Hermaphrodite Specific Neurons (HSNs) as they drive egg-laying behavior. By co-expressing mCherry, a Ca2+-insensitive fluorescent protein, we can track the position of the HSN within ~ 1 &#181;m and correct for fluctuations in fluorescence caused by changes in focus or movement. Simultaneous, infrared brightfield imaging allows for behavior recording and animal tracking using a motorized stage. By integrating these microscopic techniques and data streams, we can record Ca2+ activity in the C. elegans egg-laying circuit as it progresses between inactive and active behavior states over tens of minutes.

Ratiometric Calcium Imaging of Individual Neurons in Behaving Caenorhabditis Elegans

This protocol describes the use of genetically encoded Ca2+ reporters to record changes in neural activity in behaving Caenorhabditis elegans worms. &#8195;

It has become increasingly clear that neural circuit activity in behaving animals differs substantially from that seen in anesthetized or immobilized ...

Localization of the Locus Coeruleus in the Mouse Brain

The locus coeruleus (LC) is a major hub of norepinephrine producing neurons that modulate a number of physiological functions. Structural or functional abnormalities of LC impact several brain regions including cortex, hippocampus, and cerebellum and may contribute to depression, bipolar disorder, anxiety, as well as Parkinson disease and Alzheimer disease. These disorders are often associated with metal misbalance, but the role of metals in LC is only partially understood. Morphologic and functional studies of LC are needed to better understand the human pathologies and contribution of metals. Mice are a widely used experimental model, but the mouse LC is small (~0.3 mm diameter) and hard to identify for a non-expert. Here, we describe a step-by-step immunohistochemistry-based protocol to localize the LC in the mouse brain. Dopamine-&#946;-hydroxylase (DBH), and alternatively, tyrosine hydroxylase (TH), both enzymes highly expressed in the LC, are used as immunohistochemical markers in brain slices. Sections adjacent to LC-containing sections can be used for further analysis, including histology for morphological studies, metabolic testing, as well as metal imaging by X-ray fluorescence microscopy (XFM).

The locus coeruleus is a small cluster of neurons involved in a variety of physiological processes. Here, we describe a protocol to prepare mouse brain sections for studies of proteins and metals in this nucleus.

The locus coeruleus (LC) is a major hub of norepinephrine producing neurons that modulate a number of physiological functions. Structural or functional ...

In vivo Calcium Imaging in Mouse Inferior Olive

Inferior olive (IO), a nucleus in the ventral medulla, is the only source of climbing fibers that form one of the two input pathways entering the cerebellum. IO has long been proposed to be crucial for motor control and its activity is currently considered to be at the center of many hypotheses of both motor and cognitive functions of the cerebellum. While its physiology and function have been relatively well studied on single-cell level in vitro, presently there are no reports on the organization of the IO network activity in living animals. This is largely due to the extremely challenging anatomical location of the IO, making it difficult to subject to conventional fluorescent imaging methods, where an optic path must be created through the entire brain located dorsally to the region of interest.
Here we describe an alternative method for obtaining state-of-the-art -level calcium imaging data from the IO network. The method takes advantage of the extreme ventral location of the IO and involves a surgical procedure for inserting a gradient-refractive index (GRIN) lens through the neck viscera to come into contact with the ventral surface of the calcium sensor GCaMP6s-expressing IO in anesthetized mice. A representative calcium imaging recording is shown to demonstrate the feasibility to record IO neuron activity after the surgery. While this is a non-survival surgery and the recordings must be conducted under anesthesia, it avoids damage to life-critical brainstem nuclei and allows conducting large variety of experiments investigating spatiotemporal activity patterns and input integration in the IO. This procedure with modifications could be used for recordings in other, adjacent regions of the ventral brainstem.

In vivo Calcium Imaging in Mouse Inferior Olive

We present a protocol to expose the brainstem of adult mouse from the ventral side. By using a gradient-refractive index lens with a miniature microscope, calcium imaging can be used to examine the activity of inferior olive neural somata in vivo.