This work was supported by the NINDS Intramural Research Program.

1. NSC culture
NOTE: Manipulation of a human NSC line will be described below but any cell line can be used for this protocol. All cell culture work is performed in a biological safety cabinet.
<ol>
	<li>Coat a 96-well plate with basement membrane/extracellular matrix (ECM).
	<ol>
		<li>Thaw aliquot of ECM (Table of Materials), which will facilitate attachment of NSC, on ice. Dilute ECM to the appropriate concentration (generally 1:100) in 10 mL base medium (Table of Materials) and add 50 &#181;L per well to each of 60 interior wells of a 96-well plate (Figure 1). Use only the interior 60 wells to avoid artifacts that may result from the edge effect16.</li>
		<li>Let the plate sit at room temperature or in a cell culture incubator (37 &#176;C, 5% CO2) for at least 30 min.</li>
	</ol>
	</li>
	<li>Dissociate and plate neural stem cells. 
	NOTE: Cells for use in this method should be grown to at least 80% confluence in a T75 flask.
	<ol>
		<li>Culture cells in a T75 flask in a cell culture incubator at 37 &#176;C and 5% CO2 in NSC medium that is composed of base medium, B27, non-essential amino acids, 2 mM glutamine, and 10 ng/mL basic fibroblast growth factor (FGFb or FGF2).</li>
		<li>Remove cells from the incubator once they reach 80% confluence and aspirate off NSC medium. Add an appropriate amount of cell dissociation reagent (3 mL for a T75 flask; Table of Materials) and incubate for 5 min in the incubator.</li>
		<li>After incubation, add 7 mL of NSC medium in the T75 flask and pipette vigorously to ensure all cells become detached. Transfer the dissociated cell solution to a 15 mL tube and centrifuge at 200 x g for 5 min.</li>
		<li>After centrifugation, remove supernatant from the tube and resuspend cells in 10 mL of NSC medium and count cells.</li>
		<li>Readjust concentration of cells to 200,000 cells/mL with NSC medium. Ensure cells are fully resuspended for homogeneous plating into wells.</li>
		<li>Plate 100 &#181;L of the cell mixture (20,000 cells) in the 60 interior wells of three 96-well plates that have been coated as described in section 1.1. Use six of the eight slots of an 8-channel multichannel pipettor to plate cells column-by-column.</li>
		<li>Add 100 &#181;L of base medium or NSC medium to all wells without cells to minimize potential evaporation from outermost wells.</li>
		<li>Under a cell culture microscope, visually inspect at least 10 wells on each of the three 96-well plates to confirm that the cells are seeded at the expected density. Do not proceed with the assay if cells are plated at a density too sparse or dense.</li>
	</ol>
	</li>
</ol>
2. Treating cells with compounds
NOTE: The home-made library tested in this demonstration contains compounds that modulate wingless/integrated (Wnt), retinoic acid, transforming growth factor-beta (TGF-&#946;), and sonic hedgehog signaling pathways as well as a variety of tyrosine kinases.
<ol>
	<li>Exploratory primary screen for toxicity/cell number
	<ol>
		<li>Aliquot 50&#8722;100 &#956;L of up to 57 test compounds (Supplemental Table 1) at a concentration of 10 mM in 100% dimethyl sulfoxide (DMSO) into the interior 60 wells of a U-bottomed, V-bottomed or round-bottomed 96-well plate with three DMSO wells as a control (see Figure 1 for a plate map). This will serve as the master compound plate with 25 &#181;L of compound that can be frozen and thawed several times. 
		NOTE: Flat bottomed plates should not be used as it will be more difficult to aspirate small volumes of compounds from them with a bench top pipettor.</li>
		<li>Remove cell culture plates from incubator 16-24 h after splitting as described in section 1 and aspirate off NSC medium column-by-column with an 8-channel multi-well pipettor using only six of the eight multi-well slots. Add 95 &#181;L of fresh NSC medium to cells in each of the three replicate plates and place plates back in incubator until step 2.1.4 below is completed.</li>
		<li>Add 49 &#181;L of NSC medium to each of the interior 60 wells of an empty U-bottomed, V-bottomed or round-bottomed 96-well plate with an 8-channel multi-well pipettor. Unseal the master compound plate and use a bench top pipettor or equivalent instrument to pipette 1 &#181;L of compound from the master plate into the 49 &#181;L of NSC medium in each of the interior 60 wells.</li>
		<li>Mix the diluted compound 3x with the bench top pipettor.</li>
		<li>Remove the three 96-well plates of NSCs from the incubator, pipette 15 &#181;L of each diluted compound with the bench top pipettor and dispense a 5 &#181;L aliquot of compound into each of the three plates. 
		NOTE: This 1:20 dilution of compound into the cells in combination with the initial 1:50 dilution in step 2.1.3 yields a 1:1000 dilution such that the final concentration of the compounds on the NSCs will be 10 &#181;M with a DMSO concentration of 0.1% and the final concentration for the DMSO controls will be 0.1%.</li>
		<li>Incubate cells with compound for 72 h and proceed with cytotoxicity assays. Shorter intervals can be used but a 72-hour incubation period should maximize the potential cytotoxic effects of tested compounds.</li>
	</ol>
	</li>
	<li>Dose response assay 
	NOTE: The set-up for the 96-well used for the dose-response is displayed in Figure 2.
	<ol>
		<li>Use column 2 for six DMSO control replicates and test triplicates of up to three different compounds at two-fold serial dilutions at six doses starting with a high dose of 10 &#181;M.</li>
		<li>Dilute 4 &#181;L of DMSO or test compound in DMSO into 196 &#181;L of NSC medium in a 1.5 mL microcentrifuge tube. Add 25 &#181;L of DMSO to the column of wells from B2-G2 and 50 &#181;L of test compounds to the row from B3-B11 with the three tested compounds in 10 mM triplicates in rows B3-B5, B6-B8, and B9-B11.</li>
		<li>Pipette 25 &#181;L of NSC medium to the remaining empty columns in the interior portion of the 96-well plate. Remove 25 &#181;L of compound from wells B3-B11 with a multichannel pipettor, add to wells C3-C11, and mix at least five times. Repeat the process for the remaining rows to generate triplicates at two-fold dilutions for a total of six doses for each of the compounds.</li>
		<li>Generate NSCs for the dose response exactly as described for the primary screen in section 2.1. The compounds for the dose response are added to and incubated on the cells exactly as described in steps 2.1.5 and 2.1.6. 
		NOTE: Three biological replicates of the dose response assay are performed by repeating the assay on the NSCs at different passages on separate days.</li>
	</ol>
	</li>
</ol>
3. Imaging cells on a plate reader
<ol>
	<li>After cells have been incubated with compounds for the allotted time, image cells on a plate reader to determine the pre-treatment cell number per well. 
	NOTE: Instructions for imaging cells are reader-specific but generally follow a similar strategy. The directions below apply to the reader used in this demonstration (Table of Materials).</li>
	<li>Remove the plate from the incubator and place it inside the plate reader. Open the imager software to set up protocol and experiment files for the study. Go to Imager Manual Mode on Task Manager and click Capture now&#8230;.</li>
	<li>Choose 96-well plate as the vessel type, select 10x for the magnification, and red fluorescent protein (RFP) 531 and 593 for imaging tdTomato. Pick a well, then click Autofocus to focus image, and Auto Expose for proper exposure time. Manually adjust focus and exposure if needed.</li>
	<li>Once proper focus and exposure have been obtained, click the camera icon to capture the picture. Then click PROCESS/ANALZYE above image to continue building the protocol and select the ANALYSIS tab.</li>
	<li>Click Cellular Analysis in ADD ANALYSIS STEP to the right of the image and click START. Image will show highlighted cells to indicate each individual cell. The Options selection may be clicked to alter parameters to better select cells based upon the fluorescence threshold or cell size. If the imager is properly counting the cells, then click ADD STEP at the bottom of the screen.</li>
	<li>Click the icon at the top of the screen to Create experiment from image set, which will open a window with the experiment. Once open, click Procedure under the Protocol tab and in the new window that opens select Read, then in the new window click full plate to select only the 60 wells that contain the cells (B2...G11). Click OK to save changes, then click OK in the Procedure window.</li>
	<li>The plate can now be imaged by this protocol and the experimental file can be saved. Click the play icon to run the plate. Once the first plate has been imaged, image the other two plates. Upon completion of the imaging, download the cell count data to a spreadsheet for analysis. Take all images at 10x magnification.</li>
</ol>
4. Terminal MTT cytotoxicity assay
NOTE: Begin the MTT assay within two hours of completing tdTomato imaging.
<ol>
	<li>Make a 5 mg/mL MTT stock solution by weighing out 25 mg of MTT and resuspending it in 5 mL of NSC medium. Vortex the solution until there are no visible precipitates of MTT, which could take several minutes.</li>
	<li>Remove cell culture plates from the incubator and aspirate off cell culture medium. Dilute MTT 1:10 in cell culture medium and add 100 &#181;L of MTT to each well of cells.</li>
	<li>Incubate cells at 37 &#176;C for 2 h. A purplish precipitate should be visible roughly in proportion to the number of cells in the well. Either aspirate the MTT solution off plates or invert the plate quickly to flick solution out of the plate.</li>
	<li>Add 50 &#181;L of 100% DMSO to each well and shake plates at room temperature for 10 min at 400 rpm. Read the absorbance of each well at 595 nm in a plate reader and export data to a spreadsheet for analysis.</li>
</ol>
5. Data analysis
<ol>
	<li>Perform an analysis of tdTomato cell counts and absorbances with appropriate software (commercial spreadsheet, R). Calculate averages for absorbance or cell count of the three DMSO replicates on each plate for normalization purposes, then divide the value for the cell counts or absorbances for each well on the plate by this average and convert to a percentage. This yields the normalized cell count or absorbance relative to DMSO control for each plate.</li>
	<li>Calculate the mean normalized count or absorbance and standard deviation for replicate wells on the three plates. 
	NOTE: At this point there should be four different sets of normalized values: one for each of the plates and one mean for the three replicate plates.</li>
	<li>Be conservative and use a normalized value at or below 25% for the average across the three replicate plates to classify a compound as toxic. Also, because only a single treatment per compound is performed on each plate, only label compounds that fall below this threshold on all three replicate plates as toxic. Examine fluorescent images of all compounds that this analysis filters as toxic to visually confirm toxicity. 
	NOTE: The identification of compounds with a growth inhibitory or growth enhancing effect is more difficult to assess in an exploratory assay of this type due to the lack of replicates on each plate. However, the following is a quick way to identify compounds that may either slow down or enhance cellular growth.</li>
	<li>Calculate the standard deviation for the three replicate DMSO controls on each plate and then filter for any compounds that have average values at least two standard deviations above or below the DMSO control. Compounds that fall out of this filter on each of the three plates may warrant further investigation.</li>
	<li>Use the same analysis strategy for the dose response as the primary toxicity screen. Calculate the averages for the DMSO controls for each biological replicate and use these values to normalize the percent live cells or percent absorbances for each compound/dose combination. Calculate the means and standard error of the means for all compound/dose combinations for the three biological replicates.</li>
	<li>Transform the concentration to its log value, generate a dose response curve for the log of concentration versus normalized viability, and fit the curve with a non-linear regression analysis (analysis can be performed in R or various commercial statistical packages). Calculate the lethal dose 50 (or technically in this case the viable dose 50) or concentration of compound that results in 50% toxicity from the equation of this curve. Many software packages will automatically calculate this figure.</li>
</ol>

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The authors have nothing to disclose.

The primary goal of this article was to describe a strategy that could efficiently and inexpensively identify compounds affecting cell growth in a low- to moderate-throughput screening. Two orthogonal techniques were utilized to assess cell number to increase confidence in the conclusions and offer additional insights that would not be available if only a single assay was used. One of the assays used a fluorescent cell imager to directly count tdTomato-positive cells and the second was dependent on the well-characterized...

One of the most important characteristics that needs to be determined for a chemical compound that has therapeutic potential is its toxicity to animal cells. This characteristic will determine whether a drug is a good candidate for more extensive study. In most instances, compounds with minimal toxicity are sought but there are situations in which a compound with the capacity to kill specific cell types is of interest, e.g., anti-tumorigenic drugs. Although whole animals are the best model systems to determine systemic toxicity, the cost and labor involved is prohibitive when more than a few compounds need to be tested. As such mammalian cell culture is generally used as the most efficient alternative1,2. Small to medium throughput drug screens are an important modality through which toxicity can be assessed in cell culture. These screens can be used to interrogate annotated libraries targeting individual signaling pathways. The general format of such a screen is to initially test all the compounds in the library at a single dose (generally 10 &#181;M) in an exploratory primary toxicity screen, and then perform an in-depth secondary dose response screen to fully characterize the toxicity profile of hits from the primary screen. The methods to implement this strategy will be described here and provide a quick, efficient, and inexpensive way to identify and characterize toxic compounds.
Multiple methods have been developed to assess cytotoxicity of small compounds and nanomaterial in mammalian cells3,4. It should be noted that certain materials can interact with the assay providing misleading results, and such interactions should be tested when characterizing hits from toxicity screens4. Cytotoxicity assays include trypan blue exclusion5, lactate dehydrogenase (LDH) release assay6, Alamar blue assay7, calcien acetoxymethyl ester (AM)8, and the ATP assay9. All these assays measure various aspects of cell metabolism which can serve as a proxy for cell number. While all offer benefits, tetrazolium salt-based assays such as 3-(4,5-dimethylthizol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 2,3-bis(2-methoxy-4-nitro-5-sulfopheny)-2H-tetrazolium-5-carboxyanilide inner salt (XTT)-1, and 4-(3-[4-Iodophenyl]-2-[4-nitrophenyl]-2H-5-tetrazolio)-1,3-benzene disulfonate (WST-1)10,11 provide good accuracy and ease of use at low cost. MTT, which will be used in this demonstration, is reduced to an insoluble formazan by a mitochondrial reductase and the rate of this conversion correlates strongly with cell number. This assay has been routinely utilized at both a small scale and for screening libraries with up to 2,000 compounds12. Direct counting of cells by a labeled marker offers another method to assess the cellular number, and unlike the MTT assay it can provide additional information about the dynamics of cellular growth. Several publicly available algorithms are available to perform automated cell count analyses and there are also proprietary algorithms that are part of software packages for imaging readers13,14. In this method description, a human neural stem cell (NSC) line that has been genetically edited to constitutively express tdTomato15 will serve as a test line to compare cellular viability results between an MTT assay and an automated cell counting assay in a screen assessing toxicity of 57 test compounds. Although the primary goal of this strategy was to identify and characterize toxic compounds, it has the additional benefit of potentially identifying growth inhibitory and growth enhancing compounds and thus provides an effective method for identifying drugs that can modulate cellular growth.

<table border="0" cellpadding="0" cellspacing="0" style="width:1292px;" width="1292">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">B-27 (50X)</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td align="right" style="width:119px;">17504001</td>
			<td style="width:720px;">Neural stem cell medium component.&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">BenchTop pipettor</td>
			<td style="width:237px;">Sorenson Bioscience</td>
			<td align="right" style="width:119px;">73990</td>
			<td>Provides ability to pipette compound library into a 96-well plate in one shot.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">BioLite 96 well multidish</td>
			<td style="width:237px;">Thermo Scientific</td>
			<td align="right" style="width:119px;">130188</td>
			<td>Any 96 well cell culture plate will work.&#160; We use these in our work.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Cell culture microscope</td>
			<td style="width:237px;">Nikon</td>
			<td style="width:119px;">Eclipse TS100</td>
			<td>Visual inspection of cells to ensure proper density.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Cytation 5/ Imaging reader</td>
			<td style="width:237px;">BioTek</td>
			<td style="width:119px;">CYT3MFV</td>
			<td>Used for cell imaging and absorbance readings.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMSO</td>
			<td style="width:237px;">Fisher Scientific</td>
			<td align="right" style="width:119px;">610420010</td>
			<td>Solvent for compounds used in screen. Dissolves MTT precipitates to facilitate absorbance measurements.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">FGF-basic</td>
			<td style="width:237px;">Peprotech</td>
			<td style="width:119px;">100-18B</td>
			<td>Neural stem cell medium component.&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">GelTrex</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td style="width:119px;">A1413202</td>
			<td>Neural stem cell basement membrane matrix.&#160; Allows cells to attach to cell culture plates.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Gen5 3.04</td>
			<td style="width:237px;">BioTek</td>
			<td style="width:119px;"></td>
			<td>Analysis software to determine cell counts for tdTomato expressing cells.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Glutamine</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td align="right" style="width:119px;">25030081</td>
			<td>Neural stem cell medium component.&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Microtest U-Bottom</td>
			<td style="width:237px;">Becton Dickinson</td>
			<td align="right" style="width:119px;">3077</td>
			<td>Storage of compound libraries.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">MTT</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td style="width:119px;">M6494</td>
			<td>Active assay reagent to determine cellular viability.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Multichannel pippette</td>
			<td style="width:237px;">Rainin</td>
			<td style="width:119px;">E8-1200</td>
			<td>Column-by-column addition of cell culture medium, MTT, or DMSO.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Neurobasal medium</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td align="right" style="width:119px;">21103049</td>
			<td>Neural stem cell base medium.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">RFP filter cube</td>
			<td style="width:237px;">BioTek</td>
			<td align="right" style="width:119px;">1225103</td>
			<td>Filter in Cytation 5 used to image tdTomato expressing cells.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">TrypLE</td>
			<td style="width:237px;">ThermoFisher Scientific</td>
			<td align="right" style="width:119px;">12605036</td>
			<td>Cell dissociation reagent.</td>
		</tr>
	</tbody>
</table>

a strategy to identify compounds that affect cell growth and survival in cultured mammalian cells at low-to-moderate throughput

Cytotoxicity is a critical parameter that needs to be quantified when studying drugs that may have therapeutic benefits. Because of this, many drug screening assays utilize cytotoxicity as one of the critical characteristics to be profiled for individual compounds. Cells in culture are a useful model to assess cytotoxicity before proceeding to follow up on promising lead compounds in more costly and labor-intensive animal models. We describe a strategy to identify compounds that affect cell growth in a tdTomato expressing human neural stem cells (NSC) line. The strategy uses two complementary assays to assess cell number. One assay works via the reduction of 3-(4,5-dimethylthizol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to formazan as a proxy for cell number and the other directly counts the tdTomato expressing NSCs. The two assays can be performed simultaneously in a single experiment and are not labor intensive, rapid, and inexpensive. The strategy described in this demonstration tested 57 compounds in an exploratory primary screen for toxicity in a 96-well plate format. Three of the hits were characterized further in a six-point dose response using the same assay set-up as the primary screen. In addition to providing excellent corroboration for toxicity, comparison of results from the two assays may be effective in identifying compounds affecting other aspects of cell growth.

The automated cell count data identified eleven compounds with less than 25% viability when normalized to the DMSO control while the MTT data identified these same compounds plus two additional ones (Table 1 and Table 2, shaded red). The two compounds found to be toxic only in the MTT assay (wells F3 and G10) had 31% and 39%, respectively, the number of tdTomato-positive cells as the control and by rank order were the next two most toxic compounds in this library after those deemed to be...

Watch this Scientific Journal Video about A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput at JoVE.com

A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput

It is often necessary to assess the potential cytotoxicity of a set of compounds on cultured cells. Here, we describe a strategy to reliably screen for toxic compounds in a 96-well format.

Cytotoxicity is a critical parameter that needs to be quantified when studying drugs that may have therapeutic benefits. Because of this, many drug ...

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Biochemistry

8.4K Views.  National Institutes of Health (NIH). It is often necessary to assess the potential cytotoxicity of a set of compounds on cultured cells. Here, we describe a strategy to reliably screen for toxic compounds in a 96-well format.

Video: A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput

Measuring Protein Binding to F-actin by Co-sedimentation

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, cross-linking and/or disassembly. This protocol describes a technique &#8211; the actin co-sedimentation, or pelleting, assay &#8211; to determine whether a protein or protein domain binds F-actin and to measure the affinity of the interaction (i.e., the dissociation equilibrium constant). In this technique, a protein of interest is first incubated with F-actin in solution. Then, differential centrifugation is used to sediment the actin filaments, and the pelleted material is analyzed by SDS-PAGE. If the protein of interest binds F-actin, it will co-sediment with the actin filaments. The products of the binding reaction (i.e., F-actin and the protein of interest) can be quantified to determine the affinity of the interaction. The actin pelleting assay is a straightforward technique for determining if a protein of interest binds F-actin and for assessing how changes to that protein, such as ligand binding, affect its interaction with F-actin.

This protocol describes a method to test the ability of a protein to co-sediment with filamentous actin (F-actin) and, if binding is observed, to measure the affinity of the interaction.

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, ...

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Intermediate filaments (IFs), together with actin filaments and microtubules, form the cytoskeleton &#8211; a critical structural element of every cell. Normal functioning IFs provide cells with mechanical and stress resilience, while a dysfunctional IF cytoskeleton compromises cellular health and has been associated with many human diseases. Post-translational modifications (PTMs) critically regulate IF dynamics in response to physiological changes and under stress conditions. Therefore, the ability to monitor changes in the PTM signature of IFs can contribute to a better functional understanding, and ultimately conditioning, of the IF system as a stress responder during cellular injury. However, the large number of IF proteins, which are encoded by over 70 individual genes and expressed in a tissue-dependent manner, is a major challenge in sorting out the relative importance of different PTMs. To that end, methods that enable monitoring of PTMs on IF proteins on an organism-wide level, rather than for isolated members of the family, can accelerate research progress in this area. Here, we present biochemical methods for the isolation of the total, detergent-soluble, and detergent-resistant fraction of IF proteins from 9 different mouse tissues (brain, heart, lung, liver, small intestine, large intestine, pancreas, kidney, and spleen). We further demonstrate an optimized protocol for rapid isolation of IF proteins by using lysing matrix and automated homogenization of different mouse tissues. The automated protocol is useful for profiling IFs in experiments with high sample volume (such as in disease models involving multiple animals and experimental groups). The resulting samples can be utilized for various downstream analyses, including mass spectrometry-based PTM profiling. Utilizing these methods, we provide new data to show that IF proteins in different mouse tissues (brain and liver) undergo parallel changes with respect to their expression levels and PTMs during aging.

In this method, we present biochemical procedures for rapid and efficient isolation of intermediate filament (IF) proteins from multiple mouse tissues. Isolated IFs can be used to study changes in post-translational modifications by mass spectrometry and other biochemical assays.

Intermediate filaments (IFs), together with actin filaments and microtubules, form the cytoskeleton &#8211; a critical structural element of every cell. ...

Analyses of Mitochondrial Calcium Influx in Isolated Mitochondria and Cultured Cells

Ca2+ handling by mitochondria is a critical function regulating both physiological and pathophysiological processes in a broad spectrum of cells. The ability to accurately measure the influx and efflux of Ca2+ from mitochondria is important for determining the role of mitochondrial Ca2+ handling in these processes. In this report, we present two methods for the measurement of mitochondrial Ca2+ handling in both isolated mitochondria and cultured cells. We first detail a plate reader-based platform for measuring mitochondrial Ca2+ uptake using the Ca2+ sensitive dye calcium green-5N. The plate reader-based format circumvents the need for specialized equipment, and the calcium green-5N dye is ideally suited for measuring Ca2+ from isolated tissue mitochondria. For our application, we describe the measurement of mitochondrial Ca2+ uptake in mitochondria isolated from mouse heart tissue; however, this procedure can be applied to measure mitochondrial Ca2+ uptake in mitochondria isolated from other tissues such as liver, skeletal muscle, and brain. Secondly, we describe a confocal microscopy-based assay for measurement of mitochondrial Ca2+ in permeabilized cells using the Ca2+ sensitive dye Rhod-2/AM and imaging using 2-dimensional laser-scanning microscopy. This permeabilization protocol eliminates cytosolic dye contamination, allowing for specific recording of changes in mitochondrial Ca2+. Moreover, laser-scanning microscopy allows for high frame rates to capture rapid changes in mitochondrial Ca2+ in response to various drugs or reagents applied in the external solution. This protocol can be applied to measure mitochondrial Ca2+ uptake in many cell types including primary cells such as cardiac myocytes and neurons, and immortalized cell lines.

Here, we present two protocols for the measurement of mitochondrial Ca2+ influx in isolated mitochondria and cultured cells. For isolated mitochondria, we detail a plate reader-based Ca2+ import assay using the Ca2+ sensitive dye calcium green-5N. For cultured cells, we describe a confocal microscopy method using the Ca2+ dye Rhod-2/AM.

Ca2+ handling by mitochondria is a critical function regulating both physiological and pathophysiological processes in a broad spectrum of cells. The ...

Dissipative Microgravimetry to Study the Binding Dynamics of the Phospholipid Binding Protein Annexin A2 to Solid-supported Lipid Bilayers Using a Quartz Resonator

The dissipative quartz crystal microbalance technique is a simple and label-free approach to measure simultaneously the mass uptake and viscoelastic properties of the absorbed/immobilized mass on sensor surfaces, allowing the measurements of the interaction of proteins with solid-supported surfaces, such as lipid bilayers, in real-time and with a high sensitivity. Annexins are a highly conserved group of phospholipid-binding proteins that interact reversibly with the negatively charged headgroups via the coordination of calcium ions. Here, we describe a protocol that was employed to quantitatively analyze the binding of annexin A2 (AnxA2) to planar lipid bilayers prepared on the surface of a quartz sensor. This protocol is optimized to obtain robust and reproducible data and includes a detailed step-by-step description. The method can be applied to other membrane-binding proteins and bilayer compositions.

Here, we present an experimental protocol that can be employed to determine the binding affinities and mode of interaction of label-free phospholipid-binding protein annexin A2 with immobilized solid-supported bilayers (SLB) by simultaneously measuring the mass uptake and the viscoelastic properties of the protein annexin A2.

The dissipative quartz crystal microbalance technique is a simple and label-free approach to measure simultaneously the mass uptake and viscoelastic ...

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for the targeted expression of genetically encoded calcium sensors. This protocol outlines the use of these sensors for the in vivo imaging of calcium dynamics in targeted cells, specifically the body wall muscles of the worms. By utilizing the co-expression of presynaptic channelrhodopsin, stimulation of acetylcholine release from excitatory motor neurons can be induced using blue light pulses, resulting in muscle depolarization and reproducible changes in cytoplasmic calcium levels. Two worm immobilization techniques are discussed with varying levels of difficulty. Comparison of these techniques demonstrates that both approaches preserve the physiology of the neuromuscular junction and allow for the reproducible quantification of calcium transients. By pairing optogenetics and functional calcium imaging, changes in postsynaptic calcium handling and homeostasis can be evaluated in a variety of mutant backgrounds. Data presented validates both immobilization techniques and specifically examines the roles of the C. elegans sarco(endo)plasmic reticular calcium ATPase and the calcium-activated BK potassium channel in the body wall muscle calcium regulation.

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

This method provides a way to couple optogenetics and genetically encoded calcium sensors to image baseline cytosolic calcium levels and changes in evoked calcium transients in the body wall muscles of the model organism C. elegans.

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for ...

Atomic Absorbance Spectroscopy to Measure Intracellular Zinc Pools in Mammalian Cells

Transition metals are essential micronutrients for organisms but can be toxic to cells at high concentrations by competing with physiological metals in proteins and generating redox stress. Pathological conditions that lead to metal depletion or accumulation are causal agents of different human diseases. Some examples include anemia, acrodermatitis enteropathica, and Wilson&#8217;s and Menkes&#8217; diseases. It is therefore important to be able to measure the levels and transport of transition metals in biological samples with high sensitivity and accuracy in order to facilitate research exploring how these elements contribute to normal physiological functions and toxicity. Zinc (Zn), for example, is a cofactor in many mammalian proteins, participates in signaling events, and is a secondary messenger in cells. In excess, Zn is toxic and can inhibit absorption of other metals, while in deficit, it can lead to a variety of potentially lethal conditions.

Graphite furnace atomic absorption spectroscopy (GF-AAS) provides a highly sensitive and effective method for determining Zn and other transition metal concentrations in diverse biological samples. Electrothermal atomization via GF-AAS quantifies metals by atomizing small volumes of samples for subsequent selective absorption analysis using wavelength of excitation of the element of interest. Within the limits of linearity of the Beer-Lambert Law, the absorbance of light by the metal is directly proportional to concentration of the analyte. Compared to other methods of determining Zn content, GF-AAS detects both free and complexed Zn in proteins and possibly in small intracellular molecules with high sensitivity in small sample volumes. Moreover, GF-AAS is also more readily accessible than inductively coupled plasma mass spectrometry (ICP-MS) or synchrotron-based X-ray fluorescence. In this method, the systematic sample preparation of different cultured cell lines for analyses in a GF-AAS is described. Variations in this trace element were compared in both whole cell lysates and subcellular fractions of proliferating and differentiated cells as proof of principle.

Cultured primary or established cell lines are commonly used to address fundamental biological and mechanistic questions as an initial approach before using animal models. This protocol describes how to prepare whole cell extracts and subcellular fractions for studies of zinc (Zn) and other trace elements with atomic absorbance spectroscopy.

Transition metals are essential micronutrients for organisms but can be toxic to cells at high concentrations by competing with physiological metals in ...

Enrichment of Mammalian Tissues and Xenopus Oocytes with Cholesterol

Cholesterol enrichment of mammalian tissues and cells, including Xenopus oocytes used for studying cell function, can be accomplished using a variety of methods. Here, we describe two important approaches used for this purpose. First, we describe how to enrich tissues and cells with cholesterol using cyclodextrin saturated with cholesterol using cerebral arteries (tissues) and hippocampal neurons (cells) as examples. This approach can be used for any type of tissue, cells, or cell lines. An alternative approach for cholesterol enrichment involves the use of low-density lipoprotein (LDL). The advantage of this approach is that it uses part of the natural cholesterol homeostasis machinery of the cell. However, whereas the cyclodextrin approach can be applied to enrich any cell type of interest with cholesterol, the LDL approach is limited to cells that express LDL receptors (e.g., liver cells, bone marrow-derived cells such as blood leukocytes and tissue macrophages), and the level of enrichment depends on the concentration and the mobility of the LDL receptor. Furthermore, LDL particles include other lipids, so cholesterol delivery is nonspecific. Second, we describe how to enrich Xenopus oocytes with cholesterol using a phospholipid-based dispersion (i.e., liposomes) that includes cholesterol. Xenopus oocytes constitute a popular heterologous expression system used for studying cell and protein function. For both the cyclodextrin-based cholesterol enrichment approach of mammalian tissue (cerebral arteries) and for the phospholipid-based cholesterol enrichment approach of Xenopus oocytes, we demonstrate that cholesterol levels reach a maximum following 5 min of incubation. This level of cholesterol remains constant during extended periods of incubation (e.g., 60 min). Together, these data provide the basis for optimized temporal conditions for cholesterol enrichment of tissues, cells, and Xenopus oocytes for functional studies aimed at interrogating the impact of cholesterol enrichment.

Enrichment of Mammalian Tissues and Xenopus Oocytes with Cholesterol

Two methods of cholesterol enrichment are presented: the application of cyclodextrin saturated with cholesterol to enrich mammalian tissues and cells, and the use of cholesterol-enriched phospholipid-based dispersions (liposomes) to enrich Xenopus oocytes. These methods are instrumental for determining the impact of elevated cholesterol levels in molecular, cellular, and organ function.

Cholesterol enrichment of mammalian tissues and cells, including Xenopus oocytes used for studying cell function, can be accomplished using a variety of ...

Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One &#945;-Synuclein Monomer at a Time

Using spectroscopic rulers to track multiple conformations of single biomolecules and their dynamics have revolutionized the understanding of structural dynamics and its contributions to biology. While the FRET-based ruler reports on inter-dye distances in the 3-10 nm range, other spectroscopic techniques, such as protein-induced fluorescence enhancement (PIFE), report on the proximity between a dye and a protein surface in the shorter 0-3 nm range. Regardless of the method of choice, its use in measuring freely-diffusing biomolecules one at a time retrieves histograms of the experimental parameter yielding separate centrally-distributed sub-populations of biomolecules, where each sub-population represents either a single conformation that stayed unchanged within milliseconds, or multiple conformations that interconvert much faster than milliseconds, and hence an averaged-out sub-population. In single-molecule FRET, where the reported parameter in histograms is the inter-dye FRET efficiency, an intrinsically disordered protein, such as the &#945;-Synuclein monomer in buffer, was previously reported as exhibiting a single averaged-out sub-population of multiple conformations interconverting rapidly. While these past findings depend on the 3-10 nm range of the FRET-based ruler, we sought to put this protein to the test using single-molecule PIFE, where we track the fluorescence lifetime of site-specific sCy3-labeled &#945;-Synuclein proteins one at a time. Interestingly, using this shorter range spectroscopic proximity sensor, sCy3-labeled &#945;-Synuclein exhibits several lifetime sub-populations with distinctly different mean lifetimes that interconvert in 10-100 ms. These results show that while &#945;-Synuclein might be disordered globally, it nonetheless attains stable local structures. In summary, in this work we highlight the advantage of using different spectroscopic proximity sensors that track local or global structural changes one biomolecule at a time.

Time-resolved single-molecule protein-induced fluorescence enhancement is a useful fluorescence spectroscopic proximity sensor sensitive to local structural changes in proteins. Here we show it can be used to uncover stable local conformations in &#945;-Synuclein, which is otherwise known as globularly unstructured and unstable when measured using the longer range FRET ruler.

Using spectroscopic rulers to track multiple conformations of single biomolecules and their dynamics have revolutionized the understanding of structural ...

Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) establish and maintain the DNA methylation pattern. Changes to the normal DNA methylation pattern are linked to cancer development and progression, making DNMTs potential cancer drug targets. Thus, identifying and characterizing novel small molecule inhibitors of these enzymes is of great importance. This paper presents a protocol that can be used to screen for DNA methyltransferase inhibitors. The continuous coupled kinetics assay allows for initial velocities of DNA methylation to be determined in the presence and absence of potential small molecule inhibitors. The assay uses the methyl-sensitive endonuclease Gla I to couple methylation of a hemimethylated DNA substrate to fluorescence generation.
This continuous assay allows for enzyme activity to be monitored in real time. Conducting the assay in small volumes in microtiter plates reduces the cost of reagents. Using this assay, a small example screen was conducted for inhibitors of DNMT1, the most abundant DNMT isozyme in humans. The highly substituted anthraquinone natural product, laccaic acid A, is a potent, DNA-competitive inhibitor of DNMT1. Here, we examine three potential small molecule inhibitors &#8212; anthraquinones or anthraquinone-like molecules with one to three substituents &#8212; at two concentrations to describe the assay protocol. Initial velocities are used to calculate the percent activity observed in the presence of each molecule. One of three compounds examined exhibits concentration-dependent inhibition of DNMT1 activity, indicating that it is a potential inhibitor of DNMT1.

DNA methyltransferases are potential cancer drug targets. Here, a protocol is presented to assess small molecules for DNA methyltransferase inhibition. This assay utilizes an endonuclease to couple DNA methylation to fluorescence generation and allows for enzyme activity to be monitored in real time.&#160;

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) ...

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

Most cellular processes are regulated by dynamic protein phosphorylation. More than three-quarters of proteins are phosphorylated, and phosphoprotein phosphatases (PPPs) coordinate over 90% of all cellular serine/threonine dephosphorylation. Deregulation of protein phosphorylation has been implicated in the pathophysiology of various diseases, including cancer and neurodegeneration. Despite their widespread activity, the molecular mechanisms controlling PPPs and those controlled by PPPs are poorly characterized. Here, a proteomic approach termed phosphatase inhibitor beads and mass spectrometry (PIB-MS) is described to identify and quantify PPPs, their posttranslational modifications, and their interactors in as little as 12 h using any cell line or tissue. PIB-MS utilizes a non-selective PPP inhibitor, microcystin-LR (MCLR), immobilized on sepharose beads to capture and enrich endogenous PPPs and their associated proteins (termed the PPPome). This method does not require the exogenous expression of tagged versions of PPPs or the use of specific antibodies. PIB-MS offers an innovative way to study the evolutionarily conserved PPPs and expand our current understanding of dephosphorylation signaling.

Here, we present a protocol for the enrichment of endogenous phosphoprotein phosphatases and their interacting proteins from cells and tissues and their identification and quantification by mass spectrometry-based proteomics.

Most cellular processes are regulated by dynamic protein phosphorylation. More than three-quarters of proteins are phosphorylated, and phosphoprotein ...

A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput

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Measuring Protein Binding to F-actin by Co-sedimentation

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Analyses of Mitochondrial Calcium Influx in Isolated Mitochondria and Cultured Cells

Dissipative Microgravimetry to Study the Binding Dynamics of the Phospholipid Binding Protein Annexin A2 to Solid-supported Lipid Bilayers Using a Quartz Resonator

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

Atomic Absorbance Spectroscopy to Measure Intracellular Zinc Pools in Mammalian Cells

Enrichment of Mammalian Tissues and Xenopus Oocytes with Cholesterol

Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One α-Synuclein Monomer at a Time

Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors