Name: a western blotting protocol for small numbers of hematopoietic stem cells
Uploaded: 2018-08-22T12:30:00
Description: Watch this Scientific Journal Video about A Western Blotting Protocol for Small Numbers of Hematopoietic Stem Cells at JoVE.com

National Institutes of Health grant R01 CA149976 (N.A.S) supported this work.

All procedures must be performed in accordance with institutional animal use and care guidelines. The procedure was developed for the analysis of murine hematopoietic stem and progenitor cells (HSCs and HPs), but can be adapted for the analysis of other cell populations.
1. Flow Cytometry Isolation of Murine HSCs and HPs
<ol>
	<li>Harvest murine bone marrow cells as described in the literature6. 
	NOTE: In data presented in Figure 1 ...

<ol>
	<li>Krutzik, P. O., Clutter, M. R., Nolan, G. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordinate+analysis+of+murine+immune+cell+surface+markers+and+intracellular+phosphoproteins+by+flow+cytometry.">Coordinate analysis of murine immune cell surface markers and intracellular phosphoproteins by flow cytometry.</a> J Immunol. 175 (4), 2357-2365 (2005).</li><li>Du, J., 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=Signaling+profiling+at+the+single-cell+level+identifies+a+distinct+signaling+signature+in+murine+hematopoietic+stem+cells.">Signaling profiling at the single-cell level identifies a distinct signaling signature in murine hematopoietic stem cells.</a> Stem Cells. 30 (7), 1447-1454 (2012).</li><li>Signer, R. A., Magee, J. A., Salic, A., Morrison, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Haematopoietic+stem+cells+require+a+highly+regulated+protein+synthesis+rate.">Haematopoietic stem cells require a highly regulated protein synthesis rate.</a> Nature. 509 (7498), 49-54 (2014).</li><li>Wang, J., 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=A+differentiation+checkpoint+limits+hematopoietic+stem+cell+self-renewal+in+response+to+DNA+damage.">A differentiation checkpoint limits hematopoietic stem cell self-renewal in response to DNA damage.</a> Cell. 148 (5), 1001-1014 (2012).</li><li>Hoshii, T., 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=mTORC1+is+essential+for+leukemia+propagation+but+not+stem+cell+self-renewal.">mTORC1 is essential for leukemia propagation but not stem cell self-renewal.</a> J Clin Invest. 122 (6), 2114-2129 (2012).</li><li>Signer, R. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+rate+of+protein+synthesis+in+hematopoietic+stem+cells+is+limited+partly+by+4E-BPs.">The rate of protein synthesis in hematopoietic stem cells is limited partly by 4E-BPs.</a> Genes Dev. 30 (15), 1698-1703 (2016).</li><li>Cai, X., 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=Runx1+deficiency+decreases+ribosome+biogenesis+and+confers+stress+resistance+to+hematopoietic+stem+and+progenitor+cells.">Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells.</a> Cell Stem Cell. , (2015).</li><li>Loven, J., 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=Revisiting+global+gene+expression+analysis.">Revisiting global gene expression analysis.</a> Cell. 151 (3), 476-482 (2012).</li><li>JoVE Science Education Database. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+a+Hemoacytometer+to+Count+Cells.">Using a Hemoacytometer to Count Cells.</a> Basic Methods in Cellular and Molecular Biology. , (2017).</li><li>JoVE Science Education Database. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Separating+Protein+with+SDS-PAGE.">Separating Protein with SDS-PAGE.</a> Basic Methods in Cellular and Molecular Biology. , (2017).</li><li>JoVE Science Education Database. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Western+Blot.">The Western Blot.</a> Basic Methods in Cellular and Molecular Biology. , (2017).</li><li>Jackson, R. J., Hellen, C. U., Pestova, T. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mechanism+of+eukaryotic+translation+initiation+and+principles+of+its+regulation.">The mechanism of eukaryotic translation initiation and principles of its regulation.</a> Nat Rev Mol Cell Biol. 11 (2), 113-127 (2010).</li><li>Eaton, S. L., 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=A+guide+to+modern+quantitative+fluorescent+western+blotting+with+troubleshooting+strategies.">A guide to modern quantitative fluorescent western blotting with troubleshooting strategies.</a> J Vis Exp. (93), e52099 (2014).</li></ol>

Western Blotting is a common technique for detecting specific proteins and the activation of signaling pathways in tissues or cells. By introducing small adjustments to a commonly used procedure, we were able to routinely detect 15 different proteins (Table of Materials) in 15,000 HSCs, and in some cases in as few as 500 HSCs. The most critical steps in this protocol are: 1) accurately counting the cells, 2) minimizing the number of transfers between tubes, and 3) lysing the cells directly with Laemmli s...

Hematopoietic stem cells (HSCs) are self-renewing cells that can give rise to all blood lineages. They are relatively rare cells in the bone marrow, rendering biochemical analyses difficult. Approaches suitable for analyzing rare cells, such as flow cytometry, have been extremely useful for quantifying relative amounts of cell surface markers and intracellular proteins. However, the analysis of intracellular proteins necessitates the use of cell permeabilization procedures to enable antibody access, and not all cell surface epitopes survive these procedures1,2. In addition, antibodies that discriminate between different protein isoforms or cleavage products are not often available for flow cytometry, and therefore investigators still rely on Western blots for certain types of analyses.
Western blot analysis of cell lysates is a routine procedure in most laboratories. Cells can be purified under native conditions that preserve the epitopes of cell surface molecules, and cell lysates can subsequently be prepared and analyzed. However, the analysis of proteins in rare primary cell populations by Western blot can require euthanizing large numbers of animals to obtain enough cells. By making small adjustments to several steps, a conventional Western blotting protocol was able to detect proteins in relatively small numbers of HSCs (500 - 15,000, depending on the protein of interest). The adjustments include accurately counting the cells, carefully handling the cell pellet, reducing transfers of cells between tubes to minimize cell loss, and lysing a defined number of cells with a concentrated loading buffer containing proteasome and phosphatase inhibitors. Many published reports include Western blots obtained with 20,000 or more HSCs3,4,5,6,7; this simple procedure will reduce the number of cells and experimental animals required to produce equivalent data by between 4 and 40 fold. The protocol is designed to normalize results on a per cell basis, rather than to an internal control. This enables detection of overall reductions in protein levels that can be overlooked if data are normalized to an internal control. The importance of normalizing on a per cell basis was described for the analysis of gene expression data8, and the same principle applies to quantifying proteins by Western blot. This optimized protocol should be useful for anyone needing to analyze small numbers of cells.

<table>
	<tbody>
		<tr>
			<td>sodium dodecyl sulfate (SDS)</td>
			<td>Fisher Scientific</td>
			<td>BP166-500</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Fisher Scientific</td>
			<td>BP150-20</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>30% Acrylamidel Bis solution</td>
			<td>Bio-Rad</td>
			<td>1610158</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>1.5M Tris-HCl pH8.8</td>
			<td>TEKNOVA</td>
			<td>T1588</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>1.0M Tris-HCl pH6.8</td>
			<td>TEKNOVA</td>
			<td>T1068</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>Ammonium Persulfate</td>
			<td>Fisher Scientific</td>
			<td>BP179-25</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>mini-protean 3 comb</td>
			<td>Bio-Rad</td>
			<td>1653360</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td> 
			Mini-PROTEAN Tetra Cell</td>
			<td>Bio-Rad</td>
			<td>1658005EDU&#160;</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>&#160;Transfer System</td>
			<td>Bio-Rad</td>
			<td>1704155EDU</td>
			<td>transfer</td>
		</tr>
		<tr>
			<td>PowerPac HC Power Supply</td>
			<td>Bio-Rad</td>
			<td>1645052EDU&#160;</td>
			<td>electrophoresis</td>
		</tr>
		<tr>
			<td>Imaging System</td>
			<td>Bio-Rad</td>
			<td>1708195&#160;</td>
			<td>signal detection</td>
		</tr>
		<tr>
			<td>4x Laemmli Sample Buffer</td>
			<td>Bio-Rad</td>
			<td>1610747EDU&#160;</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>10x Tris/Glycine/SDS Electrophoresis Buffer</td>
			<td>Bio-Rad</td>
			<td>1610732EDU&#160;</td>
			<td>electrophoresis</td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol</td>
			<td>Bio-Rad</td>
			<td>1610710EDU</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>&#160;RTA Mini PVDF Transfer Kit, for 40 blots</td>
			<td>Bio-Rad</td>
			<td>1704272&#160;</td>
			<td>transfer</td>
		</tr>
		<tr>
			<td>Protease Inhibitor Cocktail</td>
			<td>Sigma</td>
			<td>11697498001</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>Phosphatase Inhibitor Cocktailrs</td>
			<td>Gold Biotechnology</td>
			<td>GB-450-1</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>EIF4G</td>
			<td>Cell signaling</td>
			<td>2469</td>
			<td>WB antibody, validated in 1000 cells 
			antibody concentration: 1:1000 
			reference(figure): Fig2</td>
		</tr>
		<tr>
			<td>p-Rps6</td>
			<td>Cell signaling</td>
			<td>4858</td>
			<td>WB antibody,validated in 1000 cells 
			antibody concentration: 1:1000 
			reference(figure): Fig2</td>
		</tr>
		<tr>
			<td>actin(HRP conjugated)</td>
			<td>abcam</td>
			<td>ab49900</td>
			<td>WB antibody,validated in 500 cells 
			antibody concentration: 1:5000 
			reference(figure): Fig1, Fig2</td>
		</tr>
		<tr>
			<td>LC-3</td>
			<td>Abcam</td>
			<td>ab48394</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig5)</td>
		</tr>
		<tr>
			<td>S6</td>
			<td>Cell Signaling</td>
			<td>2317</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig4)</td>
		</tr>
		<tr>
			<td>4EBP1</td>
			<td>Cell Signaling</td>
			<td>9644</td>
			<td>WB antibody, validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig4)</td>
		</tr>
		<tr>
			<td>p-4EBP1</td>
			<td>Cell Signaling</td>
			<td>2855</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig4)</td>
		</tr>
		<tr>
			<td>TSC2</td>
			<td>Cell Signaling</td>
			<td>4308</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig4)</td>
		</tr>
		<tr>
			<td>HSP90</td>
			<td>Cell Signaling</td>
			<td>4877</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (Fig5)</td>
		</tr>
		<tr>
			<td>PTEN</td>
			<td>Cell Signaling</td>
			<td>9188</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (FigS1)</td>
		</tr>
		<tr>
			<td>mTOR</td>
			<td>Cell Signaling</td>
			<td>2983</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (FigS1)</td>
		</tr>
		<tr>
			<td>p-mTOR</td>
			<td>Cell Signaling</td>
			<td>5536</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (FigS1)</td>
		</tr>
		<tr>
			<td>PP2AB</td>
			<td>Cell Signaling</td>
			<td>4953</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (FigS1)</td>
		</tr>
		<tr>
			<td>p-AMPKa</td>
			<td>Cell Signaling</td>
			<td>2535</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:1000 
			reference(figure): ref5 (FigS1)</td>
		</tr>
		<tr>
			<td>actin</td>
			<td>Santa Cruz</td>
			<td>sc-47778</td>
			<td>WB antibody,validated in 15000 cells 
			antibody concentration: 1:3000 
			reference(figure): ref5 (Fig4)</td>
		</tr>
		<tr>
			<td>lineage depletion kit (mouse)</td>
			<td>Miltenyi Biotec</td>
			<td>130-090-858</td>
			<td>hematopoietic stem and progenitor cells purification</td>
		</tr>
		<tr>
			<td>LS columns</td>
			<td>Miltenyi Biotec</td>
			<td>130-041-305</td>
			<td>hematopoietic stem and progenitor cells purification</td>
		</tr>
		<tr>
			<td>SCF</td>
			<td>PeproTech</td>
			<td>250-03</td>
			<td>phosphorylation stimulation</td>
		</tr>
		<tr>
			<td>APC-Cy7 c-kit antibody</td>
			<td>ThermoFisher</td>
			<td>A15423</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>anti-B220</td>
			<td>ThermoFisher</td>
			<td>48-0452-82</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>anti-CD3e</td>
			<td>ThermoFisher</td>
			<td>48-0031-82</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>anti-Mac1</td>
			<td>ThermoFisher</td>
			<td>48-0112-82</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>anti-Gr1</td>
			<td>ThermoFisher</td>
			<td>48-5931-82</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>anti-Ter119</td>
			<td>ThermoFisher</td>
			<td>48-5921-82</td>
			<td>cell sorting</td>
		</tr>
		<tr>
			<td>Spacer Plates with 1.0 mm Integrated Spacers</td>
			<td>Bio-Rad</td>
			<td>1653311</td>
			<td>&#160;SDS-PAGE</td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Research Products International</td>
			<td>A30075</td>
			<td>membrane blocking</td>
		</tr>
		<tr>
			<td>serum</td>
			<td>Atlanta Biologicals</td>
			<td>A12450</td>
			<td>medium supplement</td>
		</tr>
		<tr>
			<td>cell counter</td>
			<td>Invitrogen</td>
			<td>AMQAF1000</td>
			<td>cell counting</td>
		</tr>
		<tr>
			<td>hemocytometer</td>
			<td>ThermoFisher</td>
			<td>&#160;S17040</td>
			<td>cell counting</td>
		</tr>
		<tr>
			<td>flim</td>
			<td>Denville Scientific</td>
			<td>E3012</td>
			<td>signal detection</td>
		</tr>
		<tr>
			<td>medical film processor</td>
			<td>Konica</td>
			<td>SRC-101A</td>
			<td>signal detection</td>
		</tr>
		<tr>
			<td>Supersignal West Femto Maximum Sensitivity Substrate</td>
			<td>Therom Scientific</td>
			<td>34096</td>
			<td>signal detection</td>
		</tr>
		<tr>
			<td>Allegra X-15R Centrifuge (Rotor SX4750A)</td>
			<td>Beckman Coulter</td>
			<td>X-15R</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>BLUEstain protein ladder</td>
			<td>Gold Biotechnology</td>
			<td>P007-500</td>
			<td>electrophoresis</td>
		</tr>
		<tr>
			<td>cell sorter</td>
			<td>BD</td>
			<td>FACSAria II</td>
			<td>sample preparation</td>
		</tr>
		<tr>
			<td>Incublock</td>
			<td>Denville Scientific</td>
			<td>I0510</td>
			<td>electrophoresis</td>
		</tr>
	</tbody>
</table>

a western blotting protocol for small numbers of hematopoietic stem cells

Hematopoietic stem cells (HSCs) are rare cells, with the mouse bone marrow containing only ~25,000 phenotypic long term repopulating HSCs. A Western blotting protocol was optimized and suitable for the analysis of small numbers of HSCs (500 - 15,000 cells). Phenotypic HSCs were purified, accurately counted, and directly lysed in Laemmli sample buffer. Lysates containing equal numbers of cells were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the blot was prepared and processed following standard Western blotting protocols. Using this protocol, 2,000 - 5,000 HSCs can be routinely analyzed, and in some cases data can be obtained from as few as 500 cells, compared to the 20,000 to 40,000 cells reported in most publications. This protocol should be generally applicable to other hematopoietic cells, and enables the routine analysis of small numbers of cells using standard laboratory procedures.

Representative results from 500 - 2,000 purified HSCs and HPs are shown in Figure 1 and Figure 2. The &#946;-actin signal in Figure 1 can be detected from as few as 500 HSCs and HPs purified from the bone marrow of one mouse. Note that loading the lysates into 1.5 mm wells produced a much stronger signal from 500 HPs than loading into 3.0 mm wells. Figure 2 is a Western ...

Watch this Scientific Journal Video about A Western Blotting Protocol for Small Numbers of Hematopoietic Stem Cells at JoVE.com

A Western Blotting Protocol for Small Numbers of Hematopoietic Stem Cells

A standard Western blotting protocol was optimized for analyzing as few as 500 hematopoietic stem or progenitor cells. Optimization involves careful handling of the cell sample, limiting transfers between tubes, and directly lysing the cells in Laemmli sample buffer.

Hematopoietic stem cells (HSCs) are rare cells, with the mouse bone marrow containing only ~25,000 phenotypic long term repopulating HSCs. A Western ...

The over goal of this western blotting protocol is to Perform western blots on small numbers of cells. This method can help answer key questions in the hematopoietic stem cell field such as the presence or abundance of specific proteins or activation of signaling pathways. The main advantage of this technique is that it requires fewer than 20, 000 cells thus fewer animals are needed to analyze rare populations of primary cells.We first had the idea for this method when we were trying to find ways to reduce the number of mice we needed to use for hematopoietic stem cell analyses. Demonstrating the procedure will be Xiongwei Cai, a post doc from my laboratory. Use a swinging bucket rotor to centrifuge 1.5 milliliter tubes containing sorted hematopoietic stem and progenitor cells at 500 times gravity for five minutes at four degrees Celsius.Once the centrifugation is over, discard all but 100 microliters of supernatant, without disturbing the cell pellet. If there are less than 5, 000 cells, and the volume of the sorted sample is less than 0.2 milliliters, first transfer the cells to low binding 0.2 milliliter PCR tubes before centrifugation. However, if there are less than 5, 000 cells, but the volume of the sorted sample is more than 0.2 milliliter, then centrifuge the cells at 500 times gravity for five minutes at four degrees Celsius.After centrifugation, discard all but 200 microliters of supernatant. Then re suspend the pellet and the remaining 200 microliters of supernatant. Next, transfer the cell suspension to 0.2 milliliter PCR tubes and again, centrifuge.Then re suspend the pellet in 20 to 30 microliters of supernatant and discard the rest. If necessary, add phosphate buffered saline in 2%fetal bovine serum, or 2%bovine serum albumin to the re suspended cells. Then use an automated cell counter to determine the cellular concentration using two to five microliters of re suspended cells.Next use a 20 or 100 microliter pipette tip to transfer a volume of 500, 1, 000, and 2, 000 hematopoietic stem and progenitor cells to new 1.5 milliliter tubes. Use a swinging bucket rotor to centrifuge the cells at four degrees Celsius at 500 times gravity for five minutes. Then follow the manufacturers instructions to dissolve phosphatase and proteasome inhibitor and DMSO to prepare a 100 fold stock solution.Next dilute the four fold Laemmli sample buffer with equivalent volumes of distilled water to make a two fold Laemmli sample buffer. Then add appropriate amounts of the 100 fold stock solution of phosphatase and proteasome inhibitor to adjust the final concentration to two fold inhibitors, and two fold Laemmli sample buffer. Adjust the volume of residual supernatant in the tube such that adding equal volumes of two fold Laemmli buffer along with the phosphatase and proteasome inhibitor will achieve a final concentration of 500 cells per microliter and one fold Laemmli buffer.And then re suspend to form the lysate. Before loading the gel, heat the sample lysates at 95 degrees Celsius in a heat block for five minutes. Using standard protocols electrophoresis one to 40 microliters of lysate equivalent to 500 to 20, 000 cells through SDS page at 100 volts.After treating poly vinylidene membrane with methanol for then seconds wash the membrane with distilled water briefly. Then transfer the protein from the gel to the membrane according to the instructions provided by the manufacturer of the transfer apparatus. After transfer, block the membrane with two milliliters of 2%bovine serum albumin and phosphate buffered saline with 0.1%Tween overnight at four degrees Celsius according to standard protocals.After blocking the membrane, incubate it with diluted antibodies overnight at four degrees celsius. Then wash the membrane thrice with phosphate buffered saline with 0.1%Tween 20 for five minutes each at room temperature. Next incubate the membrane with two milliliters of enhanced chemiluminescence buffer for one minute at room temperature.Detect the signals using an imaging system. To compare the beta actin signals lysates were prepared from urine hematopoietic stem and progenitor cells and subjected to western plot analysis. It is clear form the amino blot that there is a decrease in beta actin signal from the lysates prepared from 2, 000 to 500 hematopoietic progenitor and stem cells loaded in 1.5 millimeter wells on a 12%SDS page gel.Further, to compare the beta actin signals obtained from different well sizes cast on the gel. Lysates were loaded in 1.5 and three millimeter wells on the gel and then subjected to western blot analysis. The blot shows that the beta actin signal obtained from the lysate prepared from 500 hematopoietic progenitors loaded in a 1.5 millimeter well is much stronger than when loaded in a three millimeter well.Next, to compare the signals for eucaryotic initiation factor 4G, actin and phosphorylation of ribosomal protein S6 in response to cytokine stem cell factor stimulation the lysates obtained were analyzed by amino blot. The blot shows the presence of stronger signal intensities for all three proteins in the hematopoietic re genitors with cytokine stem cell factor stimulation. In comparison to the control in vitro it is also clear that there is and increasing signal intensity for all three proteins from different hematopoietic stem cell volumes.Once mastered this technically can be done in 48 hours. If it is approached properly. While attempting this procedure it's important to remember to accurately count the cells and to direct the lysate cells with a loading buffer.After this development it is technically pelleted away for the researchers in the field of stem cell research to explore signal pathways in small number of cells. After watching this video you should have a good understanding of how to do western plotting with a small number of address pieces. Be careful with the regions you're using for SDS page.Thank you for watching. Good luck with your experiments.

a-western-blotting-protocol-for-small-numbers-hematopoietic-stem

Research

JoVE Journal

Biochemistry

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating these studies, reincorporation of detergent-solubilized membrane proteins into liposomes is a stochastic process where protein topology is impossible to enforce. This paper offers an alternative method to these challenging techniques that utilizes a liposome-based scaffold. Protein solubility is enhanced by deletion of the transmembrane domain, and these amino acids are replaced with a tethering moiety, such as a His-tag. This tether interacts with an anchoring group (Ni2+ coordinated by nitrilotriacetic acid (NTA(Ni2+)) for His-tagged proteins), which enforces a uniform protein topology at the surface of the liposome. An example is presented wherein the interaction between Dynamin-related protein 1 (Drp1) with an integral membrane protein, Mitochondrial Fission Factor (Mff), was investigated using this scaffold liposome method. In this work, we have demonstrated the ability of Mff to efficiently recruit soluble Drp1 to the surface of liposomes, which stimulated its GTPase activity. Moreover, Drp1 was able to tubulate the Mff-decorated lipid template in the presence of specific lipids. This example demonstrates the effectiveness of scaffold liposomes using structural and functional assays and highlights the role of Mff in regulating Drp1 activity.

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

This paper describes a method for assessing the interactions and assemblies of integral membrane proteins in vitro with various partner factors in a lipid-proximal environment.

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating ...

SorLA and CLC:CLF-1-dependent Downregulation of CNTFR&#945; as Demonstrated by Western Blotting, Inhibition of Lysosomal Enzymes, and Immunocytochemistry

The heterodimeric cytokine Cardiotrophin-like Cytokine:Cytokine-like Factor-1 (CLC:CLF-1) targets the glycosylphosphatidylinositol (GPI)-anchored CNTFR&#945; to form a trimeric complex that subsequently recruits glycoprotein 130/Leukemia Inhibitory Factor Receptor-&#946; (gp130/LIFR&#946;) for signaling. Both CLC and CNTFR&#945; are necessary for signaling but so far CLF-1 has only been known as a putative facilitator of CLC secretion. However, it has recently been shown that CLF-1 contains three binding sites: one for CLC; one for CNTFR&#945; (that may promote assembly of the trimeric complex); and one for the endocytic receptor sorLA. The latter site provides high affinity binding of CLF-1, CLC:CLF-1, as well as the trimeric (CLC:CLF-1:CNTFR&#945;) complex to sorLA, and in sorLA-expressing cells the soluble ligands CLF-1 and CLC:CLF-1 are rapidly taken up and internalized. In cells co-expressing CNTFR&#945; and sorLA, CNTFR&#945; first binds CLC:CLF-1 to form a membrane-associated trimeric complex, but it also connects to sorLA via the free sorLA-binding site in CLF-1. As a result, CNTFR&#945;, which has no capacity for endocytosis on its own, is tugged along and internalized by the sorLA-mediated endocytosis of CLC:CLF-1.
The present protocol describes the experimental procedures used to demonstrate i) the sorLA-mediated and CLC:CLF-1-dependent downregulation of surface-membrane CNTFR&#945; expression; ii) sorLA-mediated endocytosis and lysosomal targeting of CNTFR&#945;; and iii) the lowered cellular response to CLC:CLF-1-stimulation upon sorLA-mediated downregulation of CNTFR&#945;.

SorLA and CLC:CLF-1-dependent Downregulation of CNTFR&amp;#945; as Demonstrated by Western Blotting, Inhibition of Lysosomal Enzymes, and Immunocytochemistry

The present protocol describes how Western blotting and immunocytochemistry combined with inhibition of lysosomal enzymes can be used to demonstrate the downregulation of Ciliary Neurotrophic Factor Receptor-&#945; (CNTFR&#945;), which is conveyed by the interaction between Cytokine-like Factor-1 (CLF-1) and the endocytic receptor sorLA.

The heterodimeric cytokine Cardiotrophin-like Cytokine:Cytokine-like Factor-1 (CLC:CLF-1) targets the glycosylphosphatidylinositol (GPI)-anchored ...

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 ...

Robust Comparison of Protein Levels Across Tissues and Throughout Development Using Standardized Quantitative Western Blotting

Western blotting is a technique that is commonly used to detect and quantify protein expression. Over the years, this technique has led to many advances in both basic and clinical research. However, as with many similar experimental techniques, the outcome of Western blot analyses is easily influenced by choices made in the design and execution of the experiment. Specific housekeeping proteins have traditionally been used to normalize protein levels for quantification, however, these have a number of limitations and have therefore been increasingly criticized over the past few years. Here, we describe a detailed protocol that we have developed to allow us to undertake complex comparisons of protein expression variation across different tissues, mouse models (including disease models), and developmental timepoints. By using a fluorescent total protein stain and introducing the use of an internal loading standard, it is possible to overcome existing limitations in the number of samples that can be compared within experiments and systematically compare protein levels across a range of experimental conditions. This approach expands the use of traditional western blot techniques, thereby allowing researchers to better explore protein expression across different tissues and samples.

This method describes a robust and reproducible approach for the comparison of protein levels in different tissues and at different developmental timepoints using a standardized quantitative western blotting approach.

Western blotting is a technique that is commonly used to detect and quantify protein expression. Over the years, this technique has led to many advances ...

A Semi-High-Throughput Adaptation of the NADH-Coupled ATPase Assay for Screening Small Molecule Inhibitors

ATPase enzymes utilize the free energy stored in adenosine triphosphate to catalyze a wide variety of endergonic biochemical processes in vivo that would not occur spontaneously. These proteins are crucial for essentially all aspects of cellular life, including metabolism, cell division, responses to environmental changes and movement. The protocol presented here describes a nicotinamide adenine dinucleotide (NADH)-coupled ATPase assay that has been adapted to semi-high throughput screening of small molecule ATPase inhibitors. The assay has been applied to cardiac and skeletal muscle myosin II's, two actin-based molecular motor ATPases, as a proof of principle. The hydrolysis of ATP is coupled to the oxidation of NADH by enzymatic reactions in the assay. First, the ADP generated by the ATPase is regenerated to ATP by pyruvate kinase (PK). PK catalyzes the transition of phosphoenolpyruvate (PEP) to pyruvate in parallel. Subsequently, pyruvate is reduced to lactate by lactate dehydrogenase (LDH), which catalyzes the oxidation of NADH in parallel. Thus, the decrease in ATP concentration is directly correlated to the decrease in NADH concentration, which is followed by change to the intrinsic fluorescence of NADH. As long as PEP is available in the reaction system, the ADP concentration remains very low, avoiding inhibition of the ATPase enzyme by its own product. Moreover, the ATP concentration remains nearly constant, yielding linear time courses. The fluorescence is monitored continuously, which allows for easy estimation of the quality of data and helps to filter out potential artifacts (e.g., arising from compound precipitation or thermal changes).

A nicotinamide adenine dinucleotide (NADH)-coupled ATPase assay has been adapted to semihigh throughput screening of small molecule myosin inhibitors. This kinetic assay is run in a 384-well microplate format with total reaction volumes of only 20 &#181;L per well. The platform should be applicable to virtually any ADP producing enzyme.

ATPase enzymes utilize the free energy stored in adenosine triphosphate to catalyze a wide variety of endergonic biochemical processes in vivo that would ...

A Rapidly Incremented Tethered-Swimming Maximal Protocol for Cardiorespiratory Assessment of Swimmers

Incremental exercise testing is the standard means of assessing cardiorespiratory capacity of endurance athletes. While the maximal rate of oxygen consumption is typically used as the criterion measurement in this regard, two metabolic breakpoints that reflect changes in the dynamics of lactate production/consumption as the work rate is increased are perhaps more relevant for endurance athletes from a functional standpoint. Exercise economy, which represents the rate of oxygen consumption relative to performance of submaximal work, is also an important parameter to measure for endurance-athlete assessment. Ramp incremental tests comprising a gradual but rapid increase in work rate until the limit of exercise tolerance is reached are useful for determining these parameters. This type of test is typically performed on a cycle ergometer or treadmill because there is a need for precision with respect to work-rate incrementation. However, athletes should be tested while performing the mode of exercise required for their sport. Consequently, swimmers are typically assessed during free-swimming incremental tests where such precision is difficult to achieve. We have recently suggested that stationary swimming against a load that is progressively increased (incremental tethered swimming) can serve as a &#34;swim ergometer&#34; by allowing sufficient precision to accommodate a gradual but rapid loading pattern that reveals the aforementioned metabolic breakpoints and exercise economy. However, the degree to which the peak rate of oxygen consumption achieved during such a protocol approximates the maximal rate that is measured during free swimming remains to be determined. In the present article, we explain how this rapidly incremented tethered-swimming protocol can be employed to assess the cardiorespiratory capacity of a swimmer. Specifically, we explain how assessment of a short-distance competitive swimmer using this protocol revealed that his rate of oxygen uptake was 30.3 and 34.8 mL&#8729;min-1&#8729;kg-1BM at his gas-exchange threshold and respiratory compensation point, respectively.

As opposed to measurement during free swimming, which presents inherent challenges and limitations, determination of important parameters of cardiorespiratory function for swimmers can be made using a more feasible and easier to administer tethered-swimming rapidly incremented protocol with gas exchange and ventilatory data collection.

Incremental exercise testing is the standard means of assessing cardiorespiratory capacity of endurance athletes. While the maximal rate of oxygen ...

A High-Throughput Enzyme-Coupled Activity Assay to Probe Small Molecule Interaction with the dNTPase SAMHD1

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this enzyme can hydrolyze dNTPs into their corresponding nucleosides and inorganic triphosphates. Due to its critical role in nucleotide metabolism, its association to several pathologies, and its role in therapy resistance, intense research is currently being carried out for a better understanding of both the regulation and cellular function of this enzyme. For this reason, development of simple and inexpensive high-throughput amenable methods to probe small molecule interaction with SAMHD1, such as allosteric regulators, substrates, or inhibitors, is vital. To this purpose, the enzyme-coupled malachite green assay is a simple and robust colorimetric assay that can be deployed in a 384-microwell plate format allowing the indirect measurement of SAMHD1 activity. As SAMHD1 releases the triphosphate group from nucleotide substrates, we can couple a pyrophosphatase activity to this reaction, thereby producing inorganic phosphate, which can be quantified by the malachite green reagent through the formation of a phosphomolybdate malachite green complex. Here, we show the application of this methodology to characterize known inhibitors of SAMHD1 and to decipher the mechanisms involved in SAMHD1 catalysis of non-canonical substrates and regulation by allosteric activators, exemplified by nucleoside-based anticancer drugs. Thus, the enzyme-coupled malachite green assay is a powerful tool to study SAMHD1, and furthermore, could also be utilized in the study of several enzymes which release phosphate species.

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase with critical roles in human health and disease. Here we present a versatile enzyme-coupled SAMHD1 activity assay, deployed in a 384-well microplate format, that allows for the evaluation of small molecules and nucleotide analogues as SAMHD1 substrates, activators, and inhibitors.

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this ...

Development of a Lateral Flow Immunochromatographic Strip for Rapid and Quantitative Detection of Small Molecule Compounds

Membrane-based lateral flow immunochromatographic strips (ICSs) are useful tools for low-cost self-diagnosis and have been efficiently applied to toxin, physiological index and clinical biomarker detection. In this protocol, we provide a detailed description of the steps to develop a rapid, sensitive and quantitative lateral-flow immunoassay (using AuNPs as a marker and mAbs as a probe). The procedure describes the preparation and characterization of colloidal gold, synthesis of the AuNP-mAb conjugate, assembly of the immunochromatographic strip, and methodological investigation of the assay. The results showed that the final strips can be further utilized for the rapid and convenient self-diagnosis of a small molecule, which may provide an alternative tool in the rapid and precise analysis of physiological and biological indices.

Membrane-based lateral flow immunochromatographic strips (ICSs) are useful tools for low-cost self-diagnosis and have been efficiently applied to toxin, ...

Generating Self-Assembling Human Heart Organoids Derived from Pluripotent Stem Cells

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in vitro. Developing more efficient organ-like platforms that can model complex in vivo phenotypes, such as organoids and organs-on-a-chip, will enhance the ability to study human heart development and disease. This paper describes a protocol to generate highly complex human heart organoids (hHOs) by self-organization using human pluripotent stem cells and stepwise developmental pathway activation using small molecule inhibitors. Embryoid bodies (EBs) are generated in a 96-well plate with round-bottom, ultra-low attachment wells, facilitating suspension culture of individualized constructs.
The EBs undergo differentiation into hHOs by a three-step Wnt signaling modulation strategy, which involves an initial Wnt pathway activation to induce cardiac mesoderm fate, a second step of Wnt inhibition to create definitive cardiac lineages, and a third Wnt activation step to induce proepicardial organ tissues. These steps, carried out in a 96-well format, are highly efficient, reproducible, and produce large amounts of organoids per run. Analysis by immunofluorescence imaging from day 3 to day 11 of differentiation reveals first and second heart field specifications and highly complex tissues inside hHOs at day 15, including myocardial tissue with regions of atrial and ventricular cardiomyocytes, as well as internal chambers lined with endocardial tissue. The organoids also exhibit an intricate vascular network throughout the structure and an external lining of epicardial tissue. From a functional standpoint, hHOs beat robustly and present normal calcium activity as determined by Fluo-4 live imaging. Overall, this protocol constitutes a solid platform for in vitro studies in human organ-like cardiac tissues.

Here, we describe a protocol to create developmentally relevant human heart organoids (hHOs) efficiently using human pluripotent stem cells by self-organization. The protocol relies on the sequential activation of developmental cues and produces highly complex, functionally relevant human heart tissues.

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in ...

Synthesis of Masarimycin, a Small Molecule Inhibitor of Gram-Positive Bacterial Growth

Peptidoglycan (PG) in the cell wall of bacteria is a unique macromolecular structure that confers shape, and protection from the surrounding environment. Central to understanding cell growth and division is the knowledge of how PG degradation influences biosynthesis and cell wall assembly. Recently, the metabolic labeling of PG through the introduction of modified sugars or amino acids has been reported. While chemical interrogation of biosynthetic steps with small molecule inhibitors is possible, chemical biology tools to study PG degradation by autolysins are underdeveloped. Bacterial autolysins are a broad class of enzymes that are involved in the tightly coordinated degradation of PG. Here, a detailed protocol is presented for preparing a small molecule probe, masarimycin, which is an inhibitor of N-acetylglucosaminidase LytG in Bacillus subtilis, and cell wall metabolism in Streptococcus pneumoniae. Preparation of the inhibitor via microwave-assisted and classical organic synthesis is provided. Its applicability as a tool to study Gram-positive physiology in biological assays is presented.

A detailed protocol is presented for preparing the bacteriostatic diamide masarimycin, a small molecule probe that inhibits the growth of Bacillus subtilis and Streptococcus pneumoniae by targeting cell wall degradation. Its application as a chemical probe is demonstrated in synergy/antagonism assays and morphological studies with B. subtilis and S. pneumoniae.

Peptidoglycan (PG) in the cell wall of bacteria is a unique macromolecular structure that confers shape, and protection from the surrounding environment. ...