We thank Daniel Chen from the Digital Video Production Team of Buchholz High School for assistance in editing the video. This research on stomatal guard cells, proteomics and metabolomics in the Chen lab has been supported by grants from the US National Science Foundation (0818051, 1158000 and 1412547). Wenwen Kong is supported by the China Scholarship Council. Dr. Qiuying Pang is supported by the China Scholarship Council and National Natural Science Foundation of China (31570396).

1. Growing Plants
<ol>
	<li>Germinate the seeds in potting mixture. Grow plants in a growth chamber with a light intensity of 140 &#181;mol photons m&#8722;2 s &#8722;1 and a photoperiod of 8 h light at 22 &#176;C and 16 h dark at 18 &#176;C for 2 weeks.</li>
	<li>Transplant seedlings of similar sizes individually into 4&#34; diameter pots containing the soil and grow for an additional 3 weeks in the same conditions described in step 1.1. 
	NOTE: Water plants with tap water twice a week to keep the soil moist.</li>
</ol>
2. Preparation of Enriched Stomata
<ol>
	<li>Remove the leaves of 5-week old A. thaliana plants individual with a scalpel.</li>
	<li>Attach each leaf to two pieces of clear Scotch tape, with one piece adhering to the abaxial (lower) side and the other piece adhering to adaxial (upper) side of the leaf. Leave the tape on the leaf for 5 s.</li>
	<li>Gentle peel apart the two pieces of tapes using the index finger and thumb on each hand to separate the abaxial side with pavement and guard cells and the adaxial side with mesophyll cells.</li>
	<li>Place the peels from the abaxial side of the leaves in 60 mL of stomata opening buffer (50 mM KCl, 10 mM MES-KOH, adjusted to pH 6.2 with 1 M KOH) in 40 mm &#215; 12 mm size Petri dishes as they are collected.
	<ol>
		<li>Repeat the above steps until all sample peels are collected.</li>
	</ol>
	</li>
	<li>Place the Petri dishes containing the peels into the growth chamber under light conditions stated in step 1.1. Leave the peels under the light for 2 h to fully open stomata.</li>
	<li>Place peels into a 150 mm x 20 mm Petri dish containing 50 mL of cell wall digesting enzyme mixture (0.7% cellulase R-10, 0.025% macerozyme R-10 , 0.1% (w/v) polyvinylpyrrolidone-40, and 0.25% (w/v) bovine serum albumin in 55% basic solution (0.55 M sorbitol, 0.5 mM CaCl2, 0.5 mM MgCl2, 0.5 mM ascorbic acid, 10 &#181;M KH2PO4, 5 mM 4-morpholineethanesulfonic acid (MES) at pH 5.7 adjusted with 1 M KOH).</li>
	<li>Shake the peels on a reciprocal shaker in a Petri dish at 50 rpm for 20 min.</li>
	<li>Remove peels from enzyme solution with tweezers after 20 min. Transfer the peels to a 150 mm x 20 mm size Petri dish containing 50 mL of water.</li>
	<li>Using a transfer pipette, rinse peels for 15 s twice with 10 mL of water to remove any residual enzyme solution.</li>
	<li>Use tweezers to place peels in a 150 mm x 20 mm size Petri dish with 50 mL of fresh stomata opening buffer as used in step 2.4. Incubate for 1 h in light conditions stated in step 1.1 to allow the stomata to recover.</li>
</ol>
3. Abscisic Acid (ABA) Treatment and Stomata Movement Assay
<ol>
	<li>In a 150 mm x 20 mm size Petri dish. Incubate the enriched stomata peels at 30&#176;C for 15 min in 50 mL of the stomatal opening buffer or in 50 mL of the stomatal opening buffer with a final concentration of 10 &#181;M ABA for the appropriate treatment time.</li>
	<li>Place peels on a shaker at 50 rpm for 5, 15 and 30 min. After each time interval remove a peel with tweezers and follow the imaging steps in step 3.3.</li>
	<li>Take images of stomata before ABA treatment and at the various time points after ABA treatment with a light microscope.
	<ol>
		<li>Take a peel and place it on a glass microscope slide.</li>
		<li>Place the slide on the microscope stage and adjust the stage so that the image of the peel can be visualized.</li>
		<li>Adjust the fine and course focus on the microscope to get a clear image of the guard cells.</li>
		<li>Take several images of multiple stomata at 40X magnification.</li>
	</ol>
	</li>
	<li>Measure 60 stomatal apertures using ImageJ8.</li>
	<li>Calculate the standard error and significance at a p-value &#60; 0.05 of the 60 stomatal aperture measurements.</li>
</ol>
4. Protein Extraction and SDS-Page Separation
<ol>
	<li>Grind the peels for 15 s in enough liquid nitrogen to cover the peels using a chilled mortar and pestle.</li>
	<li>Per 50 peels, add 3 mL of Tris saturated phenol (pH 8.8) and 3 mL protein extraction buffer (0.9 M sucrose, 0.1 M Tris-HCl, 0.01 M EDTA, 0.4% 2-Mercaptoethanol, 10 &#181;L of 1 mM protease and phosphatase inhibitor) with a pipette to the mortar and then grind the peels for 5 additional minutes in a fume hood.</li>
	<li>Transfer the extract using a pipette and the peels using metal tweezers to an Oakridge centrifuge tube and agitate on a shaker at 50 rpm for 1 h at 4 &#176;C.</li>
	<li>Remove the peels from the Oakridge centrifuge tube and centrifuge the extract at 5,000 x g for 10 min. Then transfer the top phenolic phase to a new clean micro-centrifuge tube using a pipette.</li>
	<li>Precipitate the phenol extracted proteins by adding 5 volumes of ice-cold 0.1 M ammonium acetate in 100% methanol. Vortex briefly and incubate overnight at -20 &#176;C.</li>
	<li>Centrifuge at 20,000 x g at 4 &#176;C for 20 min, decant the supernatant by slowly pouring it out of the tube and retain the protein pellet in the tube.</li>
	<li>Wash the protein pellet twice with 0.1 M ammonium acetate in methanol, and then twice with 80% acetone and once with 100% cold acetone. 
	NOTE: Washes are done by adding 10 mL of specified reagent to the tube of protein. Agitate on a shaker at 50 rpm for 5 min, followed by centrifugation at 15,000 x g at 4 &#176;C for 10 min. Then pour the reagent out of the tube retaining only the protein pellet.</li>
	<li>Add 1 mL of 100% cold acetone to the pellet and re-suspend by slowly pipetting up and down.</li>
	<li>Transfer protein suspension via pipette to a 2 mL micro-centrifuge tube then centrifuge at 20,000 x g at 4 &#176;C for 5 min.</li>
	<li>Remove the acetone by decanting it from tube and dry the pellet in fume hood for 10 min.</li>
	<li>Dissolve the protein in a micro-centrifuge tube with 200 &#181;L of dissolution buffer (8 M urea, 0.5% SDS, 30 mM Tris-HCl at pH 8.5) and vortex for 30 min. Centrifuge at 20,000 x g at 15 &#176;C for 20 min and collect the supernatant in a new tube.</li>
	<li>Quantify the protein concentration following the protein quantification protocol9.</li>
	<li>Use protein samples for protein separation by gel electrophoresis following the protocol10.</li>
</ol>

<ol>
	<li>Acharya, B., Assmann, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hormone+interactions+in+stomatal+function.">Hormone interactions in stomatal function.</a> Plant Molecular Biology. 69 (4), 451-462 (2009).</li><li>Schroeder, J. I., Allen, G. J., Hugouvieux, V., Kwak, J. M., Waner, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Guard+cell+signal+transduction.">Guard cell signal transduction.</a> Annual Review of Plant Physiology and Plant Molecular Biology. 52, 627-658 (2001).</li><li>Obulareddy, N., Panchal, S., Melotto, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Guard+Cell+Purification+and+RNA+Isolation+Suitable+for+High-Throughput+Transcriptional+Analysis+of+Cell-Type+Responses+to+Biotic+Stresses.">Guard Cell Purification and RNA Isolation Suitable for High-Throughput Transcriptional Analysis of Cell-Type Responses to Biotic Stresses.</a> Molecular Plant-Microbe Interactions. 26 (8), 844-849 (2013).</li><li>Pandey, S., Wang, X. Q., Coursol, S. A., Assmann, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+and+applications+of+Arabidopsis+thaliana+guard+cell+protoplasts.">Preparation and applications of Arabidopsis thaliana guard cell protoplasts.</a> New Phytologist. 153 (3), 517-526 (2002).</li><li>Schroeder, J. I., Raschke, K., Neher, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Voltage+Dependence+Of+K++Channels+In+Guard-Cell+Protoplasts.">Voltage Dependence Of K+ Channels In Guard-Cell Protoplasts.</a> Proceedings of the National Academy of Sciences of the United States of America. 84 (12), 4108-4112 (1987).</li><li>Wu, F. H., 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=Tape-Arabidopsis+Sandwich+-+a+simpler+Arabidopsis+protoplast+isolation+method.">Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method.</a> Plant Methods. 5, 10 (2009).</li><li>Svozil, J., Gruissem, W., Baerenfaller, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteasome+targeting+of+proteins+in+Arabidopsis+leaf+mesophyll,+epidermal+and+vascular+tissues.">Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues.</a> Frontiers in Plant Science. 6, (2015).</li><li>Schneider, C., Rasband, W., Eliceiri, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NIH+Image+to+ImageJ:+25+years+of+image+analysis.">NIH Image to ImageJ: 25 years of image analysis.</a> Nature Methods. 9 (7), 671-675 (2012).</li><li>Agnew, B., Murray, D., Patton, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+solid-phase+fluorescence-based+protein+assay+for+quantitation+of+protein+electrophoresis+samples+containing+detergents,+chaotropes,+dyes,+and+reducing+agents.">A rapid solid-phase fluorescence-based protein assay for quantitation of protein electrophoresis samples containing detergents, chaotropes, dyes, and reducing agents.</a> Electrophoresis. 25 (15), 2478-2485 (2004).</li><li>He, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laemmli-SDS-PAGE.">Laemmli-SDS-PAGE.</a> Bio-protocol. Bio101 (80), (2011).</li><li>Thompson, 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=Tandem+mass+tags:+A+novel+quantification+strategy+for+comparative+analysis+of+complex+protein+mixtures+by+MS/MS+(vol+75,+pg+1895).">Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS (vol 75, pg 1895).</a> Analytical Chemistry. 78 (12), 4235-4235 (2006).</li><li>Wiese, S., Reidegeld, K. A., Meyer, H. E., Warscheid, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+labeling+by+iTRAQ:+A+new+tool+for+quantitative+mass+spectrometry+in+proteome+research.">Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research.</a> Proteomics. 7 (3), 340-350 (2007).</li></ol>

No conflicts of interest declared.

Guard cells are a model system for studying signal transduction mechanisms in plants and it is important to ensure that the preparation of samples used in the study is the most appropriate to answering biological questions. Despite the increasing interest in guard cells within the plant research community, there is no universal method on how to prepare stomatal guard cells that would allow both the stomatal movement and physiology as well as the molecular changes to be studied in one system. The challenge to isolate them...

Stomata play an important role in the overall physiology and fitness of plants. These tiny plant specific structures are formed by two specialized epidermal cells known as guard cells and are found most abundantly on the abaxial surface of leaves. Stomata are necessary for the exchange of gasses between the plant and the atmosphere, as well as the control of water loss through transpiration. Guard cells regulate stomata aperture through the integration of different external (e.g., light, humidity, pathogen contact, carbon dioxide levels) and internal (e.g., endogenous hormones) stimuli1,2. In the last 20 years, this cell type has become a model system for studying cell signaling processes in plants. These cells make up a small fraction of the total cells in a leaf; thus, to investigate their unique cellular, biochemical and molecular properties in a single-cell manner, it is necessary to isolate them from other leaf cell types. In the past, guard cell studies have often involved the preparation of guard cell protoplasts (GCP)3,4,5. This typically requires the use of large amounts of cell-wall degrading enzymes and or mechanical disruption via blending and has proven to be costly and time-consuming as it generally takes many hours to prepare a GCP sample, often times with little yield. More importantly, because guard cells act as complete pairs to regulate stomata aperture, the use of GCP can be seen as an artificial system to studying guard cell signaling. 
Here, we have developed a method to prepare stomata in which intact guard cells are enriched and maintain physiological responses to stimuli. This method was inspired by a method that was used to isolate mesophyll cell protoplasts6,7. In our method, stomata are prepared using clear Scotch tape to first separate the majority of mesophyll cells attached to the adaxial layer of the leaf from the abaxial layer containing the pavement and guard cells. This is done by affixing a piece of tape to each side of the leaf and peeling them apart. The cells from the abaxial layer are allowed to recover under light in a stomata-opening buffer. Later the remaining pavement cells are removed using a small quantity of cell wall degrading enzymes, leaving behind guard cell that are enriched on the tape. 
In this simple method, stomatal guard cells that are both viable and responsive can quickly and efficiently be prepared, taking less than an hour to obtain enriched stomatal guard cells from 50 peels with minimal cost. The method here imposes less damage to the plant cells than previous methods where protoplasts are prepared. In addition, materials collected from this method yield desirable protein amounts. Most importantly, because the leaf is not subjected to blending or lengthy digestion times and guard cells remain intact, the results of studies will more closely be relevant to that of a guard cell's natural biology. With this method, stomatal movements can be correlated in real time with changes at the molecular level. Thus, the knowledge gained from studies using this preparation method would be important for a more comprehensive understanding of guard cell signaling. 
We used the plant Arabidopsis thaliana as a model; however this protocol can be applied to the enrichment of stomatal guard cells in other plant species such as Brassica napus with small modifications in digestion time. As a proof of concept, we have demonstrated that stomatal guard cells enriched via this method are viable and responsive to stimuli as shown by the fluorescein diacetate (FDA) assay and studies utilizing the plant hormone abscisic acid (ABA), respectively. In addition, we have demonstrated that high-quality proteins can be isolated from these guard cells. Here, we describe a detailed protocol of this process.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Stainless Steel Surgical Scalpel</td>
			<td style="width:297px;">Feather&#160;</td>
			<td style="width:119px;">&#160;NC9999403</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Scotch Tape (3M)</td>
			<td style="width:297px;">ULINE</td>
			<td style="width:119px;">S-9781</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Petri Dish</td>
			<td style="width:297px;">Sigma-Aldrich</td>
			<td>BR455701</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cellulase (Onozuka R-10)&#160;</td>
			<td>Yakult Pharmaceutical Industry Co., Ltd.</td>
			<td>21560003-3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Macerozyme R-10</td>
			<td>Yakult Pharmaceutical Industry Co., Ltd.</td>
			<td>21560003-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">DM6000B Microscope&#160;</td>
			<td>Leica Microsystems</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Protease and Phosphatase Inhibitor Cocktails</td>
			<td style="width:297px;">Thermo Fisher Scientific&#160;</td>
			<td>&#160;PI78443</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Oak Ridge High-Speed PPCO Centrifuge Tubes</td>
			<td>Thermo Fisher Scientific</td>
			<td>3119-0030</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">EZQ Protein Quantitation Kit</td>
			<td style="width:297px;">Thermo Fisher Scientific</td>
			<td>R33200</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluorescein Diacetate (FDA)</td>
			<td style="width:297px;">Thermo Fisher Scientific</td>
			<td>F1303</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Abscisic Acid</td>
			<td>Sigma-Aldrich</td>
			<td>A4906</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Metro Mix 500</td>
			<td style="width:297px;">BWI Companies&#160;</td>
			<td style="width:119px;">TX-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Laemmli Sample Buffer</td>
			<td style="width:297px;">Bio-Rad</td>
			<td style="width:119px;">161-0737</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Bio-Safe Comassie (G-250)</td>
			<td style="width:297px;">Bio-Rad</td>
			<td style="width:119px;">161-0786</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Microcentrifuge Tube (2mL)</td>
			<td style="width:297px;">USA Scientific, Inc.</td>
			<td style="width:119px;">1620-2700</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">ImageJ software</td>
			<td style="width:297px;">National Institute of Health</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">Tweezers&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>F4017-1EA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:307px;">12% Mini-PROTEAN TGX Precast Gel</td>
			<td style="width:297px;">Bio-Rad</td>
			<td style="width:119px;">456-1043</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Microscope slides</td>
			<td style="width:297px;">Fisherbrand</td>
			<td>12-550-A3</td>
			<td></td>
		</tr>
	</tbody>
</table>

stomata tape-peel: an improved method for guard cell sample preparation

The study of guard cells is essential to the knowledge of the specific contributions of this cell type to the overall function of plants. However, it is often difficult to isolate and thus studying them often provides a challenge. 
This study establishes a stomatal guard cell enrichment method. The protocol utilizes Scotch tape to isolate guard cells and extract proteins from the cells. This method improves the integrity and yield of guard cell during isolation and provides a reliable sample for the study of cell signaling processes and how they correlate to stomatal movement phenotypes. In this method, the plant leaves were partitioned between two portions of tape and peeled apart to remove the abaxial side. This protocol was applied to Arabidopsis leaf tissue to isolate guard cells. The cells were treated with fluorescein diacetate (FDA) to determine viability and with abscisic acid (ABA) to assess stomata movement in response to ABA. In conclusion, this protocol proves useful for preparing enriched stomatal guard cells and isolating proteins. The quality of the cells and proteins obtained here enable physiological and other biological studies.

A representative image of Arabidopsis&#160;guard cells before and after digestion of the mesophyll and epidermal cells is shown in Figure 1. Guard cell viability before and after the removal of mesophyll and epidermal cells can be observed using FDA to measure enzymatic activity and cell membrane integrity (Figure 1B and 1D). Figure 2 illustrates stomatal movement of Arabidopsis in r...

Watch this Scientific Journal Video about Stomata Tape-Peel: An Improved Method for Guard Cell Sample Preparation at JoVE.com

Stomata Tape-Peel: An Improved Method for Guard Cell Sample Preparation

This protocol describes a method of preparing enriched stomatal guard cells that is useful for physiological and other biological studies.

The study of guard cells is essential to the knowledge of the specific contributions of this cell type to the overall function of plants. However, it is ...

stomata-tape-peel-an-improved-method-for-guard-cell-sample-preparation

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14.9K Views.  University of Florida. This protocol describes a method of preparing enriched stomatal guard cells that is useful for physiological and other biological studies.

Video: Stomata Tape-Peel: An Improved Method for Guard Cell Sample Preparation

MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) 1,2. The ultra-thin layer method involves the production of a substrate layer of matrix crystals (alpha-cyano-4-hydroxycinnamic acid) on the sample plate, which serves as a seeding ground for subsequent crystallization of a matrix/analyte mixture. Advantages of the ultra-thin layer method over other sample deposition approaches (e.g. dried droplet) are that it provides (i) greater tolerance to impurities such as salts and detergents, (ii) better resolution, and (iii) higher spatial uniformity. This method is especially useful for the accurate mass determination of proteins. The protocol was initially developed and optimized for the analysis of membrane proteins and used to successfully analyze ion channels, metabolite transporters, and receptors, containing between 2 and 12 transmembrane domains 2. Since the original publication, it has also shown to be equally useful for the analysis of soluble proteins. Indeed, we have used it for a large number of proteins having a wide range of properties, including those with molecular masses as high as 380 kDa 3. It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement.

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption ...

Assembly, Loading, and Alignment of an Analytical Ultracentrifuge Sample Cell

The analytical ultracentrifuge (AUC) is a powerful biophysical tool that allows us to record macromolecular sedimentation profiles during high speed centrifugation. When properly planned and executed, an AUC sedimentation velocity or sedimentation equilibrium experiment can reveal a great deal about a protein in regards to size and shape, sample purity, sedimentation coefficient, oligomerization states and protein-protein interactions.
This technique, however, requires a rigorous level of technical attention. Sample cells hold a sectored center piece sandwiched between two window assemblies. They are sealed with a torque pressure of around 120-140 in/lbs. Reference buffer and sample are loaded into the centerpiece sectors and then after sealing, the cells are precisely aligned into a titanium rotor so that the optical detection systems scan both sample and reference buffer in the same radial path midline through each centerpiece sector while rotating at speeds of up to 60, 000 rpm and under very high vacuum
Not only is proper sample cell assembly critical, sample cell components are very expensive and must be properly cared for to ensure they are in optimum working condition in order to avoid leaks and breakage during experiments. Handle windows carefully, for even the slightest crack or scratch can lead to breakage in the centrifuge. The contact between centerpiece and windows must be as tight as possible; i.e. no Newton s rings should be visible after torque pressure is applied. Dust, lint, scratches and oils on either the windows or the centerpiece all compromise this contact and can very easily lead to leaking of solutions from one sector to another or leaking out of the centerpiece all together. Not only are precious samples lost, leaking of solutions during an experiment will cause an imbalance of pressure in the cell that often leads to broken windows and centerpieces. In addition, plug gaskets and housing plugs must be securely in place to avoid solutions being pulled out of the centerpiece sector through the loading holes by the high vacuum in the centrifuge chamber. Window liners and gaskets must be free of breaks and cracks that could cause movement resulting in broken windows.
This video will demonstrate our procedures of sample cell assembly, torque, loading and rotor alignment to help minimize component damage, solution leaking and breakage during the perfect AUC experiment.

The analytical ultracentrifuge (AUC) sample cell holds sample and reference buffer and during experiments and is exposed to high vacuum and rotor speeds up to 60,000 rpm. This video will demonstrate the rigorous attention to detail necessary for assembly, loading and alignment of this very important component of an AUC experiment.

The analytical ultracentrifuge (AUC) is a powerful biophysical tool that allows us to record macromolecular sedimentation profiles during high speed ...

Western Blotting: Sample Preparation to Detection

Western blotting is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.

Western blotting is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract.

Western blotting is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel ...

Preparation of Quality Inositol Pyrophosphates

Myo-inositol is present in nature either unmodified or in more complex phosphorylated derivates. Of the latest, the two most abundant in eukaryotic cells are inositol pentakisphosphate (IP5) and inositol hexakisphosphate (phytic acid or IP6). IP5 and IP6 are the precursors of inositol pyrophosphate molecules that contain one or more pyrophosphate bonds1. Phosphorylation of IP6 generates diphoshoinositolpentakisphosphate (IP7 or PP-IP5) and bisdiphoshoinositoltetrakisphosphate (IP8 or (PP)2-IP4). Inositol pyrophosphates have been isolated from all eukaryotic organisms so far studied. In addition, the two distinct classes of enzymes responsible for inositol pyrophosphate synthesis are highly conserved throughout evolution2-4.
The IP6 kinases (IP6Ks) posses an enormous catalytic flexibility, converting IP5 and IP6 to PP-IP4 and IP7 respectively and subsequently, by using these products as substrates, promote the generation of more complex molecules5,6. Recently, a second class of pyrophosphate generating enzymes was identified in the form of the yeast protein VIP1 (also referred as PP-IP5K), which is able to convert IP6 to IP7 and IP87,8.
Inositol pyrophosphates regulate many disparate cellular processes such as insulin secretion9, telomere length10,11, chemotaxis12, vesicular trafficking13, phosphate homeostasis14 and HIV-1 gag release15. Two mechanisms of actions have been proposed for this class of molecules. They can affect cellular function by allosterically interacting with specific proteins like AKT16. Alternatively, the pyrophosphate group can donate a phosphate to pre-phosphorylated proteins17. The enormous potential of this research field is hampered by the absence of a commercial source of inositol pyrophosphates, which is preventing many scientists from studying these molecules and this new post-translational modification. The methods currently available to isolate inositol pyrophosphates require sophisticated chromatographic apparatus18,19. These procedures use acidic conditions that might lead to inositol pyrophosphate degradation20 and thus to poor recovery. Furthermore, the cumbersome post-column desalting procedures restrict their use to specialized laboratories.
In this study we describe an undemanding method for the generation, isolation and purification of the products of the IP6-kinase and PP-IP5-kinases reactions. This method was possible by the ability of polyacrylamide gel electrophoresis (PAGE) to resolve highly phosphorylated inositol polyphosphates20. Following IP6K1 and PP-IP5K enzymatic reactions using IP6 as the substrate, PAGE was used to separate the generated inositol pyrophosphates that were subsequently eluted in water.

Inositol pyrophosphates play an important role in human pathologies such cancer, diabetes and obesity; however, the exact mechanism of action is a matter of dispute. The lack of commercially available inositol pyrophosphates renders detailed studies problematic. Here we describe a simple protocol to produce and isolate milligrams of inositol pyrophosphates.

Myo-inositol is present in nature either unmodified or in more complex phosphorylated derivates. Of the latest, the two most abundant in eukaryotic cells ...

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a &#34;drop tube&#34; to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens.

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Here we describe a method for rapid and accurate measurement of flight performance in Drosophila, enabling high-throughput screening.

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an ...

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

The attachment of virions to a surface is a requirement for single virion imaging by Super-resolution fluorescence imaging or atomic force microscopy (AFM). Here we demonstrate a sample preparation method for controlled adhesion of virions to glass surfaces suitable for use in AFM and super-resolution fluorescence imaging.

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule ...

Improved Swiss-rolling Technique for Intestinal Tissue Preparation for Immunohistochemical and Immunofluorescent Analyses

Understanding the role of factors that regulate intestinal epithelial homeostasis and response to injury and regeneration is important. The current literature describes several different methodological approaches to obtain images of intestinal tissues for data validation. In this paper, we delineate a common protocol relating to the derivation and processing of mouse intestinal tissues. Proper fixation of intestinal tissues and Swiss-roll techniques that enhance intestinal epithelial morphology are discussed. Postresection processing and reorientation of embedded intestinal tissues are critical in obtaining paraffin-embedded blocks that display intact intestinal structural features after sectioning. The Swiss-rolling technique helps in histological assessment of the complete intestinal or colonic sections examined. An ability to differentiate intestinal structural features can be vital in quantitative measurements of intestinal inflammation and tumorigenesis along the entire length. Finally, paraffin-embedded sections are ideal for robust processing using both immunohistochemical and immunofluorescent detection methods. Nonfluorescent immunohistochemical sections provide a vibrant image of the tissue detailing different cellular structural features but do not provide flexibility for intracellular co-localization experiments. Multiple fluorescent channels can be appropriately utilized with immunofluorescent detection for co-localization experiments, lending support to mechanistic studies.

Accurate identification and location of epithelial cells along the intestinal mucosal lining are essential to define different cell lineages. Proper imaging of intestinal tissues is crucial for identification of protein expression patterns with maximum resolution. This study aims to delineate the optimal methods and conditions for processing mouse intestinal tissues.

Understanding the role of factors that regulate intestinal epithelial homeostasis and response to injury and regeneration is important. The current ...

Sample Preparation for Mass Cytometry Analysis

Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities for deep analysis well beyond what is possible with conventional fluorescence-based flow cytometry. As with any new technology, there are critical steps that help ensure the reliable generation of high-quality data. Presented here is an optimized protocol that incorporates multiple techniques for the processing of cell samples for mass cytometry analysis. The methods described here will help the user avoid common pitfalls and achieve consistent results by minimizing variability, which can lead to inaccurate data. To inform experimental design, the rationale behind optional or alternative steps in the protocol and their efficacy in uncovering new findings in the biology of the system being investigated is covered. Lastly, representative data is presented to illustrate expected results from the techniques presented here.

This article describes the collection and processing of samples for mass cytometry analysis.

Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities ...

An Alternative Approach for Sample Preparation with Low Cell Number for TEM Analysis

Transmission electron microscopy (TEM) provides details of the cellular organization and ultrastructure. However, TEM analysis of rare cell populations, especially cells in suspension such as hematopoietic stem cells (HSCs), remains limited due to the requirement of a high cell number during sample preparation. There are a few cytospin or monolayer approaches for TEM analysis from scarce samples, but these approaches fail to get significant quantitative data from the limited number of cells. Here, an alternative and novel approach for sample preparation in TEM studies is described for rare cell populations that enables quantitative analysis.
A relatively low cell number, i.e., 10,000 HSCs, was successfully used for TEM analysis compared to the millions of cells typically used for TEM studies. In particular, Evans blue staining was performed after paraformaldehyde-glutaraldehyde (PFA-GA) fixation to visualize the tiny cell pellet, which facilitated embedding in agarose. Clusters of numerous cells were observed in ultra-thin sections. The cells had a well preserved morphology, and the ultra-structural details of the Golgi complex and several mitochondria were visible. This efficient, easy and reproducible protocol allows sample preparation from a low cell number and can be used for qualitative and quantitative TEM analysis on rare cell populations from limited biological samples.

Here, we present a protocol to prepare samples with low cell numbers for transmission electron microscopy (TEM) analysis.

Transmission electron microscopy (TEM) provides details of the cellular organization and ultrastructure. However, TEM analysis of rare cell populations, ...

Hybrid-Cut: An Improved Sectioning Method for Recalcitrant Plant Tissue Samples

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some plant cells have rigid cell walls, tough fibers and crystals (calcium oxalate, silica, etc.), and high water content that often disrupt tissue integrity during plant tissue sectioning.
This study establishes a simple Hybrid-Cut tissue sectioning method. This protocol modifies a paraffin-based sectioning technique and improves the integrity of tissue sections from different plants. Plant tissues were embedded in paraffin before sectioning in a cryostat at -16 &#176;C. Sectioning under low temperature hardened the paraffin blocks, reduced tearing and scratching, and improved tissue integrity significantly. This protocol was successfully applied to calcium oxalate-rich Phalaenopsis orchid tissues as well as recalcitrant tissues such as reproductive organs and leaves of rice, maize, and wheat. In addition, the high quality of tissue sections from Hybrid-Cut could be used in combination with in situ hybridization (ISH) to provide spatial expression patterns of genes of interest. In conclusion, this protocol is particularly useful for recalcitrant plant tissue containing high crystal or silica content. Good quality tissue sections enable morphological and other biological studies.

This protocol describes a simple Hybrid-Cut tissue sectioning method that is useful for recalcitrant plant tissues. Good quality tissue sections enable anatomical studies and other biological studies including in situ hybridization (ISH).

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some ...