This work was supported by the Cornell University Agricultural Experiment Station (CUAES) NYC-125433 Hatch Grant and Cornell Start-Up Grant awarded to O.K.V.

Part 1. Preparation of solid medium for growing plants.
We typically culture plants on concentrated Murasige and Skoog (MS) medium supplemented with 1% sucrose and 0.7% agar. It contains all necessary ingredients to keep plants healthy.
For preparing 1L of MS, media pH 5.7
<ol>
	<li>Add 2.15 g of MS powder into 800 ml of water in 1.5 -2.0L autoclavable bottle.</li>
	<li>Place a stirring bar into the bottle and dissolve MS powder by stirring medium on a stirring plate.</li>
	<li>While stirring, add, drop by drop, 1N KOH to adjust pH of MS medium to 5.7.</li>
	<li>Add 10 g of sucrose, keep stirring.</li>
	<li>Add 7 g of agar *.</li>
	<li>Adjust the final volume of the prepared medium to 1000 ml and sterilize by autoclaving.*</li>
	<li>Place autoclaved medium on a stirring plate and cool it down while stirring, so that agar will not precipitate at the bottom of the bottle. Cool down medium to ~ 60 &#176;C.*</li>
	<li>Pour 100 mm Petri plates. Keep plates at 4 &#176;C.</li>
</ol>
*Tip 1: Do not attempt to dissolve agar. It will solubilize during autoclaving. 
*Tip 2: Keep the stirring bar in a bottle during autoclaving, you will need it later. 
*Tip 3: If you can keep you hands on the autoclaved bottle for 10 s, it means that the medium has cooled down sufficiently and you can start pouring plates.
Part 2. Plant material and growth conditions.
<ol>
	<li>Sterilize seeds of Arabidopsis thaliana
	<ol>
		<li>Place 100 mg of seeds into eppendorf microcentrifuge tubes and add 1 ml of 70% ethanol. Mix well and incubate for 2 min. Spin seeds down, aspirate the supernatant.</li>
		<li>Add 1 ml of 1.8 % bleach solution* containing 0.1% Tween-20. Mix for 10 min. Spin down seeds and aspirate bleach solution.</li>
		<li>This step has to be done in a laminar flow hood. Add 1 ml of sterile water to seeds, mix well. Spin down seeds, aspirate water. Repeat this step 5 times.</li>
	</ol>
	</li>
	<li>Spread seeds onto the prepared in step 1 plates (100 seeds/plate).</li>
	<li>Keep seeded plates for 24-48 h at 4 &#176;C in the dark for stratification.</li>
	<li>Grow plants for 14 days in the growth chamber with 8 h light/16 h dark photoperiod (at a photosynthetic photon flux density of 250 &#956;mol m-2s-1) at 23 /19 &#176;C light/dark temperature regime and 75% relative humidity.</li>
</ol>
*Tip 1: Bleach solution is made-up by dilution a household Clorox, containing 6% sodium hypochlorite and adding Tween-20 to a final concentration of 0.1%.
Part 3. Isolation of protoplasts from Arabidopsis seedlings.
<ol>
	<li>Slice 2 g of 14-day-old seedlings with a fresh razor blade in 15 ml of filter-sterilized TVL Solution. We chop plant material in sterile disposable Petri dishes.</li>
	<li>Transfer chopped tissues into 200 ml beaker, add 20 ml of filter-sterilized Enzyme Solution, swirl the beaker to let tissues mix with Enzyme Solution, cover with parafilm and aluminum foil.</li>
	<li>Shake plant tissues at 35 rpm in the dark at room temperature for 16-18 h.</li>
	<li>Collect the released protoplasts into 50 ml Falcon tube by sieving through 8 layers of the cheese cloth, pre-wet in W5 Solution.</li>
	<li>Sieve protoplasts from the cheese-cloth one more time by washing the cloth with 15 ml of W5 Solution.</li>
	<li>Carefully overlay protoplasts with 10 ml of W5 Solution, do not disturb the sugar gradient; centrifuge for 7 min at 100 g.</li>
	<li>Collect 10 ml of protoplasts at the interface of Enzyme Solution and W5 Solution (Fig. 1B) and transfer to a new 50 ml Falcon tube.</li>
	<li>Add 15 ml W5 Solution, centrifuge for 5 min at 60 g. Remove the supernatant.</li>
	<li>Wash protoplasts free from Enzyme Solution by resuspending protoplasts in 15ml of W5 Solution, centrifuge for 5min at 60 g</li>
	<li>Remove the supernatant, resuspend pelleted protoplasts in 1-3ml W5 Solution.</li>
	<li>Evaluate protoplast yield by cell counting with a hemocytometer.</li>
</ol>
Part 4. Reagents:
TVL: 0.3 M sorbitol; 50 mM CaCL2 Filter-sterilize and store at -20 &#176;C.
Enzyme Solution: 0.5 M sucrose, 10 mM MES-KOH [pH 5.7], 20 mM CaCl2, 40 mM KCl, 1% Cellulase (Onozuka R-10), 1% Macerozyme (R10). Filter-sterilize and freshly use.
W5 Solution: 0.1% (w/v) glucose, 0.08% (w/v) KCl, 0.9% (w/v) NaCl, 1.84% (w/v) CaCl2, 2 mM MES-KOH pH 5.7. Filter-sterilize and store at room temperature.
Part 5: Representative Results:
Using Arabidopsis culture conditions described in Parts 1 and 2 renders healthy seedlings, suitable for isolating protoplasts (Fig. 1A). Protoplast are purified by sucrose density gradient centrifugation and collected at the interface of W5 and Enzyme solutions (Fig. 1B). Using protoplast isolation procedure described in Part 3 we typically harvest 5-10 106 of intact protoplasts (Fig. 1C) from one gram of fresh seedlings.
<img alt="Figure 1" src="/files/ftp_upload/1149/1149fig1.jpg" /> 
Figure 1. Isolation of protoplasts from Arabidopsis seedlings. A,Tissues from 14-day-old seedlings of Arabidopsis were collected and converted to protoplasts by a modified procedure of (Chen and Halkier, 2000). B, Protoplasts were purified by sucrose density gradient centrifugation and collected at the interface of enzyme solution and W5 uffer (White arrows). C, Bright-field microscopy of protoplasts. Microphotographs were collected using a cooled CCD camera interfaced with the Zeiss Axioscope 2 plus microscope.

<ol>
	<li>Cocking, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Method+for+the+Isolation+of+Plant+Protoplasts+and+Vacuoles.">A Method for the Isolation of Plant Protoplasts and Vacuoles.</a> Nature. 187, 962-963 (1960).</li><li>Chen, S., Halkier, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+glucosinolate+uptake+by+leaf+protoplasts+of+Brassica+napus.">Characterization of glucosinolate uptake by leaf protoplasts of Brassica napus.</a> J Biol Chem. 275, 22955-22960 (2000).</li><li>Robert, S., Zouhar, J., Carter, C., Raikhel, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+intact+vacuoles+from+Arabidopsis+rosette+leaf-derived+protoplasts.">Isolation of intact vacuoles from Arabidopsis rosette leaf-derived protoplasts.</a> Nat. Protocols. 2, 259-262 (2007).</li><li>Yoo, S. D., Cho, Y. H., Sheen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arabidopsis+mesophyll+protoplasts:+a+versatile+cell+system+for+transient+gene+expression+analysis.">Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis.</a> Nat Protoc. 2, 1565-1572 (2007).</li><li>Zhai, Z., Sooksa-nguan, T., Vatamaniuk, O. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishing+RNAi+as+a+reverse+genetic+approach+for+gene+functional+analysis+in+protoplasts.">Establishing RNAi as a reverse genetic approach for gene functional analysis in protoplasts.</a> Plant Phys. 149, 642-652 (2009).</li></ol>

The provisional patent describing this procedure for its use in functional analyses of plant genes have been filed with Cornell Center For Technology Enterprise and Commercialization (CCTEC), June 2008. Docket No 50341/015001: Vatamaniuk, O.K., and Zhai, Z. Method for rapid functional analyses of plant genes.

To ensure the high yield of intact protoplast it is very important to start-up with healthy plants. Use filter-sterilize solutions for isolating protoplasts. Remember that protoplasts are fragile. Therefore, when you are handling protoplasts, do not mix, pipet or vortex them vigorously since it will brake them. Instead, mix protoplasts by slowly rotating or taping the centrifuge tube. The described procedure yield intact protoplasts that are viable for at least 96 h. Therefore, protoplasts can be used to study a var...

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<td>Murashige and Skoog Basal Salt Mixture (MS)</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>M5524</td>
<td>&nbsp;</td>
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<td>Agar</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>A1296</td>
<td>&nbsp;</td>
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<td>&nbsp;</td>
<td>Kreckeler Scientific</td>
<td>82-4001</td>
<td>&nbsp;</td>
<tr>
<td>Cellulase (Onozuka R&#x2010;10)</td>
<td>&nbsp;</td>
<td>RPI Corp</td>
<td>C32200</td>
<td>&nbsp;</td>
<tr>
<td>Macerozyme (R10)</td>
<td>&nbsp;</td>
<td>RPI Corp</td>
<td>M22010</td>
<td>&nbsp;</td>
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<td>Cheesecloth wipes</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>06-665-29</td>
<td>&nbsp;</td>
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<td>Lab Rotator</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>1167152Q</td>
<td>&nbsp;</td>
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<td>Allegra X&#x2010;15R Centrifuge</td>
<td>&nbsp;</td>
<td>VWR</td>
<td>392932</td>
<td>&nbsp;</td>
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<td>Axioskop2 Plus Microscope</td>
<td>&nbsp;</td>
<td>Zeiss</td>
<td>&nbsp;</td>
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isolation of protoplasts from tissues of 14-day-old seedlings of arabidopsis thaliana

Protoplasts are plant cells that have had their cell walls enzymatically removed. Isolation of protoplasts from different plant tissues was first reported more than 40 years ago 1 and has since been adapted to study a variety of cellular processes, such as subcellular localization of proteins, isolation of intact organelles and targeted gene-inactivation by double stranded RNA interference (RNAi) 2-5. Most of the protoplast isolation protocols use leaf tissues of mature Arabidopsis (e.g. 35-day-old plants) 2-4. We modified existing protocols by employing 14-day-old Arabidopsis seedlings. In this procedure, one gram of 14-day-old seedlings yielded 5 106-107 protoplasts that remain intact at least 96 hours. The yield of protoplasts from seedlings is comparable with preparations from leaves of mature Arabidopsis, but instead of 35-36 days, isolation of protoplasts is completed in 15 days. This allows decreasing the time and growth chamber space that are required for isolating protoplasts when mature plants are used, and expedites the downstream studies that require intact protoplasts.

Watch this Scientific Journal Video about Isolation of Protoplasts from Tissues of 14-day-old Seedlings of Arabidopsis thaliana at JoVE.com

Isolation of Protoplasts from Tissues of 14-day-old Seedlings of Arabidopsis thaliana

This video shows a procedure for isolating intact protoplasts from tissues of 14-day-old seedlings of Arabidopsis. Given that the isolated protoplasts remain intact for at least 96h and are isolated from seedlings instead of one-month-old mature plants, this procedure expedites assays requiring intact protoplasts.

Isolation of Protoplasts from Tissues of 14-day-old Seedlings of Arabidopsis thaliana

Protoplasts are plant cells that have had their cell walls enzymatically removed. Isolation of protoplasts  from different plant tissues was first ...

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35.8K Views.  Cornell University. This video shows a procedure for isolating intact protoplasts from tissues of 14-day-old seedlings of Arabidopsis. Given that the isolated protoplasts remain intact for at least 96h and are isolated from seedlings instead of one-month-old mature plants, this procedure expedites assays requiring intact protoplasts.

Video: Isolation of Protoplasts from Tissues of 14-day-old Seedlings of Arabidopsis thaliana

Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds

In flowering plants, the embryo develops within a nourishing tissue - the endosperm - surrounded by the maternal seed integuments (or seed coat). As a consequence, the isolation of plant embryos at early stages (1 cell to globular stage) is technically challenging due to their relative inaccessibility. Efficient manual dissection at early stages is strongly impaired by the small size of young Arabidopsis seeds and the adhesiveness of the embryo to the surrounding tissues. Here, we describe a method that allows the efficient isolation of young Arabidopsis embryos, yielding up to 40 embryos in 1 hr to 4 hr, depending on the downstream application. Embryos are released into isolation buffer by slightly crushing 250-750 seeds with a plastic pestle in an Eppendorf tube. A glass microcapillary attached to either a standard laboratory pipette (via a rubber tube) or a hydraulically controlled microinjector is used to collect embryos from droplets placed on a multi-well slide on an inverted light microscope. The technical skills required are simple and easily transferable, and the basic setup does not require costly equipment. Collected embryos are suitable for a variety of downstream applications such as RT-PCR, RNA sequencing, DNA methylation analyses, fluorescence in situ hybridization (FISH), immunostaining, and reporter gene assays.

Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds

We report an efficient and simple method to isolate embryos at early stages of development from Arabidopsis thaliana seeds. Up to 40 embryos can be isolated in 1 hr to 4 hr, depending on the downstream application. The procedure is suitable for transcriptome, DNA methylation, reporter gene expression, immunostaining and fluorescence in situ hybridization analyses.

In flowering plants, the embryo develops within a nourishing tissue - the endosperm - surrounded by the maternal seed integuments (or seed coat). As a ...

Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements

Arabidopsis thaliana is a model organism commonly used to understand and manipulate various cellular processes in plants, and it has been used extensively in the study of secondary cell wall formation. Secondary cell wall deposition occurs after the primary cell wall is laid down, a process carried out exclusively by specialized cells such as those forming vessel and fiber tissues. Most secondary cell walls are composed of cellulose (40&#8211;50%), hemicellulose (25&#8211;30%), and lignin (20&#8211;30%). Several mutations affecting secondary cell wall biosynthesis have been isolated, and the corresponding mutants may or may not exhibit obvious biochemical composition changes or visual phenotypes since these mutations could be masked by compensatory responses. Staining procedures have historically been used to show differences on a cellular basis. These methods are exclusively visual means of analysis; nevertheless their role in rapid and critical analysis is of great importance. Congo red and calcofluor white are stains used to detect polysaccharides, whereas M&#228;ule and phloroglucinol are commonly used to determine differences in lignin, and toluidine blue O is used to differentially stain polysaccharides and lignin. The seemingly simple techniques of sectioning, staining, and imaging can be a challenge for beginners. Starting with sample preparation using the A. thaliana model, this study details the protocols of a variety of staining methodologies that can be easily implemented for observation of cell and tissue organization in secondary cell walls of plants.

Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements

Plant cell wall composition varies between tissue types and can include lignin, cellulose, hemicelluloses, and pectin. Various staining techniques have been developed to visualize differences at the cell-type level. This paper is a compilation of commonly used cell wall staining techniques.

Arabidopsis thaliana is a model organism commonly used to understand and manipulate various cellular processes in plants, and it has been used extensively ...

Rapid Analysis of Circadian Phenotypes in Arabidopsis Protoplasts Transfected with a Luminescent Clock Reporter

The plant circadian clock allows the anticipation of daily changes to the environment. This anticipation aids the responses to temporally predictable biotic and abiotic stress. Conversely, disruption of circadian timekeeping severely compromises plant health and reduces agricultural crop yields. It is therefore imperative that we understand the intricate regulation of circadian rhythms in plants, including the factors that affect motion of the transcriptional clockwork itself.
Testing circadian defects in the model plant Arabidopsis thaliana (Arabidopsis) traditionally involves crossing specific mutant lines to a line rhythmically expressing firefly luciferase from a circadian clock gene promoter. This approach is laborious, time-consuming, and could be fruitless if a mutant has no circadian phenotype. The methodology presented here allows a rapid initial assessment of circadian phenotypes. Protoplasts derived from mutant and wild-type Arabidopsis are isolated, transfected with a rhythmically expressed luminescent reporter, and imaged under constant light conditions for 5 days. Luminescent traces will directly reveal whether the free-running period of mutant plants is different from wild-type plants. The advantage of the method is that any Arabidopsis line can efficiently be screened, without the need for generating a stably transgenic luminescent clock marker line in that mutant background.

The circadian clock regulates about a third of the Arabidopsis transcriptome, but the percentage of genes that feed back into timekeeping remains unknown. Here we visualize a method to rapidly assess circadian phenotypes in any mutant line of Arabidopsis using luminescent imaging of a circadian reporter transiently expressed in protoplasts.

The plant circadian clock allows the anticipation of daily changes to the environment. This anticipation aids the responses to temporally predictable ...

Analysis of Arabidopsis thaliana Growth Behavior in Different Light Qualities

Plant biologists often need to observe the growth behavior of their chosen species. To this end, the plants need constant environmental and stable light conditions, which are preferably variable in quantity and quality so that studies under different setups can be conducted. These requirements are met by climatic chambers featuring light emitting diodes (LED) lights, which can &#8211; in contrast to fluorescent lights &#8211; be set to different wavelengths. LEDs are energy conserving and emit virtually no heat even at light intensities, which often constitutes a problem with other light sources. The presented protocol provides a step-by-step guidance of how to program a climatic chamber equipped with variable LED lights as well as describing several approaches for in depth analysis of growth phenotypes. Depending on the experimental set-up various characteristics of the growing plants can be observed and analyzed. Here we describe how to determine fresh weight, leaf area, photosynthetic activity, and stomatal density. We demonstrate that in order to obtain reliable data and draw valid conclusions it is mandatory to use a sufficient number of individuals for statistical evaluation. Taking too few plants for this kind of analysis results in high statistical errors and consequently in less clear interpretations of the data.

Analysis of Arabidopsis thaliana Growth Behavior in Different Light Qualities

Here, we present a protocol for studying plant growth behavior and especially phenotypes in a reproducible manner. We show how to provide variable and at the same time stable light conditions. Proper analyses depend on sufficient sample numbers and valid statistical evaluations.

Plant biologists often need to observe the growth behavior of their chosen species. To this end, the plants need constant environmental and stable light ...

Spatiotemporal Investigation of ERL1 Dynamics via Confocal Imaging

Image-Based Methods to Study Membrane Trafficking Events in Stomatal Lineage Cells

In eukaryotic cells, membrane components, including proteins and lipids, are spatiotemporally transported to their destination within the endomembrane system. This includes the secretory transport of newly synthesized proteins to the cell surface or the outside of the cell, the endocytic transport of extracellular cargoes or plasma membrane components into the cell, and the recycling or shuttling transport of cargoes between the subcellular organelles, etc. Membrane trafficking events are crucial to the development, growth, and environmental adaptation of all eukaryotic cells and, thus, are under stringent regulation. Cell-surface receptor kinases, which perceive ligand signals from the extracellular space, undergo both secretory and endocytic transport. Commonly used approaches to study the membrane trafficking events using a plasma membrane-localized leucine-rich-repeat receptor kinase, ERL1, are described here. The approaches include plant material preparation, pharmacological treatment, and confocal imaging setup. To monitor the spatiotemporal regulation of ERL1, this study describes the co-localization analysis between ERL1 and a multi-vesicular body marker protein, RFP-Ara7, the time series analysis of these two proteins, and the z-stack analysis of ERL1-YFP treated with the membrane trafficking inhibitors brefeldin A and wortmannin.

Author Spotlight: Image-Based Methods to Study Membrane Trafficking Events in Stomatal Lineage Cells  

Several commonly used methods are introduced here to study the membrane trafficking events of a plasma membrane receptor kinase. This manuscript describes detailed protocols including the plant material preparation, pharmacological treatment, and confocal imaging setup.

In eukaryotic cells, membrane components, including proteins and lipids, are spatiotemporally transported to their destination within the endomembrane ...

An Improved Method to Measure Pollen Hydration Profiles in Arabidopsis thaliana

A High-Resolution, Single-Grain, In Vivo Pollen Hydration Bioassay for Arabidopsis thaliana

Sexual reproduction in flowering plants requires initial interaction between the pollen grain and the stigmatic surface, where a molecular dialog is established between the interacting partners. Studies across a range of species have revealed that a series of molecular checkpoints regulate the pollen-stigma interaction to ensure that only compatible, generally intraspecific pollen is successful in effecting fertilization. In species that possess a 'dry stigma', such as the model plant Arabidopsis thaliana, the first post-pollination, prezygotic compatibility checkpoint is the establishment of pollen hydration. 
This phase of pollination is tightly regulated, whereby signals from the pollen grain elicit the release of water from the stigma, thus permitting pollen hydration. The ability to accurately measure and track pollen hydration over time is key to the design of experiments directed at understanding the regulation of this critical step in reproduction. Published protocols frequently utilize flowers that have been excised from the parent plant, maintained on liquid or solid media, and bulk pollinated. 
This paper describes a noninvasive, in vivo pollination bioassay that permits minute-by-minute hydration tracking of individual A. thaliana pollen grains at high resolution. The assay is highly reproducible, able to detect very subtle variations of pollen hydration profiles, and thus is suitable for the analysis of mutants that affect pathways regulating pollination. Although the protocol is lengthier than those described for bulk pollinations, the precision and reproducibility it provides, along with its in vivo nature, make it ideal for the detailed dissection of pollination phenotypes.

Author Spotlight: A High-Resolution, Single-Grain, In Vivo Pollen Hydration Bioassay for Arabidopsis thaliana  

An improved method to measure pollen hydration profiles in Arabidopsis thaliana is described here. The new method offers higher resolution, is noninvasive, and is highly reproducible. The protocol represents a new tool for a finer dissection of the processes that regulate the early stages of pollination.

Sexual reproduction in flowering plants requires initial interaction between the pollen grain and the stigmatic surface, where a molecular dialog is ...