The work was supported by the National Science Foundation (IOS-1901566) to S. Xiao. The authors would like to thank F. Coker and C. Hooks for the maintenance of the plant growth facility, and Jorge Zamora for technical help associated with fabrication of the inoculation box and chamber.

1. Making a standard inoculation box with a removable top lid mounted with a mesh
<ol>
	<li>Purchase a roll of 50 &#181;m nylon membrane mesh or 48 &#181;m stainless steel mesh (recommended) from stores. Make sure to order enough for cutting into multiple pieces of 14 in x 26 in for replacement of worn mesh.</li>
	<li>Purchase one 1/4 in x 2 ft x 4 ft medium density fiberboard or plywood, and cut two 24-1/2 in x 10 in pieces and two 12 in x 10 in pieces for making an inoculation box.Use 8 corner clamps for supporting the four sides. 
	NOTE: If facing the broad side of the enclosure, the left 12 in x 10 in side is attached permanently and the right 12 in x 10 in side is a removable door held in place by four magnetic catches (Figure 1A,B).</li>
	<li>Place four 2-in corner braces two in each inside corner of the left side, an inch from the top and an inch from the bottom, mark and drill a hole. Use screws to permanently attach the left short side to two long sides (front and back). The inner distance between the two long sides should be 12 in and not 11-1/2 in.</li>
	<li>With the corner clamps still in place and proper alignment of the right door, mark and drill the location of the 4 magnetic catches to hold the right detachable door in place. Install a button knob to the door. The top of the door catches under the top lid (Figure 1A,B).</li>
	<li>To make a removable top lid with a mesh, cut the long wooden square dowel into 2 sets of 26 in and 12-3/4 in. Glue and nail the four pieces in such a way that it will fit around the box - the inside dimensions of the frame being a little bigger than the outside dimensions of the box, as the screen mesh will be attached to this frame.</li>
	<li>Cut the screen mesh to a little less than 14 in x 26 in. Do not allow the screen to protrude past the frame so as to prevent sharp edges. Have assistance to stretch the screen on the frame. Hold the mesh with the frame by clamps (Figure 1C) and use a stapler gun with the right staples to secure the screen to the frame.</li>
	<li>Cut two sets of shorter wooden square dowel (21 in and 9 in), and use screws to tightly sandwich the mesh along the frame using the 4 shorter pieces of wooden square dowel (Figure 1C, D).</li>
</ol>
2. Making an inoculation chamber
<ol>
	<li>Purchase clear acrylic sheets and hardware items from appropriate stores. Cut a 7 in x 20 in opening window on the front side acrylic sheet of the box as shown in Figure 2C.</li>
	<li>Assemble the left and right sides, front (with window) and rear acrylic sheets into a box using 8 corner clamps as shown in Figure 2A. Ensure that the inner measurements of the chamber are equal to the dimensions of the top sheet. 
	NOTE: The right side is there for support and will not be attached to the front or rear sheets. It is &#189; in shorter than the other sheets on purpose. This right side will become a &#34;draw down&#34; &#34;flap&#34; door held in place by a right angle&#160;hinge at the bottom and two magnetic catches at the top as shown in Figure 2C,D.</li>
	<li>Use corner braces to secure the panels together (Figure 2B,C). Hold the braces in place, mark with a sharpie marker, center punch and then drill the hole. 
	NOTE: Drilling acrylic is different from drilling anything else, do not force or the side of the hole opposite the drill may crack. Use rivets or screws. Do not overtighten the screws or the acrylic may crack with time.</li>
	<li>Turn the enclosure on its rear side and remove the 4 corner clamps and position the top sheet in place. Mark and drill.</li>
	<li>Install the right angle hinge, made out of a &#190; in angle brace. Use a nylon retaining lock nut as a hinge rod. Do not tighten, leave a gap so the door will rotate on this hinge.</li>
	<li>Mark, center punch, drill and attach the two magnetic door magnets with #6-32x3/4&#34; pan head screws. Then attach the catch plates with #6-32x3/8&#34; flat head screws, see Figure 2C,D.</li>
</ol>
3. Inoculating plants in flats
<ol>
	<li>Prepare fresh powdery mildew spores as inocula (e.g., Arabidopsis powdery mildew Golovinomyces cichoracearum UCSC1). Grow clean Arabidopsis immune-compromised pad4-1 mutant plants 11 in a growth chamber (22 &#176;C, 65% relative humidity for 6-8 weeks), and inoculate one or half flat of pad4-1 plants to build up sufficient fresh powdery mildew spores (Figure 3A).</li>
	<li>Grow the plants for determining infection phenotypes in standard 11 in x 21 in x 2.5 in flats. 
	NOTE: Arabidopsis plants grown under short-day (8 h light, 16 h dark; 22 &#176;C) for six to eight weeks are good for infection tests with powdery mildew.</li>
	<li>When fresh powdery mildew spores from infected plants at 8-10 days post-inoculation (dpi) are available, move a flat of plants for infection test into the inoculation box inside the inoculation chamber (Figure 1B,2C).</li>
	<li>Cut 15-20 heavily infected Arabidopsis leaves (or 4-6 infected rosettes, depending on the leaf/rosette size and level of inoculation), let the leaves dry if there is condensed water.</li>
	<li>Grab 1-2 leaves or a rosette with a pair of long forceps using one hand and face the leaves upside down. Then, put both hands through the opening of the chamber and gently hit the arm of the forceps with a pair of scissors while slowly moving the leaves/rosette above the mesh mounted on the inoculation box (Figure 3B). Repeat this until all the leaves or rosettes are used. 
	NOTE: Mature spores will dislodge easily from conidiophores of the infected leaves. Try to dislodge spores on the mesh as evenly as possible.</li>
	<li>Use one or two fine fan-blender brushes to gently brush the spores through the mesh (Figure 3C). Ensure to brush the entire surface of the mesh in different directions for four or more times to maximize even distribution of spores onto the plants in the bottom of the inoculation box (Figure 3D). Gently pat the mesh for a few times with the brushes to shake off the spores that are stuck in the mesh.</li>
	<li>Let the spores settle down for half a minute. Then, move out the flat containing the inoculated plants from the inoculation box. Cover the flat with a plastic dome and place it in a growth chamber (22 &#176;C, 65% relative humidity). Disease phenotyping can be performed at 5, or 8 to 12 dpi 12.</li>
</ol>
4. Inoculate plants with smaller inoculation boxes
NOTE: In cases where fewer plants are to be inoculated, the standard inoculation box can still be used. Make sure to place the plants in the middle of the box. Dislodge and brush spores in the area of the mesh that covers the plants to ensure all plants are inoculated while saving inocula. Alternatively, and preferably, smaller inoculation boxes can be used (as described below).
<ol>
	<li>Convert cardboard boxes to an inoculation box. Simply remove the top and bottom sides of the box, tape the corner to firm it if necessary, and mount a suitably sized 50 &#181;m mesh on the top by gluing or stapling (Figure&#160;4A,B).</li>
	<li>Move the flat containing the plants inside the inoculation chamber, place the smaller inoculation box on top of the flat to cover the plants.</li>
	<li>Dislodge and brush spores as described above.</li>
</ol>
5. Inoculate detached leaves in Petri dishes
NOTE: In cases where (i) fresh powdery mildew spores are very limited and/or (ii) plants must be kept clean while disease phenotypes and/or protein subcellular localization in infected cells need to be assessed, detached leaves can be used for infection in MS-agar plates.
<ol>
	<li>Make a mini inoculation box that is only slightly bigger than a Petri dish.</li>
	<li>Prepare &#189;-strength Murashige and Skoog (MS) medium agar (1.5%) plates. Add thiabendazole (40 mg/L) to reduce mold contamination if required. Store the plates at 4 &#176;C in a fridge until use.</li>
	<li>Cut one or two fully expanded leaves from the base of the petiole for each individual plant to be tested. Insert the petiole of the detached leaves into agar medium at an angle of ~30&#176;. 
	NOTE: Each plate can contain 20-40 leaves depending on the size of the leaves and the plate used (Figure 4C).</li>
	<li>Inoculate the leaves inside the inoculation chamber as described above. Move the plate with the lid to a growth chamber.</li>
	<li>Cut a small section of a leaf and check the subcellular localization of proteins at specific time-points.</li>
	<li>For assessing infection phenotypes, transfer the leaves to a fresh aseptic MS-agar plate at 4 or 5 dpi. Cut the base of the petiole before inserting the leaves into the fresh agar medium. Assess the disease phenotypes at 8 or 9 dpi.</li>
</ol>

<ol>
	<li>Huckelhoven, R., Panstruga, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+bi+ology+of+the+plant-powdery+mildew+interaction.">Cell bi ology of the plant-powdery mildew interaction.</a> Current Opinion in Plant Biology. 14 (6), 738-746 (2011).</li><li>Dean, R., 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+top+10+fungal+pathogens+in+molecular+plant+pathology.">The top 10 fungal pathogens in molecular plant pathology.</a> Molecular Plant Pathology. 13 (4), 414-430 (2012).</li><li>Sakurai, H., Hirata, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Some+observations+on+the+relation+between+the+penetration+hypha+and+haustorium+of+barley+powdery+mildew+and+host+cell.+V.+Influence+of+water+spray+on+the+pathogen+and+host+tissue.">Some observations on the relation between the penetration hypha and haustorium of barley powdery mildew and host cell. V. Influence of water spray on the pathogen and host tissue.</a> Annual Phytopathology Society of Japan. 24, 239-245 (1959).</li><li>Shomari, S. H., Kennedy, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Survival+of+Oidium+anacardii+on+cashew+(Anacardium+occidentale)+in+southern+Tanzania.">Survival of Oidium anacardii on cashew (Anacardium occidentale) in southern Tanzania.</a> Plant Pathology. 48 (4), 505-513 (1999).</li><li>Sitterly, W. R., Spencer, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Powdery Mildews. , 369 (1978).</li><li>Reuveni, M., Agapov, V., Reuveni, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+systemic+resistance+to+powdery+mildew+and+growth+increase+in+cucumber+by+phosphates.">Induction of systemic resistance to powdery mildew and growth increase in cucumber by phosphates.</a> Biological Agriculture &amp; Horticulture. 9 (4), 305-315 (1993).</li><li>Reifschneider, F. J. B., Boiteux, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+vacuum-operated+settling+tower+for+inoculation+of+powdery+mildew+fungi.">A vacuum-operated settling tower for inoculation of powdery mildew fungi.</a> Phytopathology. 78 (11), 1463-1465 (1988).</li><li>Chowdhury, A., Bremer, G. B., Salt, D. W., Miller, P., Ford, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+method+of+delivering+Blumeria+graminis+f.+sp+hordei+spores+for+laboratory+experiments.">A novel method of delivering Blumeria graminis f. sp hordei spores for laboratory experiments.</a> Crop Protection. 22 (7), 917-922 (2003).</li><li>Xiao, S., 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=Broad-spectrum+mildew+resistance+in+Arabidopsis+thaliana+mediated+by+RPW8.">Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8.</a> Science. 291 (5501), 118-120 (2001).</li><li>Xiao, S., Ellwood, S., Findlay, K., Oliver, R. P., Turner, J. G. <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+three+loci+controlling+resistance+of+Arabidopsis+thaliana+accession+Ms-0+to+two+powdery+mildew+diseases.">Characterization of three loci controlling resistance of Arabidopsis thaliana accession Ms-0 to two powdery mildew diseases.</a> The Plant Journal. 12 (4), 757-768 (1997).</li><li>Reuber, T. 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=Correlation+of+defense+gene+induction+defects+with+powdery+mildew+susceptibility+in+Arabidopsis+enhanced+disease+susceptibility+mutants.">Correlation of defense gene induction defects with powdery mildew susceptibility in Arabidopsis enhanced disease susceptibility mutants.</a> The Plant Journal. 16 (4), 473-485 (1998).</li><li>Xiao, S., 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+atypical+resistance+gene,+RPW8,+recruits+components+of+basal+defence+for+powdery+mildew+resistance+in+Arabidopsis.">The atypical resistance gene, RPW8, recruits components of basal defence for powdery mildew resistance in Arabidopsis.</a> The Plant Journal. 42 (1), 95-110 (2005).</li></ol>

The authors have nothing to disclose.

Our meshed-box-based inoculation method has several advantages over other inoculation methods. First, it can achieve even distribution of spores if operated properly, as demonstrated in Figure 5. Second, the use of ~50 &#181;m mesh, plus spore-dislodging by gentle shaking of infected leaves can reduce plant infection by thrips or other plant-infecting insects that are present in source plants. Third, the use of different-sized inoculation boxes for inoculating plants or detached leaves insid...

Powdery mildew is one of the most common and important diseases of numerous food crops and ornamental plants1. Studies of powdery mildew diseases have been very popular, as evidenced by over 10,500 publications as the search result with "powdery mildew" as key word at the Web of Science (as of November 2020). Indeed, powdery mildew (represented by Blumeria graminis) is considered to be one of the top 10 fungal pathogens by the journal of Molecular Plant Pathology2. Quantification of disease susceptibility is a necessary step in characterization of plant genes contributing to disease resistance or susceptibility, or functional identification of candidate effector genes in powdery mildew. However, reliable disease phenotyping is far more challenging with powdery mildew compared to that with most other fungal pathogens, partly because, unlike spores of the latter, spores of powdery mildew species (such as Golovinomyces cichoracearum UCSC1 based on our lab experience) show reduced viability after going through a water-suspension process3,4. Inadequate and/or uneven inoculation of test plants with a particular powdery mildew pathogen may lead to inaccurate phenotyping results.
A number of inoculation methods were reported for powdery mildew studies. These include (i) brushing spores directly from infected leaves to test plants5, (ii) spraying a spore suspension to test plants6, (iii) blowing spores using a vacuum-operated settling tower to plants at the bottom of the tower7, and (iv) spore delivery by the combinatorial use of a nylon mesh membrane and sound-based vibration8. The spore-brushing (or dusting) method is easy to perform but uneven in nature, thus it may not be accurate for quantitative assessment. Spore-spraying is convenient and even, but as stated above may result in poor spore germination4. The latter two (i.e., iii-iv) are much-improved methods capable of achieving even inoculation; however, both are not flexible in adjusting their inoculation capacity in terms of the number of plants to be inoculated in a single event, making either apparatus is not trivial, and their operation is restricted to lab areas where there is a vacuum and/or electricity source.
Our lab has been working with plant-powdery mildew interaction for over 20 years9,10. Over the past decade, we tested a number of inoculation methods and recently developed a simple and yet effective powdery mildew inoculation method. This mesh-based spore-brushing method can ensure even inoculation, and is simple and scalable, thus should be easily adopted by any laboratory working with powdery mildew.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >&#160;48 &#181;m stainless steel grid mesh screen; Size: 24&#34; X 48&#34;&#160;</td>
			<td >Amazon</td>
			<td >NA</td>
			<td >For making the lid of an inoculation box</td>
		</tr>
		<tr >
			<td >#6-32 x &#190;&#34; machine screws, flat washers and nuts&#160;</td>
			<td >Home Depot</td>
			<td >NA</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >#6-32 zinc plated nylon lock nut (4-Pack)</td>
			<td >Home Depot</td>
			<td >NA</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >#6-32x3/8&#8221; Phillips flat head machine screws, flat washers and nuts&#160;</td>
			<td >Home Depot</td>
			<td >NA</td>
			<td>For securing&#160; magnet door catch plates</td>
		</tr>
		<tr >
			<td >#8-32x1/2&#34; machine screws, flat washers and nuts</td>
			<td >Home Depot</td>
			<td >NA</td>
			<td>For securing corner braces and door hinge</td>
		</tr>
		<tr >
			<td >0.250 thick clear extruded acrylic film-masked sheet;&#160; Size: 17 &#189;&#34; X 20&#34;</td>
			<td >Professional Plastics</td>
			<td >SACR.250CEF</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >0.250 thick clear extruded acrylic film-masked sheet; Size: 18&#34; X 20&#34;&#160;&#160;</td>
			<td >Professional Plastics</td>
			<td >&#160;SACR.250CEF</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >0.250 thick clear extruded acrylic film-masked sheet; Size: 18&#34; X 30&#34;&#160;</td>
			<td >Professional Plastics</td>
			<td >SACR.250CEF</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >0.250 thick clear extruded acrylic film-masked sheet; Size: 20&#34; X 29 &#189; &#34;</td>
			<td >Professional Plastics</td>
			<td >SACR.250CEF</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >1-5/8&#34; cabinet door magnetic catch white</td>
			<td >Home Depot</td>
			<td >Model #P110-W</td>
			<td>For making an inoculation chamber</td>
		</tr>
		<tr >
			<td >2&#34; steel zinc-plated corner brace (8-Pack)&#160;</td>
			<td >Home Depot</td>
			<td >&#160;Model #13611&#160;</td>
			<td>For making an inoculation box &#38; chamber</td>
		</tr>
		<tr >
			<td >3&#34; Corner Clamp</td>
			<td>Harbor Freight Tools</td>
			<td>SKU 63653, 1852, 60589</td>
			<td>For making inoculation chamber</td>
		</tr>
		<tr >
			<td >3/4&#34;&#160; steel zinc plated corner brace (4-Pack)</td>
			<td >Home Depot</td>
			<td >Model #13542</td>
			<td>For making an inoculation box &#38; chamber</td>
		</tr>
		<tr >
			<td >4-7/8&#34; zinc-plated light duty door pull handles</td>
			<td >Home Depot</td>
			<td >Model #15184</td>
			<td>For making an inoculation box</td>
		</tr>
		<tr >
			<td >Fine fan-blender brushes</td>
			<td>Michaels Store</td>
			<td>M10472846&#160;</td>
			<td>For inoculation</td>
		</tr>
		<tr >
			<td >Kelleher 3/4&#34; x 3/4&#34; x 36&#34; wood square dowel&#160;</td>
			<td >Home Depot</td>
			<td >NA</td>
			<td>For making the lid of an inoculation box</td>
		</tr>
		<tr >
			<td >Medium density fiberboard (1/4&#34; x 2&#39; x 4&#39;);&#160;</td>
			<td >Home Depot</td>
			<td >Model# 1508104</td>
			<td>For making an inoculation box</td>
		</tr>
		<tr >
			<td >Round glass coverslips with a 500 &#181;m grid</td>
			<td >ibidi USA Inc.</td>
			<td >10816</td>
			<td>For determining&#160; spore density</td>
		</tr>
	</tbody>
</table>

an easy and flexible inoculation method for accurately assessing powdery mildew-infection phenotypes of arabidopsis and other plants

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in turn requires accurate determination of disease phenotypes of plants upon infection with a particular fungal pathogen. However, accurate disease phenotyping with unculturable biotrophic fungal pathogens such as powdery mildew is not easy to achieve and can be a rate-limiting step of a research project. Here, we have developed a safe, efficient, and easy-to-operate disease phenotyping system using the Arabidopsis-powdery mildew interaction as an example. This system mainly consists of three components: (i) a wooden inoculation box fitted with a removable lid mounted with a stainless steel or nylon mesh of ~50 &#181;m pores for inoculating a flat of plants with fungal spores, (ii) a transparent plastic chamber with a small front opening for minimizing spore escape while conducting inoculation inside, and (iii) a spore-dislodging and distribution method for even and effective inoculation. The protocols described here include the steps and parameters for making the inoculation box and the plastic chamber at a low cost, and a video demonstration of how to use the system to enable even inoculation with powdery mildew spores, thereby improving accuracy and reproducibility of disease phenotyping.

Here, we present a new powdery mildew spore inoculation method that is easy to prepare, operate and adjust. Figure 1 shows the assembly of the standard inoculation box with emphasis on the make of the removable lid mounted with a 50 &#181;m membrane mesh. Figure 2 shows the assembly of the inoculation chamber. Figure 3 illustrates the key steps of the inoculation process using this system. Figure 4 show...

Watch this Scientific Journal Video about An Easy and Flexible Inoculation Method for Accurately Assessing Powdery Mildew-Infection Phenotypes of Arabidopsis and Other Plants at JoVE.com

An Easy and Flexible Inoculation Method for Accurately Assessing Powdery Mildew-Infection Phenotypes of Arabidopsis and Other Plants

We present a protocol for constructing a simple spore-distribution system consisting of an inoculation box with a ~50 &#181;m mesh and a transparent plastic chamber. This can be used to evenly inoculate plants with powdery mildew spores, thereby enabling accurate and reproducible assessment of disease phenotypes of plants under study.

Reducing crop losses due to fungal diseases requires improved understanding of the mechanisms governing plant immunity and fungal pathogenesis, which in ...

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2.6K Views.  University of Maryland. We present a protocol for constructing a simple spore-distribution system consisting of an inoculation box with a ~50 µm mesh and a transparent plastic chamber. This can be used to evenly inoculate plants with powdery mildew spores, thereby enabling accurate and reproducible assessment of disease phenotypes of plants under study. 

Video: An Easy and Flexible Inoculation Method for Accurately Assessing Powdery Mildew-Infection Phenotypes of Arabidopsis and Other Plants

An Improved Method of RNA Isolation from Loblolly Pine (P. taeda L.) and Other Conifer Species

Tissues isolated from conifer species, particularly those belonging to the Pinaceae family, such as loblolly pine (Pinus taeda L.), contain high concentrations of phenolic compounds and polysaccharides that interfere with RNA purification. Isolation of high-quality RNA from these species requires rigorous tissue collection procedures in the field and the employment of an RNA isolation protocol comprised of multiple organic extraction steps in order to isolate RNA of sufficient quality for microarray and other genomic analyses. The isolation of high-quality RNA from field-collected loblolly pine samples can be challenging, but several modifications to standard tissue and RNA isolation procedures greatly improve results. The extent of general RNA degradation increases if samples are not properly collected and transported from the field, especially during large-scale harvests. Total RNA yields can be increased significantly by pulverizing samples in a liquid nitrogen freezer mill prior to RNA isolation, especially when samples come from woody tissues. This is primarily due to the presence of oxidizing agents, such as phenolic compounds, and polysaccharides that are both present at high levels in extracts from the woody tissues of most conifer species. If not removed, these contaminants can carry over leading to problems, such as RNA degradation, that result in low yields and a poor quality RNA sample. Carryover of phenolic compounds, as well as polysaccharides, can also reduce or even completely eliminate the activity of reverse transcriptase or other polymerases commonly used for cDNA synthesis. In particular, RNA destined to be used as template for double-stranded cDNA synthesis in the generation of cDNA libraries, single-stranded cDNA synthesis for PCR or qPCR's, or for the synthesis of microarray target materials must be of the highest quality if researchers expect to obtain optimal results. RNA isolation techniques commonly employed for many other plant species are often insufficient in their ability to remove these contaminants from conifer samples and thus do not yield total RNA samples suitable for downstream manipulations. In this video we demonstrate methods for field collection of conifer tissues, beginning with the felling of a forty year-old tree, to the harvesting of phloem, secondary xylem, and reaction wood xylem. We also demonstrate an RNA isolation protocol that has consistently yielded high-quality RNA for subsequent enzymatic manipulations.

An Improved Method of RNA Isolation from Loblolly Pine P. taeda L. and Other Conifer Species

Many plant tissues, including phloem and xylem from loblolly pine (Pinus taeda L.), contain high levels of phenolics and polysaccharides that interfere with RNA purification. This presentation discusses techniques for the harvest of field-grown tissues and isolation of RNA of sufficient quality for microarrays and other genomic analyses.

Tissues isolated from conifer species, particularly those belonging to the Pinaceae family, such as loblolly pine (Pinus taeda L.), contain high ...

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping project is to collect a tissue sample from each individual plant. The traditional approach to this task is to sample plants one-at-a-time. If one wishes to genotype hundreds or thousands of individuals, however, using this strategy results in a significant bottleneck in the genotyping pipeline. The Ice-Cap method that we describe here provides a high-throughput solution to this challenge by allowing one scientist to collect tissue from several thousand seedlings in a single day 1,2. This level of throughput is made possible by the fact that tissue is harvested from plants 96-at-a-time, rather than one-at-a-time.
The Ice-Cap method provides an integrated platform for performing seedling growth, tissue harvest, and DNA extraction. The basis for Ice-Cap is the growth of seedlings in a stacked pair of 96-well plates. The wells of the upper plate contain plugs of agar growth media on which individual seedlings germinate. The roots grow down through the agar media, exit the upper plate through a hole, and pass into a lower plate containing water. To harvest tissue for DNA extraction, the water in the lower plate containing root tissue is rapidly frozen while the seedlings in the upper plate remain at room temperature. The upper plate is then peeled away from the lower plate, yielding one plate with 96 root tissue samples frozen in ice and one plate with 96 viable seedlings. The technique is named "Ice-Cap" because it uses ice to capture the root tissue. The 96-well plate containing the seedlings can then wrapped in foil and transferred to low temperature. This process suspends further growth of the seedlings, but does not affect their viability. Once genotype analysis has been completed, seedlings with the desired genotype can be transferred from the 96-well plate to soil for further propagation. We have demonstrated the utility of the Ice-Cap method using Arabidopsis thaliana, tomato, and rice seedlings. We expect that the method should also be applicable to other species of plants with seeds small enough to fit into the wells of 96-well plates.

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

The Ice-Cap method allows one to grow plants in 96-well plates and non-destructively harvest root tissue from each seedling. DNA extracted from this root tissue can be used for genotyping reactions. We have found that Ice-Cap works well for Arabidopsis thaliana, tomato, and rice seedlings.

It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping ...

A Simple Method for Imaging Arabidopsis Leaves Using Perfluorodecalin as an Infiltrative Imaging Medium

The problem of acquiring high-resolution images deep into biological samples is widely acknowledged1. In air-filled tissue such as the spongy mesophyll of plant leaves or vertebrate lungs further difficulties arise from multiple transitions in refractive index between cellular components, between cells and airspaces and between the biological tissue and the rest of the optical system. Moreover, refractive index mismatches lead to attenuation of fluorophore excitation and signal emission in fluorescence microscopy. We describe here the application of the perfluorocarbon, perfluorodecalin (PFD), as an infiltrative imaging medium which optically improves laser scanning confocal microscopy (LSCM) sample imaging at depth, without resorting to damaging increases in laser power and has minimal physiological impact2. We describe the protocol for use of PFD with Arabidopsis thaliana leaf tissue, which is optically complex as a result of its structure (Figure 1). PFD has a number of attributes that make it suitable for this use3. The refractive index of PFD (1.313) is comparable with that of water (1.333) and is closer to that of cytosol (approx. 1.4) than air (1.000). In addition, PFD is readily available, non-fluorescent and is non-toxic. The low surface tension of PFD (19 dynes cm-1) is lower than that of water (72 dynes cm-1) and also below the limit (25 - 30 dyne cm-1) for stomatal penetration4, which allows it to flood the spongy mesophyll airspaces without the application of a potentially destructive vacuum or surfactant. Finally and crucially, PFD has a great capacity for dissolving CO2 and O2, which allows gas exchange to be maintained in the flooded tissue, thus minimizing the physiological impact on the sample. These properties have been used in various applications which include partial liquid breathing and lung inflation5,6, surgery7, artificial blood8, oxygenation of growth media9, and studies of ice crystal formation in plants10. Currently, it is common to mount tissue in water or aqueous buffer for live confocal imaging. We consider that the use of PFD as a mounting medium represents an improvement on existing practice and allows the simple preparation of live whole leaf samples for imaging.

A Simple Method for Imaging Arabidopsis Leaves Using Perfluorodecalin as an Infiltrative Imaging Medium

We describe the use of perfluorodecalin as an infiltrative mounting medium. This is a simple method for improving depth of imaging in Arabidopsis thaliana leaf tissue with minimal physiological impact.

The problem of acquiring high-resolution images deep into biological samples is widely acknowledged1. In air-filled tissue such as the spongy mesophyll of ...

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the adult plant. The female SMC (megaspore mother cell, MMC) differentiates in the ovule primordium and undergoes meiosis. The selected haploid megaspore then undergoes mitosis to form the multicellular female gametophyte, which will give rise to the gametes, the egg cell and central cell, together with accessory cells. The limited accessibility of the MMC, meiocyte and female gametophyte inside the ovule is technically challenging for cytological and cytogenetic analyses at single cell level. Particularly, direct or indirect immunodetection of cellular or nuclear epitopes is impaired by poor penetration of the reagents inside the plant cell and single-cell imaging is demised by the lack of optical clarity in whole-mount tissues.
Thus, we developed an efficient method to analyze the nuclear organization and chromatin modification at high resolution of single cell in whole-mount embedded Arabidopsis ovules. It is based on dissection and embedding of fixed ovules in a thin layer of acrylamide gel on a microscopic slide. The embedded ovules are subjected to chemical and enzymatic treatments aiming at improving tissue clarity and permeability to the immunostaining reagents. Those treatments preserve cellular and chromatin organization, DNA and protein epitopes. The samples can be used for different downstream cytological analyses, including chromatin immunostaining, fluorescence in situ hybridization (FISH), and DNA staining for heterochromatin analysis. Confocal laser scanning microscopy (CLSM) imaging, with high resolution, followed by 3D reconstruction allows for quantitative measurements at single-cell resolution.

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis

We provide here an efficient and reliable protocol for immunostaining, Fluorescence in&#160;situ Hybridization, DNA staining followed by quantitative, high-resolution imaging in whole-mount Arabidopsis thaliana ovules. This method was successfully used to analyze chromatin modifications and nuclear architecture.

In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the ...

Measuring Spatial and Temporal Ca2+ Signals in Arabidopsis Plants

Developmental and environmental cues induce Ca2+ fluctuations in plant cells. Stimulus-specific spatial-temporal Ca2+ patterns are sensed by cellular Ca2+ binding proteins that initiate Ca2+ signaling cascades. However, we still know little about how stimulus specific Ca2+ signals are generated. The specificity of a Ca2+ signal may be attributed to the sophisticated regulation of the activities of Ca2+ channels and/or transporters in response to a given stimulus. To identify these cellular components and understand their functions, it is crucial to use systems that allow a sensitive and robust recording of Ca2+ signals at both the tissue and cellular levels. Genetically encoded Ca2+ indicators that are targeted to different cellular compartments have provided a platform for live cell confocal imaging of cellular Ca2+ signals. Here we describe instructions for the use of two Ca2+ detection systems: aequorin based FAS (film adhesive seedlings) luminescence Ca2+ imaging and case12 based live cell confocal fluorescence Ca2+ imaging. Luminescence imaging using the FAS system provides a simple, robust and sensitive detection of spatial and temporal Ca2+ signals at the tissue level, while live cell confocal imaging using Case12 provides simultaneous detection of cytosolic and nuclear Ca2+ signals at a high resolution.

Measuring Spatial and Temporal Ca2+ Signals in Arabidopsis Plants

Ca2+ signaling regulates diverse biological processes in plants. Here we present approaches for monitoring abiotic stress induced spatial and temporal Ca2+ signals in Arabidopsis cells and tissues using the genetically encoded Ca2+ indicators Aequorin or Case12.

Developmental and environmental cues induce Ca2+ fluctuations in plant cells. Stimulus-specific spatial-temporal Ca2+ patterns are sensed by cellular Ca2+ ...

Construction of an Affordable and Easy-to-Build Zebrafish Facility

In vivo biomedical research is pivotal to translate in vitro findings into clinical advances. Small academic institutions with limited resources find it virtually impossible to build and maintain typical rodent facilities for research. Zebrafish research has been demonstrated to be a valuable alternative for in vivo research in pharmacology, physiology, development and genetic studies. This article demonstrates that a functional zebrafish facility can be built in an easy and affordable manner. We demonstrate that such a facility could be built in about one working day with minimal tools and expertise. The cost of the 27 1.8 L fish tank zebrafish facility constructed in this study was approximately $1,500. We estimate that the maintenance of an initial working 150 fish colony for 3 months is $1,000. This project involved students, who were introduced to aquaculturing of zebrafish for research proposes.

A Zebrafish facility suitable for breeding and in vivo research is built in an easy and affordable manner. Maintenance is minimal. This facility is ideal for student involvement and independent research.

In vivo biomedical research is pivotal to translate in vitro findings into clinical advances. Small academic institutions with limited resources find it ...

An Easy Method for Plant Polysome Profiling

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the analysis of translational regulation. The method described here is an easy and economical way for fractionating polysomes from various plant tissues. A sucrose gradient is made without the need for a gradient maker by sequentially freezing each layer. Cytosolic extracts are then prepared in a buffer containing cycloheximide and chloramphenicol to immobilize the cytosolic and chloroplastic ribosomes to mRNA and are loaded onto the sucrose gradient. After centrifugation, six fractions are directly collected from the bottom to the top of the gradient, without piercing the ultracentrifugation tube. During collection, the absorbance at 260 nm is read continuously to generate a polysome profile that gives a snapshot of global translational activity. Fractions are then pooled to prepare three different mRNA populations: the polysomes, mRNAs bound to several ribosomes; the monosomes, mRNAs bound to one ribosome; and mRNAs that are not bound to ribosomes. mRNAs are then extracted. This protocol has been validated for different plants and tissues including Arabidopsis thaliana seedlings and adult plants, Nicotiana benthamiana, Solanum lycopersicum, and Oryza sativa leaves.

This protocol describes an easy method to extract and fractionate transcripts from plant tissues on the basis of the number of bound ribosomes. It allows a global estimate of translation activity and the determination of the translational status of specific mRNAs.

Translation of mRNA to protein is a fundamental and highly regulated biological process. Polysome profiling is considered as a gold standard for the ...

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 ...

An Efficient and Flexible Cell Aggregation Method for 3D Spheroid Production

Monolayer cell culture does not adequately model the in vivo behavior of tissues, which involves complex cell-cell and cell-matrix interactions. Three-dimensional (3D) cell culture techniques are a recent innovation developed to address the shortcomings of adherent cell culture. While several techniques for generating tissue analogues in vitro have been developed, these methods are frequently complex, expensive to establish, require specialized equipment, and are generally limited by compatibility with only certain cell types. Here, we describe a rapid and flexible protocol for aggregating cells into multicellular 3D spheroids of consistent size that is compatible with growth of a variety of tumor and normal cell lines. We utilize varying concentrations of serum and methyl cellulose (MC) to promote anchorage-independent spheroid generation and prevent the formation of cell monolayers in a highly reproducible manner. Optimal conditions for individual cell lines can be achieved by adjusting MC or serum concentrations in the spheroid formation medium. The 3D spheroids generated can be collected for use in a wide range of applications, including cell signaling or gene expression studies, candidate drug screening, or in the study of cellular processes such as tumor cell invasion and migration. The protocol is also readily adapted to generate clonal spheroids from single cells, and can be adapted to assess anchorage-independent growth and anoikis-resistance. Overall, our protocol provides an easily modifiable method for generating and utilizing 3D cell spheroids in order to recapitulate the 3D microenvironment of tissues and model the in vivo growth of normal and tumor cells.

Here, we describe a rapid and flexible protocol for the formation of 3D cell spheroids through cell aggregation. This is easily adapted to multiple cell types and is suitable for use in a variety of applications including cell migration, invasion, or anoikis assays, and for imaging and quantifying cell-matrix interactions.

Monolayer cell culture does not adequately model the in vivo behavior of tissues, which involves complex cell-cell and cell-matrix interactions. ...

Standardized Method for High-throughput Sterilization of Arabidopsis Seeds

Arabidopsis thaliana (Arabidopsis) seedlings often need to be grown on sterile media. This requires prior seed sterilization to prevent the growth of microbial contaminants present on the seed surface. Currently, Arabidopsis seeds are sterilized using two distinct sterilization techniques in conditions that differ slightly between labs and have not been standardized, often resulting in only partially effective sterilization or in excessive seed mortality. Most of these methods are also not easily scalable to a large number of seed lines of diverse genotypes. As technologies for high-throughput analysis of Arabidopsis continue to proliferate, standardized techniques for sterilizing large numbers of seeds of different genotypes are becoming essential for conducting these types of experiments. The response of a number of Arabidopsis lines to two different sterilization techniques was evaluated based on seed germination rate and the level of seed contamination with microbes and other pathogens. The treatments included different concentrations of sterilizing agents and times of exposure, combined to determine optimal conditions for Arabidopsis seed sterilization. Optimized protocols have been developed for two different sterilization methods: bleach (liquid-phase) and chlorine (Cl2) gas (vapor-phase), both resulting in high seed germination rates and minimal microbial contamination. The utility of these protocols was illustrated through the testing of both wild type and mutant seeds with a range of germination potentials. Our results show that seeds can be effectively sterilized using either method without excessive seed mortality, although detrimental effects of sterilization were observed for seeds with lower than optimal germination potential. In addition, an equation was developed to enable researchers to apply the standardized chlorine gas sterilization conditions to airtight containers of different sizes. The protocols described here allow easy, efficient, and inexpensive seed sterilization for a large number of Arabidopsis lines.

The objective of this study was to determine the effects of bleach and chlorine gas sterilization on seed germination of a range of Arabidopsis genotypes grown on sterile media. Optimized sterilization protocols have been developed to prevent the growth of microbial contaminants while providing satisfactory seed survival.

Arabidopsis thaliana (Arabidopsis) seedlings often need to be grown on sterile media. This requires prior seed sterilization to prevent the growth of ...