This work was supported by grants from Shanghai Natural Science Foundation (Grant Number: 21ZR1429300/BS1500016),&#160;Shanghai Jiao Tong University (Agri-X program, Grant Number:AF1500088/002), Shanghai Collaborative Innovation Center of Agri-Seeds (Grant Number: ZXWH2150201/001)&#160;to Jiangbo Fan,&#160;and by the Medical-Engineering Collaboration Project of Shanghai Jiao Tong Univesity (grant number: 21X010301734) to Can Li.

NOTE: The protocol is applicable to different plant tissues. Rice sheath and leaf discs were used in this protocol for ROS detection upon PAMP elicitation. As differences mainly arise due to the method of sampling, only the common procedures are described below, with specific steps being mentioned wherever necessary.
1. Plant culture
<ol>
	<li>Sterilize the dehusked rice seeds with 70% ethanol for 1 min, then with 40% sodium hypochlorite (NaClO) for 1 h. Then, rinse the seeds 5x with sterile water to remove residual chlorine.</li>
	<li>Plate the seeds aseptically on 1/2 MS medium (2.37 g/L Murashige and Skoog (MS) medium, 30 g/L sucrose, 2.1 g/L phytagel, pH 5.7, autoclaved).
	<ol>
		<li>In the rice sheath method, directly plate the seeds in the sterile glass vessel with MS medium.</li>
		<li>In the leaf disc method, plate the seeds on MS plates for 5-7 days and transplant them to growth matrix or soil (Figure 1A).</li>
	</ol>
	</li>
	<li>Grow the seedlings in a growth room with a 12 h light/12 h dark photoperiod.</li>
</ol>
2. Tissue preparation and pretreatment
<ol>
	<li>Rice sheath
	<ol>
		<li>Cut the sheath from 10-day-old rice seedlings into 3 mm segments with a sharp razor blade or surgical blade for pretreatment 1 day before the ROS assay (Figure 1B).</li>
		<li>Place five sheath segments in an individual well of a 96-well microtiter plate containing 100 &#181;L of ddH2O for 10-12 h, in the dark at 25 &#176;C, which allows wound injury-related ion leakage and defense responses to abate (Figure 2). 
		NOTE: Taking care to keep the cuts vertical to ensure a consistent cutting surface area exposed to the elicitation solution is an important step to obtain highly reproducible results. Move the segments gently. Do not make extra cuts or wounds on the segments, which could be a source of data variation. As a principle, each test must contain at least five replicates since the variation of the ROS value is large. The more replicates set, the more reliable the data are.</li>
	</ol>
	</li>
	<li>Leaf disc
	<ol>
		<li>Cut the leaf discs (4 mm in diameter) from 4-6-week-old rice plants using a biopsy punch with a plunger. Always cut leaf discs from the middle third of the second leaf (numbered from the top) of the main tiller to reduce data variation (Figure 1C).</li>
		<li>Place one leaf disc in an individual well of a 96-well microtiter plate containing 100 &#181;L of ddH2O for 10-12 h for pretreatment, which allows wounding-related responses to abate as these could interfere with the induction of ROS by PAMPs (Figure 2). 
		NOTE: Operate the leaf discs gently. Do not make extra cuts or wounds on the discs in the experiment, which could result in data variation. The induction of ROS mostly occurs from the cells of the cut edge, since the surfaces of rice tissues (leaves or sheaths), are covered with hydrophobic layers. Only the cells of the cut edges are in contact with the elicitation solution (refer to the discussion section).</li>
		<li>Keep all the leaf disks floating, with the abaxial surface facing up, in the wells of a microtiter plate for water pretreatment to avoid leaf side-associated variation.</li>
	</ol>
	</li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64776/64776fig01.jpg" /> 
Figure 1: The growth condition and stages of rice seedlings for sheath sampling and parts of the rice sheath and rice leaves used in the assay. (A) Rice seedlings grown on 1/2 MS medium under sterile conditions for 10 days can be sampled for ROS assay. Sterilized rice seeds were cultured on 1/2 MS medium and grown in a 12 h light/12 h dark photoperiod in clear glass vial, 8.5 cm in diameter and 15 cm in height. (B) Schematic diagram of the sampling parts of leaf sheaths. Leaf sheaths were cut from 10-day-old rice seedlings. The positions of leaf sheaths were above the roots and below the first leaf. (C) Schematic diagram of the sampling position of leaf discs. The leaf discs can be cut from the middle third of the second leaf (count from the top) of the main tiller of healthy rice plants at any growth stage. Abbreviations: ROS = reactive oxygen species; MS = Murashige and Skoog. <a href="https://www.jove.com/files/ftp_upload/64776/64776fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/64776/64776fig02.jpg" /> 
Figure 2: Schematic diagram of the plate setup for measuring ROS production with different lines of Oryza sativa. Pretreatment and test of rice tissues using a 96-well plate. Line 1, Line 2, and Line 3 (up to eight lines on one plate) can be any material of interest, different cultivars, mutants, or transgenic lines. The tissues were stimulated with elicitation solutions with PAMP (PAMP, white) or without PAMP (ddH2O, gray) to measure ROS response. It should be noted that the more the samples to be tested, the longer the time interval between readings. Abbreviations: ROS = reactive oxygen species; PAMP = pathogen-associated molecular pattern; ddH2O = double-distilled water. <a href="https://www.jove.com/files/ftp_upload/64776/64776fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
3. Preparing the elicitation solution
<ol>
	<li>Dissolve L-012 powder into 20 mM (6.23 mg/mL) aqueous solution with ddH2O to make the stock solution. Then, dilute the stock solution with 50 mM Tris HCl buffer (pH 7.5) to make the working solution at the final concentration of 500 &#181;M L-012. Keep the stock solution frozen and dilute to the working solution before use.</li>
	<li>Prepare the elicitation solution containing PAMP, L-012, and horseradish peroxidase (HRP; 10 mg/mL in ddH2O). For a 10 mL elicitation solution, mix 9.4 mL of 50 mM Tris HCl (pH 7.5) solution, 400 &#181;L of the L-012 solution, 100 &#181;L of HRP, and 100 &#181;L of flg22 (PAMP; 10 mM in ddH2O). For the negative control, add 100 &#181;L of ddH2O instead of PAMP. 
	NOTE: Keep the prepared elicitation solutions at room temperature to avoid cold stress to rice tissues. Other PAMPs can also be used for treatment as required, such as chitin (20 ng/mL in final concentration). Since L-012 is light-sensitive, cover all the tubes containing L-012 solution with aluminum foil.</li>
</ol>
4. Starting the software and setting up the protocol with the referenced microplate reader (see Table of Materials)
NOTE: It takes some time to set up the parameters of the microplate reader software. It is recommended to get the machine and protocol ready (one click to proceed) before adding the elicitation solution.
<ol>
	<li>Start the software. Click the Experiments button to create a new protocol or use an existing protocol.</li>
	<li>Click Procedure in the pop-up to set up the plate. Select the wells from the plate to be monitored.</li>
	<li>Click Start Kinetic to set up the total run time and reading interval. Set the Run time to 35 min or longer, depending on the experimental requirements. To obtain readings as frequently as possible, select Minimum Interval. For integration time, choose 1 s or longer, depending on the signal intensity. 
	NOTE: The reading interval depends on the number of samples and signal integration duration.</li>
	<li>Click Validate | OK to confirm the settings.</li>
	<li>Click on Detect the new plate in the pop-up and wait for the software to prompt the load plate dialog box. Place the plate to be tested on the carrier.</li>
	<li>Stop here to wait for the elicitation system to be established (in the next section). As soon as the elicitation system is ready, click on Run to start the reading.</li>
</ol>
5. Establishing the elicitation system and measuring real-time ROS production
<ol>
	<li>Carefully remove the ddH2O from the wells containing the pretreated tissues, avoiding any tissue damage or desiccation.</li>
	<li>Use a multichannel pipette to add 200 &#181;L of the elicitation solution to the wells containing the tissues.</li>
	<li>Gently shake to mix. Click Run to begin detection. 
	NOTE: With PAMP treatment, plant tissues respond and produce ROS very quickly. Therefore, it is suggested that the negative control without PAMP be treated first to reduce the operation time, when there are multiple treatments. Operate as quickly as possible to reduce the elicitation delay between treatments. The shorter the time between the addition of the elicitation solution and the start of detection, the better the capture of important experimental data will be.</li>
</ol>

<ol>
	<li>Gechev, T. S., Van Breusegem, F., Stone, J. M., Denev, I., Laloi, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+oxygen+species+as+signals+that+modulate+plant+stress+responses+and+programmed+cell+death.">Reactive oxygen species as signals that modulate plant stress responses and programmed cell death.</a> Bioessays. 28 (11), 1091-1101 (2006).</li><li>Mittler, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ROS+are+good.">ROS are good.</a> Trends in Plant Science. 22 (1), 11-19 (2017).</li><li>Gilroy, 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=ROS,+calcium,+and+electric+signals:+key+mediators+of+rapid+systemic+signaling+in+plants.">ROS, calcium, and electric signals: key mediators of rapid systemic signaling in plants.</a> Plant Physiology. 171 (3), 1606-1615 (2016).</li><li>Mittler, R., Vanderauwera, S., Gollery, M., Van Breusegem, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+oxygen+gene+network+of+plants.">Reactive oxygen gene network of plants.</a> Trends in Plant Science. 9 (10), 490-498 (2004).</li><li>Marino, D., Dunand, C., Puppo, A., Pauly, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+burst+of+plant+NADPH+oxidases.">A burst of plant NADPH oxidases.</a> Trends in Plant Science. 17 (1), 9-15 (2012).</li><li>Mittler, R., Zandalinas, S. I., Fichman, Y., Van Breusegem, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+oxygen+species+signalling+in+plant+stress+responses.">Reactive oxygen species signalling in plant stress responses.</a> Nature Reviews Molecular Cell Biology. 23 (10), 663-679 (2022).</li><li>Suzuki, N., Koussevitzky, S., Mittler, R., Miller, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ROS+and+redox+signalling+in+the+response+of+plants+to+abiotic+stress.">ROS and redox signalling in the response of plants to abiotic stress.</a> Plant, Cell &amp; Environment. 35 (2), 259-270 (2012).</li><li>Suzuki, N., 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=Respiratory+burst+oxidases:+the+engines+of+ROS+signaling.">Respiratory burst oxidases: the engines of ROS signaling.</a> Current Opinion in Plant Biology. 14 (6), 691-699 (2011).</li><li>Kadota, Y., Shirasu, K., Zipfel, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+the+NADPH+oxidase+RBOHD+during+plant+immunity.">Regulation of the NADPH oxidase RBOHD during plant immunity.</a> Plant and Cell Physiology. 56 (8), 1472-1480 (2015).</li><li>Segonzac, C., Zipfel, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activation+of+plant+pattern-recognition+receptors+by+bacteria.">Activation of plant pattern-recognition receptors by bacteria.</a> Current Opinion in Microbiology. 14 (1), 54-61 (2011).</li><li>Roda, 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=Progress+in+chemical+luminescence-based+biosensors:+A+critical+review.">Progress in chemical luminescence-based biosensors: A critical review.</a> Biosensors and Bioelectronics. 76, 164-179 (2016).</li><li>Hong, D., Joung, H. -. 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The authors have no conflicts of interest to disclose.

The purpose of this study was to establish a highly efficient method to quantify early ROS production in response to PAMP in rice tissues. This method provides a standardized procedure for the real-time determination of apoplast ROS produced from treated rice tissues. This method is simple in operation, low in cost, clear in composition, and independent of commercial kits. Using this method, researchers can study the real-time production of apoplast ROS when plants are subjected to biotic or abiotic stresses.
<p clas...

Reactive oxygen species (ROS) comprise a series of chemically active oxygen derivatives, including superoxide anion radicals (O2-) and its derivatives, hydroxyl radicals (OH-), hydrogen peroxide, and products of singlet oxygen or oxidation-reduction reactions, which are constantly produced in plastids and chloroplasts, mitochondria, peroxisomes, and other subcellular locations1. ROS play important roles in many biological processes and are essential for all plants2,3,4. The broad spectrum of ROS functions varies from the regulation of growth and development to the perception of abiotic and biotic stresses5,6,7,8.
In the plant immune system, plant cell plasma membrane-localized receptors-so-called pattern recognition receptors (PRRs)-perceive pathogen-derived chemicals-pathogen-associated molecular patterns (PAMPs). This recognition triggers a series of fast immune responses, including calcium influx, ROS burst, and MAPK cascade; thus, this layer&#160;of immunity is named PAMP-triggered immunity (PTI). ROS burst is a hallmark PTI response, the determination of which is widely applied to PTI-related studies9,10. ROS production triggered by PAMPs is attributed to plasma membrane-resident NADPH oxidase, or respiratory burst oxidase homolog (RBOH) family proteins, which transfer electrons from cytosolic NADPH or NADH to extracellular oxygen to produce superoxide (O2-) which is spontaneously converted to hydrogen peroxide (H2O2) by superoxide dismutase8. PAMP-triggered ROS burst is quite rapid, appearing only a few minutes after PAMP treatment and peaking at ~10-12 min. The vast majority of the ROS molecules comprise hydrogen peroxide (H2O2), which can be easily and steadily detected with a chemiluminescence assay.
In chemiluminescence, the chemiluminescence reagent reacts with active oxygen, under the action of a catalyst, to produce the excited state intermediates. Then, the electrons in the product return to the ground state through non-radiative transition and emit photons. Common chemiluminescence reagents include luminol and L-012, with luminol dominating the application11,12,13. However, more researchers are choosing L-012 to detect ROS production, since L-012 has a much higher light emission efficiency under neutral or near neutral pH conditions compared to luminol.
This paper describes an optimized chemiluminescence method, based on L-012, for the real-time detection of ROS production after the elicitation of PAMPs in rice (Oryza sativa) tissues-leaf discs and sheath. The method provided here is simple, stable, and standardized, and is highly adaptable to meet different experimental needs. The data obtained with this method are highly reproducible under firmly controlled conditions.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>96-well microtiter plate</td>
			<td>WHB</td>
			<td>WHB-96-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>Innochem</td>
			<td>A43543</td>
			<td></td>
		</tr>
		<tr>
			<td>flg22</td>
			<td>Sangon Biotech</td>
			<td>p20973</td>
			<td>PAMP</td>
		</tr>
		<tr>
			<td>Gen5</td>
			<td>BioTek</td>
			<td></td>
			<td>software</td>
		</tr>
		<tr>
			<td>L-012</td>
			<td>FUJIFILM</td>
			<td>120-04891</td>
			<td>8-amino-5-chloro-7-phenyl-2,3-dihydropyrido [3,4-d] pyridazine-1,4-dione, CAS #:143556-24-5</td>
		</tr>
		<tr>
			<td>Microplate reader</td>
			<td>BioTek</td>
			<td>Synergy 2</td>
			<td></td>
		</tr>
		<tr>
			<td>MS Medium</td>
			<td>Solarbio</td>
			<td>M8521</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCLO</td>
			<td>Aladdin</td>
			<td>S101636</td>
			<td></td>
		</tr>
		<tr>
			<td>Peroxidase from horseradish (HRP)</td>
			<td>Sigma</td>
			<td>P8375</td>
			<td></td>
		</tr>
		<tr>
			<td>Phytagel</td>
			<td>Sigma</td>
			<td>P8169</td>
			<td></td>
		</tr>
		<tr>
			<td>Sampler</td>
			<td>Miltex&#160;</td>
			<td>15110-40</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sangon Biotech</td>
			<td>A502792</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Sangon Biotech</td>
			<td>A610195</td>
			<td></td>
		</tr>
	</tbody>
</table>

real-time detection of reactive oxygen species production in immune response in rice with a chemiluminescence assay

Reactive oxygen species (ROS) play vital roles in a variety of biological processes, including the sensing of abiotic and biotic stresses. Upon pathogen infection or challenge with pathogen-associated chemicals (pathogen-associated molecular patterns [PAMPs]), an array of immune responses, including a ROS burst, are quickly induced in plants, which is called PAMP-triggered immunity (PTI). A ROS burst is a hallmark PTI response, which is catalyzed by a group of plasma membrane-localized NADPH oxidases-the RBOH family proteins. The vast majority of ROS comprise hydrogen peroxide (H2O2), which can be easily and steadily detected by a luminol-based chemiluminescence method. Chemiluminescence is a photon-producing reaction in which luminol, or its derivative (such as L-012), undergoes a redox reaction with ROS under the action of a catalyst. This paper describes an optimized L-012-based chemiluminescence method to detect apoplast ROS production in real-time upon PAMP elicitation in rice tissues. The method is easy, steady, standardized, and highly reproducible under firmly controlled conditions.

Here, we take rice material as an example to determine the ROS produced with flg22 treatment. The generation of ROS after elicitation is transient. In rice, the increase in ROS production was first detected in 1-2 min, peaked at 10-12 min, and returned to the baseline in ~30-35 min (Figure 3). Compared to the control test, in which PAMP was absent in the elicitation solution resulting in no obvious ROS induction, a specific ROS burst was induced only when the elicitation solution containing ...

Watch this Scientific Journal Video about Real-Time Detection of Reactive Oxygen Species Production in Immune Response in Rice with a Chemiluminescence Assay at JoVE.com

Real-Time Detection of Reactive Oxygen Species Production in Immune Response in Rice with a Chemiluminescence Assay

Here, we describe a method for the real-time detection of apoplastic reactive oxygen species (ROS) production in rice tissues in pathogen-associated molecular pattern-triggered immune response. This method is simple, standardized, and generates highly reproducible results under controlled conditions.

Reactive oxygen species (ROS) play vital roles in a variety of biological processes, including the sensing of abiotic and biotic stresses. Upon pathogen ...

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3.3K Views.  Shanghai Jiao Tong University. Here, we describe a method for the real-time detection of apoplastic reactive oxygen species (ROS) production in rice tissues in pathogen-associated molecular pattern-triggered immune response. This method is simple, standardized, and generates highly reproducible results under controlled conditions.

Video: Real-Time Detection of Reactive Oxygen Species Production in Immune Response in Rice with a Chemiluminescence Assay

Detecting, Visualizing and Quantitating the Generation of Reactive Oxygen Species in an Amoeba Model System

Reactive oxygen species (ROS) comprise a range of reactive and short-lived, oxygen-containing molecules, which are dynamically interconverted or eliminated either catalytically or spontaneously. Due to the short life spans of most ROS and the diversity of their sources and subcellular localizations, a complete picture can be obtained only by careful measurements using a combination of protocols. Here, we present a set of three different protocols using OxyBurst Green (OBG)-coated beads, or dihydroethidium (DHE) and Amplex UltraRed (AUR), to monitor qualitatively and quantitatively various ROS in professional phagocytes such as Dictyostelium. We optimised the beads coating procedures and used OBG-coated beads and live microscopy to dynamically visualize intraphagosomal ROS generation at the single cell level. We identified lipopolysaccharide (LPS) from E. coli as a potent stimulator for ROS generation in Dictyostelium. In addition, we developed real time, medium-throughput assays using DHE and AUR to quantitatively measure intracellular superoxide and extracellular H2O2 production, respectively.

We adapted a set of protocols for the measurement of reactive oxygen species (ROS) that can be applied in various amoeba and mammalian cellular models for qualitative and quantitative studies.

Reactive oxygen species (ROS) comprise a range of reactive and short-lived, oxygen-containing molecules, which are dynamically interconverted or ...

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3&#8217;-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.

Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

The last decades have witnessed the explosion of scientific interest around gene expression control mechanisms at the RNA level. This branch of molecular biology has been greatly fueled by the discovery of noncoding RNAs as major players in post-transcriptional regulation. Such a revolutionary perspective has been accompanied and triggered by the development of powerful technologies for profiling short RNAs expression, both at the high-throughput level (genome-wide identification) or as single-candidate analysis (steady state accumulation of specific species). Although several state-of-art strategies are currently available for dosing or visualizing such fleeing molecules, Northern Blot assay remains the eligible approach in molecular biology for immediate and accurate evaluation of RNA expression. It represents a first step toward the application of more sophisticated, costly technologies and, in many cases, remains a preferential method to easily gain insights into RNA biology. Here we overview an efficient protocol (Enhanced Northern Blot) for detecting weakly expressed microRNAs (or other small regulatory RNA species) from Drosophila melanogaster whole embryos, manually dissected larval/adult tissues or in vitro cultured cells. A very limited amount of RNA is required and the use of material from flow cytometry-isolated cells can be also envisaged.

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster

The aim of this publication is to visualize and discuss the operative steps of an Enhanced Northern Blot protocol on RNA extracted from Drosophila melanogaster embryos, cells, and tissues. This protocol is particularly useful for the efficient detection of small RNA species.

The last decades have witnessed the explosion of scientific interest around gene expression control mechanisms at the RNA level. This branch of molecular ...

Measuring Glutathione-induced Feeding Response in Hydra

Hydra is among the most primitive organisms possessing a nervous system and chemosensation for detecting reduced glutathione (GSH) for capturing the prey. The movement of prey organisms causes mechanosensory discharge of the stinging cells called nematocysts from hydra, which are inserted into the prey. The feeding response in hydra, which includes curling of the tentacles to bring the prey towards the mouth, opening of the mouth and consequent engulfing of the prey, is triggered by GSH present in the fluid released from the injured prey. To be able to identify the molecular mechanism of the feeding response in hydra which is unknown to date, it is necessary to establish an assay to measure the feeding response. Here, we describe a simple method for the quantitation of the feeding response in which the distance between the apical end of the tentacle and mouth of hydra is measured and the ratio of such distance before and after the addition of GSH is determined. The ratio, called the relative tentacle spread, was found to give a measure of the feeding response. This assay was validated using a starvation model in which starved hydra show an enhanced feeding response in comparison with daily fed hydra.

Here we describe a simple assay for the quantification of the feeding response in hydra induced by the reduced form of glutathione. This assay relies on measuring the distance between the apical end of the tentacle and mouth of hydra.

Hydra is among the most primitive organisms possessing a nervous system and chemosensation for detecting reduced glutathione (GSH) for capturing the prey. ...

Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Provided is a protocol for developing a real-time recombinase polymerase amplification assay to quantify initial concentration of DNA samples using either a thermal cycler or a microscope and stage heater. Also described is the development of an internal positive control. Scripts are provided for processing raw real-time fluorescence data.

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII1, and one synthetic chromosome arm, synIXR2, have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis. However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

Designer chromosomes of the Synthetic Yeast Genome project, Sc2.0, can be distinguished from their native counterparts using a PCR-based genotyping assay called PCRTagging, which has a presence/absence endpoint. Here we describe a high-throughput real time PCR detection method for PCRTag genotyping.

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic ...

Stimulation of Stem Cell Niches and Tissue Regeneration in Mouse Skin by Switchable Protoporphyrin IX-Dependent Photogeneration of Reactive Oxygen Species In Situ

Here, we describe a protocol to induce switchable in vivo photogeneration of endogenous reactive oxygen species (ROS) in mouse skin. This transient production of ROS in situ efficiently activates cell proliferation in stem cell niches and stimulates tissue regeneration as strongly manifested through the acceleration of burn healing and hair follicle growth processes. The protocol is based on a regulatable photodynamic treatment that treats the tissue with precursors of the endogenous photosensitizer protoporphyrin IX and further irradiates the tissue with red light under tightly controlled physicochemical parameters. Overall, this protocol constitutes an interesting experimental tool to analyze ROS biology.

The aim of this protocol is to induce transient in vivo production of nonlethal levels of reactive oxygen species (ROS) in mouse skin, further promoting physiological responses in the tissue.

Here, we describe a protocol to induce switchable in vivo photogeneration of endogenous reactive oxygen species (ROS) in mouse skin. This transient ...

Analyzing Oxidative Stress in Murine Intestinal Organoids using Reactive Oxygen Species-Sensitive Fluorogenic Probe

Reactive oxygen species (ROS) play essential roles in intestinal homeostasis. ROS are natural by-products of cell metabolism. They are produced in response to infection or injury at the mucosal level as they are involved in antimicrobial responses and wound healing. They are also critical secondary messengers, regulating several pathways, including cell growth and differentiation. On the other hand, excessive ROS levels lead to oxidative stress, which can be deleterious for cells and favor intestinal diseases like chronic inflammation or cancer. This work provides a straightforward method to detect ROS in the intestinal murine organoids by live imaging and flow cytometry, using a commercially available fluorogenic probe. Here the protocol describes assaying the effect of compounds that modulate the redox balance in intestinal organoids and detect ROS levels in specific intestinal cell types, exemplified here by the analysis of the intestinal stem cells genetically labeled with GFP. This protocol may be used with other fluorescent probes.

The present protocol describes a method to detect reactive oxygen species (ROS) in the intestinal murine organoids using qualitative imaging and quantitative cytometry assays. This work can be potentially extended to other fluorescent probes to test the effect of selected compounds on ROS.

Reactive oxygen species (ROS) play essential roles in intestinal homeostasis. ROS are natural by-products of cell metabolism. They are produced in ...

Adipose Tissue-Derived Stem Cell Isolation and Characterization

Isolation and Identification of Mesenchymal Stem Cells Derived from Adipose Tissue of Sprague Dawley Rats

Adult mesenchymal cells have revolutionized molecular and cell biology in recent decades. They can differentiate into different specialized cell types, in addition to their great capacity for self-renewal, migration, and proliferation. Adipose tissue is one of the least invasive and most accessible sources of mesenchymal cells. It has also been reported to have higher yields compared to other sources, as well as superior immunomodulatory properties. Recently, different procedures for obtaining adult mesenchymal cells from different tissue sources and animal species have been published. After evaluating the criteria of some authors, we standardized a methodology that is applicable to different purposes and easily reproducible. A pool of stromal vascular fraction (SVF) from perirenal and epididymal adipose tissue allowed us to develop primary cultures with optimal morphology and functionality. The cells were observed adhered to the plastic surface for 24 h, and exhibited a fibroblast-like morphology, with prolongations and a tendency to form colonies. Flow cytometry (FC) and immunofluorescence (IF) techniques were used to assess the expression of the membrane markers CD105, CD9, CD63, CD31, and CD34. The ability of adipose-derived stem cells (ASCs) to differentiate into the adipogenic lineage was also assessed using a cocktail of factors (4 &#181;M insulin, 0.5 mM 3-methyl-iso-butyl-xanthine, and 1 &#181;M dexamethasone). After 48 h, a gradual loss of fibroblastoid morphology was observed, and at 12 days, the presence of lipid droplets positive to oil red staining was confirmed. In summary, a procedure is proposed to obtain optimal and functional ASC cultures for application in regenerative medicine.

Author Spotlight: Isolation and Identification of Mesenchymal Stem Cells Derived from Adipose Tissue of Sprague Dawley Rats  

This protocol describes a methodology for isolating and identifying adipose tissue-derived mesenchymal stem cells (MSCs) from Sprague Dawley rats.

Adult mesenchymal cells have revolutionized molecular and cell biology in recent decades. They can differentiate into different specialized cell types, in ...

Quantification of Skeletal Muscle Fatty Infiltration via Decellularization

Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration

Fatty infiltration is the accumulation of adipocytes between myofibers in skeletal muscle and is a prominent feature of many myopathies, metabolic disorders, and dystrophies. Clinically in human populations, fatty infiltration is assessed using noninvasive methods, including computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound (US). Although some studies have used CT or MRI to quantify fatty infiltration in mouse muscle, costs and insufficient spatial resolution remain challenging. Other small animal methods utilize histology to visualize individual adipocytes; however, this methodology suffers from sampling bias in heterogeneous pathology. This protocol describes the methodology to qualitatively view and quantitatively measure fatty infiltration comprehensively throughout intact mouse muscle and at the level of individual adipocytes using decellularization. The protocol is not limited to specific muscles or specific species and can be extended to human biopsy. Additionally, gross qualitative and quantitative assessments can be made with standard laboratory equipment for little cost, making this procedure more accessible across research laboratories.

Author Spotlight: Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration  

The present study describes decellularization-based methodologies for visualizing and quantifying intramuscular adipose tissue (IMAT) deposition through intact muscle volume, as well as quantifying metrics of individual adipocytes that comprise IMAT.