This work was supported by grants from the Japan Society for the Promotion of Science (17H05007 and 18H05491) to MT, the National Science Foundation (IOS1557899 and MCB2016177) and the National Aeronautics and Space Administration (NNX14AT25G and 80NSSC19K0126) to SG.

1. Plant material preparation
<ol>
	<li>In a 1.5 mL microtube, surface sterilize the seeds of Arabidopsis thaliana (Col-0 accession) plant expressing either GCaMP3 or CHIB-iGluSnFR by shaking with 20% (v/v) NaClO for 3 min and then wash 5 times with sterile distilled water. 
	NOTE: The transgenic lines of Arabidopsis expressing GCaMP3 or CHIB-iGluSnFR have been described previously6.</li>
	<li>In a sterile hood, sow 13 surface-sterilized seeds on a 10 cm square plastic Petri dish filled with 30 mL sterile (autoclaved) Murashige and Skoog (MS) medium [1x MS salts, 1% (w/v) sucrose, 0.01% (w/v) myoinositol, 0.05% (w/v) MES&#160;and 0.5% (w/v) gellan gum; pH 5.7 adjusted with 1N KOH]. Replace the lid and wrap with surgical tape.</li>
	<li>After incubation in dark at 4 &#176;C for 2 days, place the plates horizontally at 22 &#176;C in a growth chamber under continuous light (90-100 &#181;mol m-2 s-1) for approximately 2 weeks before use. After 2 weeks, count the number of Arabidopsis leaves from oldest to youngest44 (Figure 1). Wound responses preferentially move from the damaged leaf (n) to leaves numbered n &#177; 3 and n &#177; 56. 
	NOTE: In this protocol, the Petri dish will be opened for imaging the wound and glutamate effects under a fluorescence microscope. Therefore, subsequent steps in this experiment should be conducted under temperature- and humidity-controlled room conditions. This is because Ca2+ signals are also elicited by changes in these environmental conditions. It is also known that the blue light, emitted from the microscope during recording for excitation of the biosensor protein&#39;s fluorescence, may elicit an increase of cytosolic Ca2+ concentration45 and so the plant should be acclimated to the blue light irradiation for several minutes before beginning the experiment.</li>
</ol>
2. Chemical preparation
<ol>
	<li>Dissolve L-Glutamate in a liquid growth medium [1/2x MS salts, 1% (w/v) sucrose&#160;and 0.05% (w/v) MES; pH 5.1 adjusted with 1N KOH] to make a 100 mM working solution. 
	NOTE: Avoid use of salts of glutamate such as sodium glutamate to prevent potential cation-related effects on Ca2+ dynamics.</li>
</ol>
3. Microscope setting and conducting real-time imaging
<ol>
	<li>Turn on the motorized fluorescence stereomicroscope equipped with a 1x objective lens (NA = 0.156) and a sCMOS camera (Figure 2) and configure the device settings to irradiate with a 470/40 nm excitation light and acquire an emission light passing through a 535/50 nm filter. 
	NOTE: Any GFP-sensitive fluorescence microscope can be used to detect GCaMP3 and iGluSnFR signals in&#160;real-time, but a low power objective lens and highly sensitive camera with a wide sCMOS chip are recommended to acquire signals from the entire plant. The low power objective allows for imaging of an entire Arabidopsis plant&#39;s response and use of a highly sensitive camera permits the fast data acquisition needed to capture the rapid time course of the wound-triggered Ca2+ wave. For the fluorescence microscope used in this study, the maximum values of the field of view and temporal resolution are 3 cm x 3 cm and 30 frames per second (fps), respectively.</li>
	<li>Remove the lid and place the dish under the objective lens.</li>
	<li>Check the fluorescence signal from the plant and then wait for approximately 30 min in the dark until plants are adapted to the new environmental conditions. This adaptation step is required because changes in humidity elicit [Ca2+]cyt elevation in plants that can interfere with any wound-related events.</li>
	<li>Adjust the focus and magnification to see the whole plant in the field of view. In the current protocol, a 0.63x magnification was used.</li>
	<li>Before starting real-time imaging, set up the acquisition parameters to detect the fluorescence signals using microscope imaging software. The settings for imaging in the current protocol are: exposure and interval times set to 1.8 s and 2 s (i.e., 0.5 fps), respectively. Set recording time to 11 min.</li>
	<li>Image for 5 min prior to starting the experiment to acclimate the plant to the blue light irradiation from the microscope, then start recording by clicking on Run Now, or the equivalent command in the microscope software being used. To determine the average baseline fluorescence, record at least 10 frames (i.e., at least 20 s in the current protocol) before wounding or glutamate application (see Section 4).
	<ol>
		<li>For real-time imaging of wound-induced [Ca2+]cyt and [Glu]apo changes, cut the petiole or the middle region of leaf L1 with scissors (Figure 3 and Figure 4).</li>
		<li>For real-time imaging of glutamate-triggered [Ca2+]cyt changes, cut the edge (approximately 1 mm from the tip) of leaf 1 across the main vein with scissors. After at least 20 min recovery period, apply 10 &#181;L of 100 mM glutamate to the leaf&#39;s cut surface (Figure 5). 
		NOTE: This pre-cutting was necessary to allow glutamate access to the leaf apoplast in order to trigger responses. In addition, applying a drop of distilled water to the cut surface of leaf L1 was found to be critical to prevent the samples from desiccating during the recovery before applying glutamate.</li>
	</ol>
	</li>
	<li>After finishing the 11 min recording, save the data.</li>
</ol>
4. Data analysis
<ol>
	<li>For fluorescence intensity analysis over time, define a region of interest (ROI) at the place where fluorescence intensity is to be analyzed (Figure 6 and Figure 7). For the velocity calculation of the Ca2+ wave, define 2 ROIs (ROI1 and ROI2) for analysis. In the imaging software, click on Time Measurement | Define | Circle. Measure the distance between ROI1 and ROI2 by clicking on Annotations and Measurement | Length | Simple Line (Figure 6).</li>
	<li>Measure the raw fluorescence values (F) in each ROI over time by clicking on Measure. Export raw data to a&#160;spreadsheet software to convert the fluorescence signal into numbers at each time point by clicking on All to Excel | Export.</li>
	<li>Determine the baseline fluorescence value, which is defined as F0, by calculating the average of F over the first 10 frames (i.e., prior to treatment) in the recorded data.</li>
	<li>Normalize the F data (by calculating &#916;F/F) using the equation &#916;F/F = (F&#8722;F0)/F0, where &#916;F is the time-dependent change in fluorescence.</li>
	<li>For Ca2+ &#160;wave velocity wave analysis, define a significant signal rise point above the pre-stimulated values as representing detection of a Ca2+ increase in each ROI (t1 and t2) using the criterion of a rise to 2&#215; the standard deviation (2x SD) that is calculated from the F0 data using statistical software. 95% of the F0 data falls within 2x SD from the mean, indicating that a rise in signal above this level by chance is &#8804;5%. Calculate the time difference of the Ca2+ increase between ROI1 and ROI2 [t2- t1 time-lag (&#916;t)] and measure the distance between ROI1 and ROI2, then determine the velocities of any Ca2+ wave.</li>
</ol>

The authors do not have any conflicts of interest.

Systemic signaling is important for plants to respond to localized external environmental stimuli and then to maintain their homeostasis at a whole plant level. Although they are not equipped with an advanced nervous system like animals, they employ rapid communication both within and between organs based on factors such as mobile electrical (and possibly hydraulic) signals and propagating waves of ROS and Ca2+&#160;46,47. The protocol described above ...

Plants cannot escape from biotic stresses, e.g., insects feeding on them, so they have evolved sophisticated stress sensing and signal transduction systems to detect and then protect themselves from challenges such as herbivory1. Upon wounding or herbivore attack, plants initiate rapid defense responses including accumulation of the phytohormone jasmonic acid (JA) not only at the wounded site but also in undamaged distal organs2. This JA then both triggers defense responses in the directly damaged tissues and preemptively induces defenses in the undamaged parts of the plant. In Arabidopsis, the accumulation of JA induced by wounding was detected in distal, intact leaves within just a few minutes of damage elsewhere in the plant suggesting that a rapid and long-distance signal is being transmitted from the wounded leaf3. Several candidates, such as Ca2+, reactive oxygen species (ROS), and electrical signals, have been proposed to serve as these long-distance wound signals in plants4,5.
Ca2+ is one of the most versatile and ubiquitous second messenger elements in eukaryotic organisms. In plants, caterpillar chewing and mechanical wounding cause drastic increases in the cytosolic Ca2+ concentration ([Ca2+]cyt) both in the wounded leaf and in unwounded distant leaves6,7. This systemic Ca2+ signal is received by intracellular Ca2+-sensing proteins, which lead&#160;to the activation of downstream defense signaling pathways, including JA biosynthesis8,9. Despite numerous such reports supporting the importance of Ca2+ signals in plant wound responses, information on the spatial and temporal characteristics of Ca2+ signals induced by wounding is limited.
Real-time imaging using genetically encoded Ca2+ indicators is a powerful tool to monitor and quantify the spatial and temporal dynamics of Ca2+ signals. To date, versions of such sensors have been developed that enable the visualization of Ca2+ signals at the level of a single cell, to tissues, organs and even whole plants10. The first genetically encoded biosensor for Ca2+ used in plants was the bioluminescent protein aequorin derived from the jellyfish Aequorea victoria11. Although this chemiluminescent protein has been used to detect Ca2+ changes in response to various stresses in plants12,13,14,15,16,17,18, it is not well-suited for real-time imaging due to the extremely low luminescent signal it produces. F&#246;rster Resonance Energy Transfer (FRET)-based Ca2+ indicators, such as the Yellow cameleons, have also been successfully used to investigate the dynamics of a range of Ca2+ signaling events in plants19,20,21,22,23,24. These sensors are compatible with imaging approaches and most commonly are composed of the Ca2+ binding protein calmodulin (CaM) and a CaM-binding peptide (M13) from a myosin light chain kinase, all fused between two fluorophore proteins, generally a Cyan Fluorescent Protein (CFP) and a Yellow Fluorescent Protein variant (YFP)10. Ca2+ binding to CaM promotes the interaction between CaM and M13 leading to a conformational change of the sensor. This change promotes energy transfer between the CFP and YFP, which increases the fluorescence intensity of the YFP while decreasing the fluorescence emission from the CFP. Monitoring this shift from CFP to YFP fluorescence then provides a measure of the increase in Ca2+ level. In addition to these FRET sensors, single fluorescent protein (FP)-based Ca2+ biosensors, such as GCaMP and R-GECO, are also compatible with plant imaging approaches and are widely used to study [Ca2+]cyt changes due to their high sensitivity and ease of use25,26,27,28,29,30. GCaMPs contain a single circularly permutated (cp) GFP, again fused to CaM and the M13 peptide. The Ca2+-dependent interaction between CaM and M13 causes a conformational change in the sensor that promotes a shift in the protonation state of the cpGFP, enhancing its fluorescent signal. Thus, as Ca2+ levels rise, the cpGFP signal increases.
To investigate the dynamics of Ca2+ signals generated in response to mechanical wounding or herbivore feeding, we have used transgenic Arabidopsis thaliana plants expressing a GCaMP variant, GCaMP3, and a wide-field fluorescence microscope6. This approach has succeeded in visualizing rapid transmission of a long-distance Ca2+ signal from the wound site on a leaf to the whole plant. Thus, an increase in [Ca2+]cyt was immediately detected at the wound site but this Ca2+ signal was then propagated to the neighboring leaves through the vasculature within a few minutes of wounding. Furthermore, we found that the transmission of this rapid systemic wound signal is abolished in Arabidopsis plants with mutations in two glutamate receptor-like genes, Glutamate Receptor Like (GLR), GLR3.3, and GLR3.66. The GLRs appear to function as amino-acid gated Ca2+ channels involved in diverse physiological processes, including wound response3, pollen tube growth31, root development32, cold response33, and innate immunity34. Despite this well-understood, broad physiological function of the GLRs, information on their functional properties, such as their ligand specificity, ion selectivity, and subcellular localization, are limited35. However, recent studies reported that GLR3.3 and GLR3.6 are localized in the phloem and xylem, respectively. Plant GLRs have similarities to ionotropic glutamate receptors (iGluRs)36 in mammals, which are activated by amino acids, such as glutamate, glycine, and D-serine in the mammalian nervous system37. Indeed, we demonstrated that the application of 100 mM glutamate, but not other amino acids, at the wound site induces a rapid, long-distance Ca2+ signal in Arabidopsis, indicating that extracellular glutamate likely acts as a wound signal in plants6. This response is abolished in the glr3.3/glr3.6 mutant suggesting that glutamate may be acting through one or both of these receptor-like channels and indeed, AtGLR3.6 was recently shown to be gated by these levels of glutamate38.
In plants, in addition to its role as a structural amino acid, glutamate has also been proposed as a key developmental regulator39; however, its spatial and temporal dynamics are poorly understood. Just as for Ca2+, several genetically encoded indicators for glutamate have been developed to monitor the dynamics of this amino acid in living cells40,41. iGluSnFR is a GFP-based single-FP glutamate biosensor composed of cpGFP and a glutamate binding protein (GltI) from Escherichia coli42,43. The conformational change of iGluSnFR, that is induced by glutamate binding to GltI, results in an enhanced GFP fluorescence emission. To investigate whether extracellular glutamate acts as a signaling molecule in plant wound response, we connected the iGluSnFR sequence with the basic chitinase signal peptide secretion sequence (CHIB-iGluSnFR) to localize this biosensor in the apoplastic space6. This approach enabled imaging of any changes in the apoplastic glutamate concentration ([Glu]apo) using transgenic Arabidopsis plants expressing this sensor. We detected rapid increases in the iGluSnFR signal at the wounding site. This data supports the idea that glutamate leaks out of the damaged cells/tissues to the apoplast upon wounding and acts as a damage signal activating the GLRs and leading to the long-distance Ca2+ signal in plants6.
Here, we describe a plant-wide real-time imaging method using genetically encoded biosensors to monitor and analyze the dynamics of long-distance Ca2+ and extracellular glutamate signals in response to wounding6. The availability of wide-field fluorescence microscopy and transgenic plants expressing genetically encoded biosensors provides a powerful, yet easily implemented approach to detect rapidly transmitted long-distance signals, such as Ca2+ waves.

<table><tbody><tr><td>&lt;em&gt;Arabidopsis &lt;/em&gt;expressing GCaMP3</td><td>Saitama University</td><td></td><td></td></tr><tr><td>&lt;em&gt;Arabidopsis &lt;/em&gt;expressing CHIB-iGluSnFR</td><td>Saitama University</td><td></td><td></td></tr><tr><td>GraphPad Prism 7</td><td>GraphPad Software</td><td></td><td></td></tr><tr><td>L-Glutamate</td><td>FUJIFILM Wako</td><td>072-00501</td><td>Dissolved in a liquid growth medium [1/2x MS salts, 1% (w/v) sucrose, and 0.05% (w/v) MES; pH 5.1 adjusted with 1N KOH].</td></tr><tr><td>Microsoft Excel</td><td>Microsoft Corporation</td><td></td><td></td></tr><tr><td>Murashige and Skoog (MS) medium</td><td>FUJIFILM Wako</td><td>392-00591</td><td>composition: 1x MS salts, 1% (w/v) sucrose, 0.01% (w/v) myoinositol, 0.05% (w/v) MES, and 0.5% (w/v) gellan gum; pH 5.7 adjusted with 1N KOH.</td></tr><tr><td>Nikon SMZ25 stereomicroscope</td><td>Nikon</td><td></td><td></td></tr><tr><td>NIS-Elements AR analysis</td><td>Nikon</td><td></td><td></td></tr><tr><td>1x objective lens (P2-SHR PLAN APO)</td><td>Nikon</td><td></td><td></td></tr><tr><td>sCMOS camera (ORCA-Flash4.0 V2)</td><td>Hamamatsu Photonics</td><td>C11440-22CU</td><td></td></tr><tr><td>Square plastic Petri dish</td><td>Simport</td><td>D210-16</td><td></td></tr></tbody></table>

wide-field, real-time imaging of local and systemic wound signals in arabidopsis

Plants respond to mechanical stresses such as wounding and herbivory by inducing defense responses both in the damaged and in the distal undamaged parts. Upon wounding of a leaf, an increase in cytosolic calcium ion concentration (Ca2+ signal) occurs at the wound site. This signal is rapidly transmitted to undamaged leaves, where defense responses are activated. Our recent research revealed that glutamate leaking from the wounded cells of the leaf into the apoplast around them serves as a wound signal. This glutamate activates glutamate receptor-like Ca2+ permeable channels, which then leads to long-distance Ca2+ signal propagation throughout the plant. The spatial and temporal characteristics of these events can be captured with real-time imaging of living plants expressing genetically encoded fluorescent biosensors. Here we introduce a plant-wide, real-time imaging method to monitor the dynamics of both the Ca2+ signals and changes in apoplastic glutamate that occur in response to wounding. This approach uses a wide-field fluorescence microscope and transgenic Arabidopsis plants expressing Green Fluorescent Protein (GFP)-based Ca2+ and glutamate biosensors. In addition, we present methodology to easily elicit wound-induced, glutamate-triggered rapid and long-distance Ca2+ signal propagation. This protocol can also be applied to studies on other plant stresses to help investigate how plant systemic signaling might be involved in their signaling and response networks.

Signal propagation of [Ca2+]cyt and [Glu]apo in response to wounding is presented in Figure 3, Figure 4, Movie S1, and Movie S2. Cutting the petiole of the leaf 1 in plants expressing GCaMP3&#160;(at 0 s) led to a significant increase in [Ca2+]cyt that was rapidly induced locally through the vasculature (at 40 s) (Figure ...

Watch this Scientific Journal Video about Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis at JoVE.com

Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

Extracellular glutamate-triggered systemic calcium signaling is critical for the induction of plant defense responses to mechanical wounding and herbivore attack in plants. This article describes a method to visualize the spatial and temporal dynamics of both these factors using Arabidopsis thaliana plants expressing calcium- and glutamate-sensitive fluorescent biosensors.

Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

Plants respond to mechanical stresses such as wounding and herbivory by inducing defense responses both in the damaged and in the distal undamaged parts. ...

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4.8K Views.  Saitama University. Extracellular glutamate-triggered systemic calcium signaling is critical for the induction of plant defense responses to mechanical wounding and herbivore attack in plants. This article describes a method to visualize the spatial and temporal dynamics of both these factors using Arabidopsis thaliana plants expressing calcium- and glutamate-sensitive fluorescent biosensors.

Video: Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.
We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging1 (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers2. This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.
Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors3.

This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, ...

Bioengineering

Live Confocal Imaging of Developing Arabidopsis Flowers

The study of plant growth and development has long relied on experimental techniques using dead, fixed tissues and lacking proper cellular resolution. Recent advances in confocal microscopy, combined with the development of numerous fluorophores, have overcome these issues and opened the possibility to study the expression of several genes simultaneously, with a good cellular resolution, in live samples. Live confocal imaging provides plant biologists with a powerful tool to study development, and has been extensively used to study root growth and the formation of lateral organs on the flanks of the shoot apical meristem. However, it has not been widely applied to the study of flower development, in part due to challenges that are specific to imaging flowers, such as the sepals that grow over the flower meristem, and filter out the fluorescence from underlying tissues. Here, we present a detailed protocol to perform live confocal imaging on live, developing Arabidopsis flower buds, using either an upright or an inverted microscope.

Live confocal imaging provides biologists with a powerful tool to study development. Here, we present a detailed protocol for the live confocal imaging of developing Arabidopsis flowers.

The study of plant growth and development has long relied on experimental techniques using dead, fixed tissues and lacking proper cellular resolution. ...

Developmental Biology

Microinjection Wound Assay and In vivo Localization of Epidermal Wound Response Reporters in Drosophila Embryos.

The Drosophila embryo develops a robust epidermal layer that serves both to protect the internal cells from a harsh external environment as well as to maintain cellular homeostasis. Puncture injury with glass needles provides a direct method to trigger a rapid epidermal wound response that activates wound transcriptional reporters, which can be visualized by a localized reporter signal in living embryos or larvae. Puncture or laser injury also provides signals that promote the recruitment of hemocytes to the wound site. Surprisingly, severe (through and through) puncture injury in late stage embryos only rarely disrupts normal embryonic development, as greater than 90% of such wounded embryos survive to adulthood when embryos are injected in an oil medium that minimizes immediate leakage of hemolymph from puncture sites. The wound procedure does require micromanipulation of the Drosophila embryos, including manual alignment of the embryos on agar plates and transfer of the aligned embryos to microscope slides. The Drosophila epidermal wound response assay provides a quick system to test the genetic requirements of a variety of biological functions that promote wound healing, as well as a way to screen for potential chemical compounds that promote wound healing. The short life cycle and easy culturing routine make Drosophila a powerful model organism. Drosophila clean wound healing appears to coordinate the epidermal regenerative response, with the innate immune response, in ways that are still under investigation, which provides an excellent system to find conserved regulatory mechanisms common to Drosophila and mammalian epidermal wounding.

Microinjection Wound Assay and In vivo Localization of Epidermal Wound Response Reporters in Drosophila Embryos.

The embryonic epidermis of very late stage Drosophila embryos provides an in vivo system for rapid puncture wound response analysis and can be combined with genetic manipulations or chemical microinjection treatments to advance studies in wound healing for translation into mammalian models.

The Drosophila embryo develops a robust epidermal layer that serves both to protect the internal cells from a harsh external environment as well as to ...

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 ...

Long-term, High-resolution Confocal Time Lapse Imaging of Arabidopsis Cotyledon Epidermis during Germination

Imaging in vivo dynamics of cellular behavior throughout a developmental sequence can be a powerful technique for understanding the mechanics of tissue patterning. During animal development, key cell proliferation and patterning events occur very quickly. For instance, in Caenorhabditis elegans all cell divisions required for the larval body plan are completed within six hours after fertilization, with seven mitotic cycles1; the sixteen or more mitoses of Drosophila embryogenesis occur in less than 24 hr2. In contrast, cell divisions during plant development are slow, typically on the order of a day 3,4,5 . This imposes a unique challenge and a need for long-term live imaging for documenting dynamic behaviors of cell division and differentiation events during plant organogenesis. Arabidopsis epidermis is an excellent model system for investigating signaling, cell fate, and development in plants. In the cotyledon, this tissue consists of air- and water-resistant pavement cells interspersed with evenly distributed stomata, valves that open and close to control gas exchange and water loss. Proper spacing of these stomata is critical to their function, and their development follows a sequence of asymmetric division and cell differentiation steps to produce the organized epidermis (Fig. 1).
This protocol allows observation of cells and proteins in the epidermis over several days of development. This time frame enables precise documentation of stem-cell divisions and differentiation of epidermal cells, including stomata and epidermal pavement cells. Fluorescent proteins can be fused to proteins of interest to assess their dynamics during cell division and differentiation processes. This technique allows us to understand the localization of a novel protein, POLAR6, during the proliferation stage of stomatal-lineage cells in the Arabidopsis cotyledon epidermis, where it is expressed in cells preceding asymmetric division events and moves to a characteristic area of the cell cortex shortly before division occurs. Images can be registered and streamlined video easily produced using public domain software to visualize dynamic protein localization and cell types as they change over time.

Long-term, High-resolution Confocal Time Lapse Imaging of Arabidopsis Cotyledon Epidermis during Germination

We describe a protocol using chamber slides and media to immobilize plant cotyledons for confocal imaging of the epidermis over several days of development, documenting stomatal differentiation. Fluorophore-tagged proteins can be tracked dynamically by expression and subcellular localization, increasing understanding of their possible roles during cell division and cell-type differentiation.

Imaging in vivo dynamics of cellular behavior throughout a developmental sequence can be a powerful technique for understanding the mechanics of tissue ...

Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Research efforts in biology increasingly require use of methodologies that enable high-volume collection of high-resolution data. A challenge laboratories can face is the development and attainment of these methods. Observation of phenotypes in a process of interest is a typical objective of research labs studying gene function and this is often achieved through image capture. A particular process that is amenable to observation using imaging approaches is the corrective growth of a seedling root that has been displaced from alignment with the gravity vector. Imaging platforms used to measure the root gravitropic response can be expensive, relatively low in throughput, and/or labor intensive. These issues have been addressed by developing a high-throughput image capture method using inexpensive, yet high-resolution, flatbed scanners. Using this method, images can be captured every few minutes at 4,800 dpi. The current setup enables collection of 216 individual responses per day. The image data collected is of ample quality for image analysis applications.

This protocol describes a process for rapid collection of images of Arabidopsis seedlings responding to a gravity stimulus using commercially-available flatbed scanners. The method allows for inexpensive, high-volume capture of high-resolution images amenable for downstream analysis algorithms.

Research efforts in biology increasingly require use of methodologies that enable high-volume collection of high-resolution data. A challenge laboratories ...

Automated Stomatal Response Measurement to Bacterial Invasion in Arabidopsis

Direct Observation and Automated Measurement of Stomatal Responses to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis thaliana

Stomata are microscopic pores found in the plant leaf epidermis. Regulation of stomatal aperture is pivotal not only for balancing carbon dioxide uptake for photosynthesis and transpirational water loss but also for restricting bacterial invasion. While plants close stomata upon recognition of microbes, pathogenic bacteria, such as Pseudomonas syringae pv. tomato DC3000 (Pto), reopen the closed stomata to gain access into the leaf interior. In conventional assays for assessing stomatal responses to bacterial invasion, leaf epidermal peels, leaf discs, or detached leaves are floated on bacterial suspension, and then stomata are observed under a microscope followed by manual measurement of stomatal aperture. However, these assays are cumbersome and may not reflect stomatal responses to natural bacterial invasion in a leaf attached to the plant. Recently, a portable imaging device was developed that can observe stomata by pinching a leaf without detaching it from the plant, together with a deep learning-based image analysis pipeline designed to automatically measure stomatal aperture from leaf images captured by the device. Here, building on these technical advances, a new method to assess stomatal responses to bacterial invasion in Arabidopsis thaliana is introduced. This method consists of three simple steps: spray inoculation of Pto mimicking natural infection processes, direct observation of stomata on a leaf of the Pto-inoculated plant using the portable imaging device, and automated measurement of stomatal aperture by the image analysis pipeline. This method was successfully used to demonstrate stomatal closure and reopening during Pto invasion under conditions that closely mimic the natural plant-bacteria interaction.

Author Spotlight: Advancing Stomatal Research with Automated Aperture Measurement

Here, we present a simple method for direct observation and automated measurement of stomatal responses to bacterial invasion in Arabidopsis thaliana. This method leverages a portable stomatal imaging device, together with an image analysis pipeline designed for leaf images captured by the device.

Stomata are microscopic pores found in the plant leaf epidermis. Regulation of stomatal aperture is pivotal not only for balancing carbon dioxide uptake ...

Immunology and Infection

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+ ...

Methods for Skin Wounding and Assays for Wound Responses in C. elegans

The C. elegans epidermis and cuticle form a simple yet sophisticated skin layer that can repair localized damage resulting from wounding. Studies of wound responses and repair in this model have illuminated our understanding of the cytoskeletal and genomic responses to tissue damage. The two most commonly used methods to wound the C. elegans adult skin are pricks with microinjection needles, and local laser irradiation. Needle wounding locally disrupts the cuticle, epidermis, and associated extracellular matrix, and may also damage internal tissues. Laser irradiation results in more localized damage. Wounding triggers a succession of readily assayed responses including elevated epidermal Ca2+ (seconds-minutes), formation and closure of an actin-containing ring at the wound site (1-2 hr), elevated transcription of antimicrobial peptide genes (2-24 hr), and scar formation. Essentially all wild type adult animals survive wounding, whereas mutants defective in wound repair or other responses show decreased survival. Detailed protocols for needle and laser wounding, and assays for quantitation and visualization of wound responses and repair processes (Ca dynamics, actin dynamics, antimicrobial peptide induction, and survival) are presented.

Methods for Skin Wounding and Assays for Wound Responses in C. elegans

The adult C. elegans skin is a tractable model for studies of epithelial wound responses, including wound closure, scar formation, and innate immunity.

The C. elegans epidermis and cuticle form a simple yet sophisticated skin layer that can repair localized damage resulting from wounding. Studies of wound ...

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

Calcium ions are predicted to be key signaling entities during biotic interactions, with calcium signaling forming an established part of the plant defense response to microbial elicitors and to wounding caused by chewing insects, eliciting systemic calcium signals in plants. However, the role of calcium in vivo during biotic stress is still unclear. This protocol describes the use of a genetically-encoded calcium sensor to detect calcium signals in plants during feeding by a hemipteran pest. Hemipterans such as aphids pierce a small number of cells with specialized, elongated sucking mouthparts, making them the ideal tool to study calcium dynamics when a plant is faced with a biotic stress, which is distinct from a wounding response. In addition, fluorescent biosensors are revolutionizing the measurement of signaling molecules in vivo in both animals and plants. Expressing a GFP-based calcium biosensor, GCaMP3, in the model plant Arabidopsis thaliana allows for the real-time imaging of plant calcium dynamics during insect feeding, with a high spatial and temporal resolution. A repeatable and robust assay has been developed using the fluorescence microscopy of detached GCaMP3 leaves, allowing for the continuous measurement of cytosolic calcium dynamics before, during, and after insect feeding. This reveals a highly-localized rapid calcium elevation around the aphid feeding site that occurs within a few minutes. The protocol can be adapted to other biotic stresses, such as additional insect species, while the use of Arabidopsis thaliana allows for the rapid generation of mutants to facilitate the molecular analysis of the phenomenon.

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

This protocol outlines a simple method for analyzing calcium signals in plants generated by feeding hemipteran insects, such as aphids. Arabidopsis thaliana transformed with the GFP calcium biosensor GCaMP3 allow for the real-time in vivo imaging of calcium dynamics with a high temporal and spatial resolution.

Calcium ions are predicted to be key signaling entities during biotic interactions, with calcium signaling forming an established part of the plant ...

Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

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Chapters in this video

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

Live Confocal Imaging of Developing Arabidopsis Flowers

Microinjection Wound Assay and In vivo Localization of Epidermal Wound Response Reporters in Drosophila Embryos.

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

Long-term, High-resolution Confocal Time Lapse Imaging of Arabidopsis Cotyledon Epidermis during Germination

Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Direct Observation and Automated Measurement of Stomatal Responses to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis thaliana

Measuring Spatial and Temporal Ca²⁺ Signals in Arabidopsis Plants

Methods for Skin Wounding and Assays for Wound Responses in C. elegans

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor