Microscopy in this work was conducted at the Institute of Transformative Bio-Molecules (WPI-ITbM) of Nagoya University and supported by the Japan Advanced Plant Science Network. This work was supported by grants from the Japan Science and Technology Agency (ERATO project to T.H. and M.U.) and from the Japan Society for the Promotion of Science: a Grant-in-Aid for Scientific Research on Innovative Areas (Nos. JP24113514, JP26113710, JP15H05962, and JP15H05955 for M.U., and Nos. JP16H06465, JP16H06464 and JP16K21727 for T.H), a Grant-in-Aid for Young Scientists (B, Nos. JP24770045 and JP26840093 for M.U.), and a Grant-in-Aid for challenging Exploratory Research (No. JP16K14753 for M.U.).

1. Preparation of the In Vitro Ovule Culture Medium
<ol>
	<li>Make the liquid medium forthe in vitro ovule culture (&#34;N5T medium&#34;) containing 1x Nitsch basal salt mixture, 5% (w/v) trehalose dihydrate, 0.05% (w/v) 2-(N-morpholino)ethanesulfonic acid (MES)-KOH (pH 5.8), and 1x Gamborg&#39;s vitamin solution.</li>
	<li>Adjust the pH to 5.8 with KOH.</li>
	<li>Sterilize the medium by autoclaving it (121 &#176;C, 20 min) or filtering it through a 0.22-&#181;m filter. 
	NOTE: The sterilized medium can be stored at 4 &#176;C for 2 - 3 months.</li>
</ol>
2. Preparation of the PDMS Micropillar Array Device
<ol>
	<li>Cut the PDMS micropillar device by a knife, razor blade or scissors to fit into the glass part (14 mm &#966;) of a 35 mm glass-bottom dish. 
	NOTE: The full procedure of the PDMS device construction is described in previous papers8,9, and thus the details are omitted here. Glass-bottom dishes with smaller volumes, such as 4-well or 96-well plates, can be used for short-term imaging without the device.</li>
	<li>Sterilize the upper side of the PDMS device under UV light for 15 min.</li>
	<li>Turn the PDMS device over by using square tip tweezers, and keep it under UV light for 15 min to sterilize the bottom.</li>
	<li>Transfer the sterilized PDMS device into a 35 mm culture dish and add the N5T medium until the device is completely soaked in the medium (approximately 5 - 7 mL).</li>
	<li>Put the dish into a vacuum chamber, and reduce the pressure to degas. Keep vacuuming for 3 h to overnight until the air in the device is replaced by medium. 
	NOTE: The device can be detached by air bubbles under a strong vacuum.</li>
	<li>Take the device from the dish by holding it with square tip tweezers and put it on a paper towel to remove the extra medium on the side and bottom. 
	NOTE:The medium on the micropillar array (upper surface) should not be removed because this will be used for the ovule cultivation.</li>
	<li>Transfer the device onto a 76 mm x 26 mm slide glass, ensuring to keep the micropillar part as the upper side, and cover the device with 35 mm culture dish lid to prevent the medium from drying out during the following ovule extraction.</li>
</ol>
3. Silique Dissection and Ovule Extraction
<ol>
	<li>Sterilize a needle (0.40 mm G) and fine tweezers by wiping with 70% ethanol. The needle is easily handled by attaching it to a syringe or wood stick.</li>
	<li>Check the inflorescence of the plant, and select the proper siliques for the experiment. The approximately 5 mm siliques contain zygotes, and the 8 - 10 mm siliques include young globular embryos.</li>
	<li>Excise the siliques by using tweezers, and place them on double-sided tape on a 76 x 26 mm slide glass. One silique contains about 40 - 60 ovules, and 3 - 4 siliques (i.e., 120 - 240 ovules) are sufficient for one device.</li>
	<li>Open the silique (ovary wall) to see the ovules inside using the sterilized needle and tweezers under a stereomicroscope. Cut only the ovary wall so that the ovules are not damaged.</li>
	<li>Transfer the opened silique into the N5T medium on the PDMS device (prepared in step 2.7), and release the ovules into the medium with the needle or tweezers.</li>
	<li>Put a small cover glass (18 mm x 18 mm) onto the PDMS device to push the ovules into the spaces in the micropillar array.</li>
	<li>Take the cover glass off by pulling it horizontally using tweezers or fingers to remove extra medium.</li>
	<li>Turn the PDMS device upside down, place it into a 35 mm glass-bottom dish, and slightly press the device by pushing using the square tip tweezers to stick it to the glass.</li>
	<li>Pour N5T medium gently into the glass-bottom dish by decanting the medium bottle until the PDMS device is completely soaked in the medium, and seal the dish with paraffin film. 
	NOTE: The PDMS device can be recycled, but devices that are too old are easily detached from the glass bottom. Additionally, the device may float if it is not completely degassed in step 2.5 or the medium is poured too quickly.</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/55975/55975fig2.jpg" /> 
Figure 2: Schematic Procedure for Sample Preparation. 
This schematic flow corresponds to steps 3.5 to 4.1. <a href="//cloudfront.jove.com/files/ftp_upload/55975/55975fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
4. Time-lapse Imaging
<ol>
	<li>Place the glass-bottom dish that was prepared in step 3.9 on an inverted microscope, and select suitable ovules to focus on. 
	NOTE: Because the ovules vary in stage, position, and direction, suitable ovules should be found by checking their marker fluorescence.</li>
	<li>Start the live-imaging according tothe manufacturer&#39;s instructions of the microscope system. 
	NOTE: The microscope equipment and parameters are diverse, and thus the users should choose the proper settings that fit to the experiment purpose. As an example, the settings used in this manuscript are listed in Table 1.</li>
</ol>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Equipment/setting</td>
			<td>Figure 3 (A) and Supplemental Videos 1 and 4</td>
			<td>Figure 3 (B) and Supplemental Video 2</td>
			<td>Supplemental Video 3</td>
		</tr>
		<tr>
			<td>Microscope</td>
			<td>laser-scanning inverted microscope (A1R MP)</td>
			<td>spinning-disk confocal inverted microscope (CSU-W1)</td>
			<td>box-type inverted confocal microscope system with a stable incubation chamber (CV1000)</td>
		</tr>
		<tr>
			<td>Laser</td>
			<td>Ti:sapphire femtosecond pulse laser</td>
			<td>488-nm and 561-nm LD lasers</td>
			<td>488-nm and 561-nm LD laser</td>
		</tr>
		<tr>
			<td>Objective lens&#160;</td>
			<td>40X water-immersion objective lens (NA = 1.15) with immersion medium</td>
			<td>60X silicone oil immersion objective lens (NA = 1.30), mounted on a Piezo focus drive</td>
			<td>40X objective lens (NA = 0.95)</td>
		</tr>
		<tr>
			<td>Detector</td>
			<td>external non-descanned GaAsP PMT detector</td>
			<td>EMCCD camera</td>
			<td>EMCCD camera</td>
		</tr>
		<tr>
			<td>Dichroic mirror</td>
			<td>DM495 and DM560</td>
			<td>DM488/561</td>
			<td>DM400-410/488/561</td>
		</tr>
		<tr>
			<td>Filter</td>
			<td>band-pass filters; 534/30 nm and 578/105 nm</td>
			<td>band-pass filters; 520/35 nm, and 593/46 nm</td>
			<td>band-pass filters; 520/50 nm and 617/73 nm</td>
		</tr>
		<tr>
			<td>Slice along z-axis</td>
			<td>31 z-stacks with 1-&#181;m intervals</td>
			<td>17 z-stacks with 3-&#181;m intervals</td>
			<td>7 z-stacks with 5-&#181;m intervals</td>
		</tr>
		<tr>
			<td>Time interval</td>
			<td>20 min</td>
			<td>5 min</td>
			<td>10 min</td>
		</tr>
	</tbody>
</table>
Table 1: The Microscope Systems and Settings Used in This Manuscript. 
The microscopes and parameters are diverse, and thus each user should choose the suitable system for the experiment.
<ol start="3">
	<li>Check the acquired image sequence, and convert it to the general movie format, such as .avi or .mov for presentation. 
	NOTE: If the microscope software cannot output the images as a movie format, it is possible to save the images as .tif and then open them in ImageJ, an open source program inspired by NIH Image, to change the file type. ImageJ is provided at: https://imagej.nih.gov/ij/. ImageJ can also be used to make a Z-stuck movie, such as the maximum-intensity projection, as described at: https://imagej.net/Z-functions.</li>
</ol>

<ol>
	<li>Natesh, S., Rau, M. A., Johri, B. 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> Embryology of Angiosperms. , 377-443 (1984).</li><li>Kranz, E., Lorz, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+fertilisation+of+maize+by+single+egg+and+sperm+cell+protoplast+fusion+mediated+by+high+calcium+and+high+pH.">In vitro fertilisation of maize by single egg and sperm cell protoplast fusion mediated by high calcium and high pH.</a> Zygote. 2 (2), 125-128 (1994).</li><li>Uchiumi, T., Uemura, I., Okamoto, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+an+in+vitro+fertilization+system+in+rice+(Oryza+sativa+L.).">Establishment of an in vitro fertilization system in rice (Oryza sativa L.).</a> Planta. 226 (3), 581-589 (2007).</li><li>Sun, M. X., Moscatelli, A., Yang, H. Y., Cresti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+double+fertilization+in+Nicotiana+tabacum+(L.):+the+role+of+cell+volume+in+cell+fusion.">In vitro double fertilization in Nicotiana tabacum (L.): the role of cell volume in cell fusion.</a> Sex Plant Rep. 13 (4), 225-229 (2001).</li><li>Tian, H. Q., Yuan, T., Russell, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationship+between+double+fertilization+and+the+cell+cycle+in+male+and+female+gametes+of+tobacco.">Relationship between double fertilization and the cell cycle in male and female gametes of tobacco.</a> Sex Plant Rep. 17 (5), 243-252 (2004).</li><li>Costa, L. M., 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=Central+cell-derived+peptides+regulate+early+embryo+patterning+in+flowering+plants.">Central cell-derived peptides regulate early embryo patterning in flowering plants.</a> Science. 344 (6180), 168-172 (2014).</li><li>Sauer, M., Friml, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+culture+of+Arabidopsis+embryos+within+their+ovules.">In vitro culture of Arabidopsis embryos within their ovules.</a> Plant J. 40 (5), 835-843 (2004).</li><li>Gooh, K., 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=Live-cell+imaging+and+optical+manipulation+of+Arabidopsis+early+embryogenesis.">Live-cell imaging and optical manipulation of Arabidopsis early embryogenesis.</a> Dev Cell. 34 (2), 242-251 (2015).</li><li>Park, J., Kurihara, D., Higashiyama, T., Arata, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fabrication+of+microcage+arrays+to+fix+plant+ovules+for+long-term+live+imaging+and+observation.">Fabrication of microcage arrays to fix plant ovules for long-term live imaging and observation.</a> Sens Act B-Chem. 191, 178-185 (2014).</li><li>Kimata, Y., 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=Cytoskeleton+dynamics+control+the+first+asymmetric+cell+division+in+Arabidopsis+zygote.">Cytoskeleton dynamics control the first asymmetric cell division in Arabidopsis zygote.</a> Proc Natl Acad Sci U S A. 113 (49), 14157-14162 (2016).</li><li>Nambo, M., 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=Combination+of+Synthetic+Chemistry+and+Live-Cell+Imaging+Identified+a+Rapid+Cell+Division+Inhibitor+in+Tobacco+and+Arabidopsis+thaliana.">Combination of Synthetic Chemistry and Live-Cell Imaging Identified a Rapid Cell Division Inhibitor in Tobacco and Arabidopsis thaliana.</a> Plant Cell Physiol. 57 (11), 2255-2268 (2016).</li><li>Mizuta, Y., Kurihara, D., Higashiyama, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-photon+imaging+with+longer+wavelength+excitation+in+intact+Arabidopsis+tissues.">Two-photon imaging with longer wavelength excitation in intact Arabidopsis tissues.</a> Protoplasma. 252 (5), 1231-1240 (2015).</li></ol>

The authors have nothing to disclose.

This manuscript introduces a simple in vitro ovule cultivation protocol that is efficient for use in the live-cell imaging of developing zygotes and embryos.
The design of the PDMS device may need optimization according to the embryo stage. The first developed device was a microcage array to adjust the orientation and to fix the position of the ovules9, and then a micropillar device was constructed to trap ovules more efficiently8. Furth...

The basic body plan of an organism develops from a unicellular zygote. In most flowering plants, zygotic division generates an apical and a basal cell, which develop into the shoot and root, respectively1. Therefore, it is important to understand how the plant body is formed during embryogenesis, but there has not been an effective tool to directly observe the dynamics of living zygotes and embryos because they develop deep in the flower. In several monocot species, such as maize and rice, an in vitro fertilization method has been established2,3. In this method, isolated sperm and egg cells are fused electrically or chemically, and the generated cell can develop into a fertile plant. However, in dicot plants, there is no in vitro fertilization method that can produce proper embryos, presumably because of the non-synchronized cell cycle state of male and female gametes4,5. In addition, the embryo-surrounding tissue (endosperm) plays important roles in embryo development6.
In a model dicot species, A. thaliana, an in vitro cultivation method was developed by focusing on the whole ovule, which contains both the embryo and endosperm7. This system was successfully used to analyze the effects of various chemical reagents on embryogenesis, but it is not suitable for time-lapse imaging because it has a low survival rate. Therefore, a novel in vitro ovule cultivation system was developed in order to start as early as the zygote stage and produce fertile plants at a high ratio8. After various trials, it was found that Nitsch medium and trehalose significantly improved the survival rate of ovules8. In addition, because the ovule expands as it grows and thus frequently moves away from the observation field of the microscope, a PDMS device was developed to fix the ovule in the medium9. The PDMS device enabled the long-term imaging for 3 - 4 days, which is sufficient to trace the development from a zygote to a heart-stage embryo. Using this method, it becomes possible to visualize the dynamics of zygote polarization and embryo patterning, not only under normal conditions, but also in the presence of chemical inhibitors or in various mutant backgrounds8,10,11.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/55975/55975fig1.jpg" /> 
Figure 1: Schematic Diagram of the Specific Fluorescent Markers used to Visualize Zygotes and Embryos Through the Ovule. 
The Arabidopsis zygote develops into an embryo in the ovule, which is generated deep inside the flower. In this in vitro cultivation system, the zygote and embryo are observed through the ovule, and thus it is important to use specific fluorescent markers that are not expressed in other ovule tissues. <a href="//cloudflare.jove.com/files/ftp_upload/55975/55975fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table><tbody><tr><td>Nitsch basal salt mixture</td><td>Duchefa</td><td>N0223</td><td></td></tr><tr><td>trehalose dihydrate</td><td>Wako Pure Chemical</td><td>206-18455</td><td></td></tr><tr><td>MES</td><td>Dojindo</td><td>345-01625</td><td></td></tr><tr><td>Gamborg&amp;rsquo;s vitamin solution</td><td>Sigma-Aldrich</td><td>G1019</td><td></td></tr><tr><td>35-mm glass-bottom dish</td><td>Matsunami Glass</td><td>D111300</td><td></td></tr><tr><td>35 mm culture dish</td><td>Corning</td><td>430588</td><td></td></tr><tr><td>PDMS</td><td>Dow Corning Co.</td><td>Sylgard184</td><td></td></tr><tr><td>76 &amp;times; 26 mm slide glass</td><td>Matsunami Glass</td><td>S1225</td><td></td></tr><tr><td>18 &amp;times; 18 mm slide glass</td><td>Matsunami Glass</td><td>C018181</td><td></td></tr><tr><td>needle (gauge 0.40 mm)</td><td>Terumo</td><td>NN-2719S</td><td></td></tr><tr><td>Immersion medium Immersol W 2010</td><td>Zeiss</td><td>444969-0000-000</td><td></td></tr><tr><td>A1R MP</td><td>Nikon</td><td>A1RsiMP(1080) Ti-E-TIRF</td><td></td></tr><tr><td>CSU-W1</td><td>Yokogawa Electric</td><td></td><td>It is a customized equipment, and thus Catalog Number is not avairable.</td></tr><tr><td>CV1000</td><td>Yokogawa Electric</td><td>CV1000-SP84</td><td></td></tr></tbody></table>

in vitro ovule cultivation for live-cell imaging of zygote polarization and embryo patterning in arabidopsis thaliana

In most flowering plants, the zygote and embryo are hidden deep in the mother tissue, and thus it has long been a mystery of how they develop dynamically; for example, how the zygote polarizes to establish the body axis and how the embryo specifies various cell fates during organ formation. This manuscript describes an in vitro ovule culture method to perform live-cell imaging of developing zygotes and embryos of Arabidopsis thaliana. The optimized cultivation medium allows zygotes or early embryos to grow into fertile plants. By combining it with a poly(dimethylsiloxane) (PDMS) micropillar array device, the ovule is held in the liquid medium in the same position. This fixation is crucial to observe the same ovule under a microscope for several days from the zygotic division to the late embryo stage. The resulting live-cell imaging can be used to monitor the real-time dynamics of zygote polarization, such as nuclear migration and cytoskeleton rearrangement, and also the cell division timing and cell fate specification during embryo patterning. Furthermore, this ovule cultivation system can be combined with inhibitor treatments to analyze the effects of various factors on embryo development, and with optical manipulations such as laser disruption to examine the role of cell-cell communication.

By using this ovule cultivation system, this method can trace the living dynamics of zygote polarization and embryo patterning. This is an achievement because previously there was no technique to visualize the real-time behavior of the zygote and embryo, which are hidden deep in the mother tissue. Figure 3A and Supplemental Video 1 show that the microtubules (MTs) in the young zygote accumulate as a transverse ring in the subapical region<sup...

Watch this Scientific Journal Video about In Vitro Ovule Cultivation for Live-cell Imaging of Zygote Polarization and Embryo Patterning in Arabidopsis thaliana at JoVE.com

In Vitro Ovule Cultivation for Live-cell Imaging of Zygote Polarization and Embryo Patterning in Arabidopsis thaliana

This manuscript describes an in vitro ovule cultivation method that enables live-cell imaging of Arabidopsis zygotes and embryos. This method is utilized to visualize the intracellular dynamics during zygote polarization and the cell fate specification in developing embryos.

In Vitro Ovule Cultivation for Live-cell Imaging of Zygote Polarization and Embryo Patterning in Arabidopsis thaliana

In most flowering plants, the zygote and embryo are hidden deep in the mother tissue, and thus it has long been a mystery of how they develop dynamically; ...

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10.8K Views.  Nagoya University. This manuscript describes an in vitro ovule cultivation method that enables live-cell imaging of Arabidopsis zygotes and embryos. This method is utilized to visualize the intracellular dynamics during zygote polarization and the cell fate specification in developing embryos.

Video: In Vitro Ovule Cultivation for Live-cell Imaging of Zygote Polarization and Embryo Patterning in Arabidopsis thaliana

Protocols for Obtaining Zygotic and Somatic Embryos for Studying the Regulation of Early Embryo Development in the Model Legume Medicago truncatula

Early embryogenesis starting from a single cell zygote goes through rapid cell division and morphogenesis, and is morphologically characterized by pre-globular, globular, heart, torpedo and cotyledon stages. This progressive development is under the tight regulation of a complex molecular network. Harvesting sufficient early embryos at a similar stage of development is essential for investigating the cellular and molecular regulation of early embryogenesis. This is not straightforward since early embryogenesis undergoes rapid morphogenesis in a short while e.g. 8 days for Medicago truncatula to reach the early cotyledon stage. Here, we address the issue by two approaches. The first one establishes a linkage between embryo development and pod morphology in helping indicate the stage of the zygotic embryo. This is particularly based on the number of pod spirals and development of the spines. An alternative way to complement the in vivo studies is via culturing leaf explants to produce somatic embryos. The medium includes an unusual hormone combination - an auxin (1-naphthaleneacetic acid), a cytokinin (6-benzylaminopurine), abscisic acid and gibberellic acid. The different stages can be discerned growing out of the callus without dissection.

Protocols for Obtaining Zygotic and Somatic Embryos for Studying the Regulation of Early Embryo Development in the Model Legume Medicago truncatula

The goal is to illustrate that the model legume Medicago truncatula can be readily utilized to investigate the regulation of early plant embryogenesis to complement the non-legume Arabidopsis model. Pod morphology is linked to zygotic embryogenesis stages and a protocol to collect embryos using tissue culture is also provided.

Early embryogenesis starting from a single cell zygote goes through rapid cell division and morphogenesis, and is morphologically characterized by ...

Characterization of Thymic Settling Progenitors in the Mouse Embryo Using In Vivo and In Vitro Assays

Characterizing thymic settling progenitors is important to understand the pre-thymic stages of T cell development, essential to devise strategies for T cell replacement in lymphopenic patients. We studied thymic settling progenitors from murine embryonic day 13 and 18 thymi by two complementary in vitro and in vivo techniques, both based on the &#8220;hanging drop&#8221; method. This method allowed colonizing irradiated fetal thymic lobes with E13 and/or E18 thymic progenitors distinguished by CD45 allotypic markers and thus following their progeny. Colonization with mixed populations allows analyzing cell autonomous differences in biologic properties of the progenitors while colonization with either population removes possible competitive selective pressures. The colonized thymic lobes can also be grafted in immunodeficient male recipient mice allowing the analysis of the mature T cell progeny in vivo, such as population dynamics of the peripheral immune system and colonization of different tissues and organs. Fetal thymic organ cultures revealed that E13 progenitors developed rapidly into all mature CD3+ cells and gave rise to the canonical &#947;&#948; T cell subset, known as dendritic epithelial T cells. In comparison, E18 progenitors have a delayed differentiation and were unable to generate dendritic epithelial T cells. The monitoring of peripheral blood of thymus-grafted CD3-/- mice further showed that E18 thymic settling progenitors generate, with time, larger numbers of mature T cells than their E13 counterparts, a feature that could not be appreciated in the short term fetal thymic organ cultures.

Characterization of Thymic Settling Progenitors in the Mouse Embryo Using In Vivo and In Vitro Assays

This article describes in vivo and in vitro methodology to characterize the thymic settling progenitors by the analysis of the kinetics of generation, phenotype and numbers of their T cell progeny.

Characterizing thymic settling progenitors is important to understand the pre-thymic stages of T cell development, essential to devise strategies for T ...

Imaging Subcellular Structures in the Living Zebrafish Embryo

In vivo imaging provides unprecedented access to the dynamic behavior of cellular and subcellular structures in their natural context. Performing such imaging experiments in higher vertebrates such as mammals generally requires surgical access to the system under study. The optical accessibility of embryonic and larval zebrafish allows such invasive procedures to be circumvented and permits imaging in the intact organism. Indeed the zebrafish is now a well-established model to visualize dynamic cellular behaviors using in vivo microscopy in a wide range of developmental contexts from proliferation to migration and differentiation. A more recent development is the increasing use of zebrafish to study subcellular events including mitochondrial trafficking and centrosome dynamics. The relative ease with which these subcellular structures can be genetically labeled by fluorescent proteins and the use of light microscopy techniques to image them is transforming the zebrafish into an in vivo model of cell biology. Here we describe methods to generate genetic constructs that fluorescently label organelles, highlighting mitochondria and centrosomes as specific examples. We use the bipartite Gal4-UAS system in multiple configurations to restrict expression to specific cell-types and provide protocols to generate transiently expressing and stable transgenic fish. Finally, we provide guidelines for choosing light microscopy methods that are most suitable for imaging subcellular dynamics.

Imaging the dynamic behavior of organelles and other subcellular structures in vivo can shed light on their function in physiological and disease conditions. Here, we present methods for genetically tagging two organelles, centrosomes and mitochondria, and imaging their dynamics in living zebrafish embryos using wide-field and confocal microscopy.

In vivo imaging provides unprecedented access to the dynamic behavior of cellular and subcellular structures in their natural context. Performing such ...

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. ...

A Method for Characterizing Embryogenesis in Arabidopsis

Given the highly predictable nature of their development, Arabidopsis embryos have been used as a model for studies of morphogenesis in plants. However, early stage plant embryos are small and contain few cells, making them difficult to observe and analyze. A method is described here for characterizing pattern formation in plant embryos under a microscope using the model organism Arabidopsis. Following the clearance of fresh ovules using Hoyer's solution, the cell number in and morphology of embryos could be observed, and their developmental stage could be determined by differential interference contrast microscopy using a 100X oil immersion lens. In addition, the expression of specific marker proteins tagged with Green Fluorescent Protein (GFP) was monitored to annotate cell identity specification during embryo patterning by confocal laser scanning microscopy. Thus, this method can be used to observe pattern formation in wild-type plant embryos at the cellular and molecular levels, and to characterize the role of specific genes in embryo patterning by comparing pattern formation in embryos from wild-type plants and embryo-lethal mutants. Therefore, the method can be used to characterize embryogenesis in Arabidopsis.

A Method for Characterizing Embryogenesis in Arabidopsis

This protocol outlines a method for observing embryogenesis in Arabidopsis via ovule clearance followed by the inspection of embryo pattern formation under a microscope.

Given the highly predictable nature of their development, Arabidopsis embryos have been used as a model for studies of morphogenesis in plants. However, ...

Evaluation of Fertilization State by Tracing Sperm Nuclear Morphology in Arabidopsis Double Fertilization

Flowering plants have a unique sexual reproduction system called &#8216;double fertilization&#39;,&#160;in which each of the sperm cells precisely fuses with an egg cell or a central cell. Thus, two independent fertilization events take place almost simultaneously. The fertilized egg cell and central cell develop into zygote and endosperm, respectively. Therefore, precise control of double fertilization is essential for the ensuing seed development. Double fertilization occurs in the female gametophyte (embryo sac), which is deeply hidden and covered with thick ovule and ovary tissues. This pistil tissue construction makes observation and analysis of double fertilization quite difficult and has created the present situation in which many questions regarding the mechanism of double fertilization remain unanswered. For the functional evaluation of a potential candidate for fertilization regulator, phenotypic analysis of fertilization is important. To judge the completion of fertilization in Arabidopsis thaliana, the shapes of fluorescence signals labeling sperm nuclei are used as indicators. A sperm cell that fails to fertilize is indicated by a condensed fluorescence signal outside of the female gametes, whereas a sperm cell that successfully fertilizes is indicated by a decondensed signal due to karyogamy with the female gametes&#8217; nucleus. The method described here provides a tool to determine successful or failed fertilization under in vivo conditions.

Evaluation of Fertilization State by Tracing Sperm Nuclear Morphology in Arabidopsis Double Fertilization

We demonstrate a method to determine successful or failed fertilization on the basis of sperm nuclear morphology in Arabidopsis double fertilization using an epifluorescence microscope.

Flowering plants have a unique sexual reproduction system called &#8216;double fertilization&#39;,&#160;in which each of the sperm cells precisely fuses ...

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 ...

Biology

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

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

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

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

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

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 ...

Live Imaging of Arabidopsis Pollen Tube Reception and Double Fertilization Using the Semi-In Vitro Cum Septum Method

In flowering plants, the growth and guidance of the pollen tube (male gametophyte) within the pistil and the reception of the pollen tube by the female gametophyte are essential for double fertilization and subsequent seed development. The interactions between male and female gametophytes during pollen tube reception culminate in pollen tube rupture and the release of two sperm cells to effect double fertilization. As pollen tube growth and double fertilization are deeply hidden within the tissues of the flower, this process is difficult to observe in vivo.
A semi-in vitro (SIV) method for the live-cell imaging of fertilization in the model plant Arabidopsis thaliana has been developed and implemented in several investigations. These studies have helped to elucidate the fundamental features of how the fertilization process occurs in flowering plants and which cellular and molecular changes occur during the interaction of the male and female gametophytes. However, because these live cell imaging experiments involve the excision of individual ovules, they are limited to a low number of observations per imaging session, making this approach tedious and very time-consuming. Among other technical difficulties, a failure of the pollen tubes to fertilize the ovules in vitro is&#160;often reported, which severely confounds such analyses.
Here, a detailed video protocol for the imaging of pollen tube reception and fertilization in an automated and high-throughput manner is provided, allowing for up to 40 observations of pollen tube reception and rupture per imaging session. Coupled with the use of genetically encoded biosensors and marker lines, this method enables the generation of large sample sizes with a reduced time investment. Nuances and critical points of the technique, including flower staging, dissection, medium preparation, and imaging, are clearly detailed in video format to facilitate future research on the dynamics of pollen tube guidance, reception, and double fertilization.

Live Imaging of Arabidopsis Pollen Tube Reception and Double Fertilization Using the Semi-In Vitro Cum Septum Method

Here, we describe an improvement of the semi-in vitro (SIV) method for observing pollen tube guidance and reception in Arabidopsis thaliana,&#160;which increases the receptivity of ovules. The high-throughput SIV cum septum method may be coupled with gametophyte marker lines and genetically encoded biosensors to monitor the dynamic process of fertilization.

In flowering plants, the growth and guidance of the pollen tube (male gametophyte) within the pistil and the reception of the pollen tube by the female ...

In Vitro Ovule Cultivation for Live-cell Imaging of Zygote Polarization and Embryo Patterning in Arabidopsis thaliana

Summary

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Evaluation of Fertilization State by Tracing Sperm Nuclear Morphology in Arabidopsis Double Fertilization

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

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

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

Live Imaging of Arabidopsis Pollen Tube Reception and Double Fertilization Using the Semi-In Vitro Cum Septum Method