We thank Sven Plath for technical support. The Glia-blue transgenic line was a kind gift from Gregor Bucher (G&#246;ttingen, Germany). The research was funded by the Cluster of Excellence Frankfurt am Main for Macromolecular Complexes (CEF-MC, EXC 115, speaker Volker D&#246;tsch) granted in part to EHKS at the Buchmann Institute for Molecular Life Sciences (BMLS, director Enrico Schleiff) at the Goethe Universit&#228;t Frankfurt am Main by the Deutsche Forschungsgemeinschaft (DFG).

The authors have nothing to disclose.
Author Contributions
FS and EHKS conceived the research. FS generated the transgenic AGOC lines. Light sheet-based fluorescence imaging was performed by FS and SK. FS and EHKS wrote the manuscript with input from SK.

Quality control
In live imaging assays, the preparation and recording procedure must be non-invasive, i.e. neither the mechanical and chemical handling (collection, dechorionation, mounting onto the sample holder) nor the integrated energy load during the observation should affect the viability of the specimen. For studies that characterize WT development, it is recommended to only use data from experiments in which the embryo survives the recording process, is retrie...

The red flour beetle Tribolium castaneum, which belongs to the large family of darkling beetles (Tenebrionidae), has a long history within the agricultural and life sciences and is the second best studied model insect model organism after the fruit fly Drosophila melanogaster. During the last four decades, it became a powerful and popular insect model organism in developmental genetics, in evolutionary developmental biology and, during the last twenty years, in embryonic morphogenesis for a variety of reasons:
Drosophila and Tribolium both belong to the Holometabola, but diverged approximately 300 million years ago1,2,3,4. While the embryonic development of Drosophila is commonly considered as highly derived, Tribolium shows a more ancestral mode of development that is found in a considerably larger proportion of insect species5,6,7,8,9. Firstly, Tribolium exhibits non-involuted head development, i.e. its mouthparts and antennae emerge already during embryogenesis10,11,12,13,14,15. Secondly, Tribolium follows the principles of short-germ development, i.e. abdominal segments are added sequentially from a posterior growth zone during germband elongation16,17,18,19. Thirdly, Tribolium develops and later degrades two extra-embryonic membranes i.e. the amnion, which covers the embryo only ventrally, and the serosa, which envelops the embryo completely20,21,22. Both membranes play a crucial morphogenetic23 as well as protective role against microorganisms24,25 and desiccation26. Fourthly, the embryonically developing legs are fully functional during the larval life stage and serve as the primordia for the adult legs during pupal metamorphosis27,28,29,30,31.
Due to their small size and modest demands, cultivation of Tribolium in the laboratory is fairly straightforward. Cultures of wild-type (WT) strains or transgenic lines typically consist of around 100-300 adults and can be kept within one-liter glass bottles (footprint 80 cm2) filled three to four centimeters high (about 50 g) with growth medium that consists of full grain wheat flour supplemented with inactive dry yeast. A water supply is not necessary. This allows even small laboratories to keep dozens of beetle cultures within small- or medium-sized commercially available insect incubators. Later developmental stages of Tribolium (larvae after approximately the fourth instar, pupae and adults) are easily separated from the growth medium by sieving. Synchronized embryos are obtained by incubating adults for short periods on egg-laying medium. For rapid development, beetle cultures are kept at 32 &#176;C (about four weeks per generation), while stock keeping is typically performed at 22-25 &#176;C (about ten weeks per generation).
Within the last decade, many standard techniques have been gradually adapted and optimized for Tribolium, as summarized in the Emerging Model Organisms books32. Of great importance are advanced genetic methods such as embryonic33, larval34,35 or parental36,37 RNA interference-based gene knockdown, germline transformation with either the piggyBac38,39 or the Minos40 transposase system and CRISPR/Cas9-based genome engineering41. Furthermore, the Tribolium genome has been sequenced about a decade ago42, and is now in the third round of genome assembly release43, which allows efficient and genome-wide identification and systematic analysis of genes44 or other genetic elements45,46. Additionally, the genomes of four other coleopteran species are available for comparative genetic approaches47,48,49,50. In association with the sequenced genome, two large-scale genetic analyses have been performed, i.e. an insertional mutagenesis screen51 and a systematic RNA interference-based gene knockdown screen52,53.
Fluorescence live imaging with widefield, confocal or light sheet-based microscopy (LSFM) allows to observe the embryonic morphology of Tribolium as a function of time (i.e. the morphogenesis) in a multi-dimensional context (Table 1). In widefield and confocal fluorescence microscopy, the excitation and emission light is guided through the same objective lens. In both approaches, the entire specimen is illuminated for every recorded two-dimensional plane. Hence, the specimens are subjected to very high energy levels. In LSFM, only the fluorophores in the focal plane are excited due to a decoupling of illumination and detection by using two perpendicularly arranged objective lenses (Figure 1). LSFM comes in two canonic implementations &#8211; the single plane illumination microscope (SPIM) and the digital scanned laser light sheet-based fluorescence microscope (DSLM, Figure 2) &#8211; and offers several crucial advantages over traditional approaches: (i) intrinsic optical sectioning capability, (ii) good axial resolution, (iii) strongly reduced level of photo-bleaching, (iv) very low photo-toxicity, (v) high signal-to-noise ratio, (vi) relatively high acquisition speed, (vii) imaging along multiple directions and (viii) deeper tissue penetration due to the usage of low numerical aperture illumination objective lenses54,55,56.
LSFM has already been successfully applied in Tribolium to document nearly the entire embryonic morphogenesis57 and to analyze the principles of extra-embryonic membrane rupture at the beginning of dorsal closure23. To raise the attractiveness of LSFM in the Tribolium community and for insect science in general, it is of great importance to establish standard operating procedures and to improve the methods, protocols and the pool of resources to a level where the microscope becomes an ease-of-use standard tool in developmental biology laboratories, and the biological questions stay in the center of attention.
This protocol begins with the basics of Tribolium cultivation, i.e. maintenance, reproduction and embryo collection. Next, two experimental strategies are illustrated: (i) live imaging of custom-made transgenic lines and (ii) imaging of fixed embryos that were stained with fluorescent dyes (Table 2). Subsequently, three mounting techniques with slightly different purposes are explained in detail (Figure 3 and Table 3): (i) the agarose column, (ii) the agarose hemisphere and (iii) the novel cobweb holder. The protocol then explains the data acquisition procedure with LSFM. Imaging modalities and key considerations are outlined. Finally, embryo retrieval is explained and suggestions for basic data processing are provided. In the representative results, live imaging data from two novel custom-made and the Glia-blue58 transgenic lines are shown and the respective imaging datasets are provided as a downloadable resource. Additionally, image data of fixed embryos that were stained with a variety of fluorescence dyes are presented. The discussion focuses on quality control, current limitations of the live imaging approach and the adaptation of the protocol to other species.
The protocol is written for light sheet-based fluorescence microscopes that are equipped with a sample chamber and a rotatable clamp mechanism for standardized sample holders54,59,60, which are typically cylinder-shaped elements made of metal, plastic or glass with a diameter in the millimeter range. The protocol is also suitable for both canonic implementations, i.e. SPIM and DSLM, as well as for setups with two or more illumination and detection arms61,62,63. The representative results show data in two spectral channels, green (illumination with a 488 nm laser, detection through a 525/50 bandpass filter) and red (illumination with a 561 nm laser, detection through a 607/70 bandpass filter), but the protocol can be expanded to three or four spectral channels.

<table border="0" cellpadding="0" cellspacing="0" width="573">
	<tbody>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">full grain wheat flour</td>
			<td style="width:119px;">Demeter e.V.</td>
			<td style="width:71px;">1.13E+08</td>
			<td style="width:167px;">US: whole wheat flour, UK: whole meal flour</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">405 fine wheat flour</td>
			<td style="width:119px;">Demeter e.V.</td>
			<td style="width:71px;">1.13E+08</td>
			<td style="width:167px;">US: pastry flour, UK: soft flour</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">inactive dry yeast</td>
			<td style="width:119px;">Flystuff / Genesee Scientific</td>
			<td style="width:71px;">62-106</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">phosphate-buffered saline (PBS), pH 7.4</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">10010-023</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">sodium hypochlorite, ~12% active Cl</td>
			<td style="width:119px;">Sigma Aldrich</td>
			<td style="width:71px;">425044-250ML</td>
			<td style="width:167px;">Caution: sodium hypochlorite is corrosive</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">low-melt agarose</td>
			<td style="width:119px;">Carl Roth</td>
			<td style="width:71px;">6351.2</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">6-well plate</td>
			<td style="width:119px;">Orange Scientific</td>
			<td style="width:71px;">4430500</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">24-well plate</td>
			<td style="width:119px;">Orange Scientific</td>
			<td style="width:71px;">4430300</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">glass capillaries, internal &#216; 0.46 mm</td>
			<td style="width:119px;">Brand GmbH + Co KG</td>
			<td style="width:71px;">7087 09</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">SYTOX Green</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">57020</td>
			<td style="width:167px;">Staining solution preparation is explained in Table 2</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">YOYO-1 Iodide</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">Y3601</td>
			<td style="width:167px;">Staining solution preparation is explained in Table 2</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">BOBO-3 Iodide</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">B3586</td>
			<td style="width:167px;">Staining solution preparation is explained in Table 2</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Alexa Fluor 488 Phalloidin</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">A12379</td>
			<td style="width:167px;">Staining solution preparation is explained in Table 2</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Alexa Fluor 546 Phalloidin</td>
			<td style="width:119px;">Thermo Fisher Scientific</td>
			<td style="width:71px;">A22283</td>
			<td style="width:167px;">Staining solution preparation is explained in Table 2</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">sieve, 800 &#181;m mesh size</td>
			<td style="width:119px;">VWR International</td>
			<td style="width:71px;">200.025.222-051</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">sieve, 710 &#181;m mesh size</td>
			<td style="width:119px;">VWR International</td>
			<td style="width:71px;">200.025.222-050</td>
			<td style="width:167px;">for growth medium preparation (step 1.1)</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">sieve, 300 &#181;m mesh size</td>
			<td style="width:119px;">VWR International</td>
			<td style="width:71px;">200.025.222-040</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">sieve, 250 &#181;m mesh size</td>
			<td style="width:119px;">VWR International</td>
			<td style="width:71px;">200.025.222-038</td>
			<td style="width:167px;">for egg laying medium preparation (step 1.2)</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">glass dish, &#216; 100 mm &#215; 20 mm</td>
			<td style="width:119px;">Sigma Aldrich</td>
			<td style="width:71px;">CLS70165102</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">cell strainer, 100 &#181;m mesh size</td>
			<td style="width:119px;">BD Biosciences</td>
			<td style="width:71px;">352360</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">paint brush, head &#216; 2 mm</td>
			<td style="width:119px;">VWR International</td>
			<td style="width:71px;">149-2121</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">syringe, 1.0 ml</td>
			<td style="width:119px;">B. Braun Medical AG</td>
			<td style="width:71px;">9166017V</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">scintillation vials</td>
			<td style="width:119px;">Sigma Aldrich</td>
			<td style="width:71px;">M1152-1000EA</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">paraformaldehyde</td>
			<td style="width:119px;">Sigma Aldrich</td>
			<td style="width:71px;">158127</td>
			<td style="width:167px;">Caution: paraformaldehyde is toxic and corrosive</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">n-heptane &#8805; 99%</td>
			<td style="width:119px;">Carl Roth</td>
			<td style="width:71px;">8654.1</td>
			<td style="width:167px;">Caution: n-heptane is flammable and toxic</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Triton X-100</td>
			<td style="width:119px;">Sigma Aldrich</td>
			<td style="width:71px;">X100-100ML</td>
			<td style="width:167px;">Caution: Trition X-100 is corrosive</td>
		</tr>
	</tbody>
</table>

light sheet-based fluorescence microscopy of living or fixed and stained tribolium castaneum embryos

The red flour beetle Tribolium castaneum has become an important insect model organism in developmental genetics and evolutionary developmental biology. The observation of Tribolium embryos with light sheet-based fluorescence microscopy has multiple advantages over conventional widefield and confocal fluorescence microscopy. Due to the unique properties of a light sheet-based microscope, three dimensional images of living specimens can be recorded with high signal-to-noise ratios and significantly reduced photo-bleaching as well as photo-toxicity along multiple directions over periods that last several days. With more than four years of methodological development and a continuous increase of data, the time seems appropriate to establish standard operating procedures for the usage of light sheet technology in the Tribolium community as well as in the insect community at large. This protocol describes three mounting techniques suitable for different purposes, presents two novel custom-made transgenic Tribolium lines appropriate for long-term live imaging, suggests five fluorescent dyes to label intracellular structures of fixed embryos and provides information on data post-processing for the timely evaluation of the recorded data. Representative results concentrate on long-term live imaging, optical sectioning and the observation of the same embryo along multiple directions. The respective datasets are provided as a downloadable resource. Finally, the protocol discusses quality controls for live imaging assays, current limitations and the applicability of the outlined procedures to other insect species.
This protocol is primarily intended for developmental biologists who seek imaging solutions that outperform standard laboratory equipment. It promotes the continuous attempt to close the gap between the technically orientated laboratories/communities, which develop and refine microscopy methodologically, and the life science laboratories/communities, which require 'plug-and-play' solutions to technical challenges. Furthermore, it supports an axiomatic approach that moves the biological questions into the center of attention.

This protocol describes an experimental framework for fluorescence imaging of living or fixed and stained Tribolium embryos with LSFM. Due to the low levels of photo-bleaching and photo-toxicity, a direct consequence of its optical sectioning capability, LSFM is particularly well suited for long-term live imaging.
The novel AGOC{ATub&#39;H2B-mEmerald} #1 transgenic line expresses a histone2B-mEmerald fusion protein unde...

Watch this Scientific Journal Video about Light Sheet-based Fluorescence Microscopy of Living or Fixed and Stained Tribolium castaneum Embryos at JoVE.com

Light Sheet-based Fluorescence Microscopy of Living or Fixed and Stained Tribolium castaneum Embryos

Imaging the morphogenesis of insect embryos with light sheet-based fluorescence microscopy has become state of the art. This protocol outlines and compares three mounting techniques appropriate for Tribolium castaneum embryos, introduces two novel custom-made transgenic lines well suited for live imaging, discusses essential quality controls and indicates current experimental limitations.

Light Sheet-based Fluorescence Microscopy of Living or Fixed and Stained Tribolium castaneum Embryos

The red flour beetle Tribolium castaneum has become an important insect model organism in developmental genetics and evolutionary developmental biology. ...

light-sheet-based-fluorescence-microscopy-living-or-fixed-stained

Research

JoVE Journal

Developmental Biology

10.5K Views.  Buchmann Institute for Molecular Life Sciences (BMLS). Imaging the morphogenesis of insect embryos with light sheet-based fluorescence microscopy has become state of the art. This protocol outlines and compares three mounting techniques appropriate for Tribolium castaneum embryos, introduces two novel custom-made transgenic lines well suited for live imaging, discusses essential quality controls and indicates current experimental limitations.

Video: Light Sheet-based Fluorescence Microscopy of Living or Fixed and Stained Tribolium castaneum Embryos

Measuring Protein Stability in Living Zebrafish Embryos Using Fluorescence Decay After Photoconversion (FDAP)

Protein stability influences many aspects of biology, and measuring the clearance kinetics of proteins can provide important insights into biological systems. In FDAP experiments, the clearance of proteins within living organisms can be measured. A protein of interest is tagged with a photoconvertible fluorescent protein, expressed in vivo and photoconverted, and the decrease in the photoconverted signal over time is monitored. The data is then fitted with an appropriate clearance model to determine the protein half-life. Importantly, the clearance kinetics of protein populations in different compartments of the organism can be examined separately by applying compartmental masks. This approach has been used to determine the intra- and extracellular half-lives of secreted signaling proteins during zebrafish development. Here, we describe a protocol for FDAP experiments in zebrafish embryos. It should be possible to use FDAP to determine the clearance kinetics of any taggable protein in any optically accessible organism.

Measuring Protein Stability in Living Zebrafish Embryos Using Fluorescence Decay After Photoconversion FDAP

Protein levels in cells and tissues are often tightly regulated by the balance of protein production and clearance. Using Fluorescence Decay After Photoconversion (FDAP), the clearance kinetics of proteins can be experimentally measured in vivo.

Protein stability influences many aspects of biology, and measuring the clearance kinetics of proteins can provide important insights into biological ...

Methods for Precisely Localized Transfer of Cells or DNA into Early Postimplantation Mouse Embryos

Manipulation and culture of early mouse embryos is a powerful yet largely under-utilized technology enhancing the value of this model system. Conversely, cell culture has been widely used in developmental biology studies. However, it is important to determine whether in vitro cultured cells truly represent in vivo cell types. Grafting cells into embryos, followed by an assessment of their contribution during development is a useful method to determine the potential of in vitro cultured cells. In this study, we describe a method for grafting cells into a defined site of early postimplantation mouse embryos, followed by ex vivo culture. We also introduce an optimized electroporation method that uses glass capillaries of known diameter, allowing precise localization and adjustment of the number of cells receiving exogenous DNA with both high transfection efficiency and low cell death. These techniques, which do not require any specialized equipment, render experimental manipulations of the gastrulation and early organogenesis-stage mouse embryo possible, allowing analysis of commitment in cultured cell subpopulations and the effect of genetic manipulations in situ on cell differentiation.

We demonstrate a method for grafting cultured cells into defined sites of early mouse embryos to determine their in vivo potential. We also introduce an optimized electroporation method that uses glass capillaries of known diameter, allowing the precise delivery of exogenous DNA into a few cells in the embryos.

Manipulation and culture of early mouse embryos is a powerful yet largely under-utilized technology enhancing the value of this model system. Conversely, ...

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Light sheet fluorescence microscopy (LSFM) is gaining more and more popularity as a method to image embryonic development. The main advantages of LSFM compared to confocal systems are its low phototoxicity, gentle mounting strategies, fast acquisition with high signal to noise ratio and the possibility of imaging samples from various angles (views) for long periods of time. Imaging from multiple views unleashes the full potential of LSFM, but at the same time it can create terabyte-sized datasets. Processing such datasets is the biggest challenge of using LSFM. In this protocol we outline some solutions to this problem. Until recently, LSFM was mostly performed in laboratories that had the expertise to build and operate their own light sheet microscopes. However, in the last three years several commercial implementations of LSFM became available, which are multipurpose and easy to use for any developmental biologist. This article is primarily directed to those researchers, who are not LSFM technology developers, but want to employ LSFM as a tool to answer specific developmental biology questions. 
Here, we use imaging of zebrafish eye development as an example to introduce the reader to LSFM technology and we demonstrate applications of LSFM across multiple spatial and temporal scales. This article describes a complete experimental protocol starting with the mounting of zebrafish embryos for LSFM. We then outline the options for imaging using the commercially available light sheet microscope. Importantly, we also explain a pipeline for subsequent registration and fusion of multiview datasets using an open source solution implemented as a Fiji plugin. While this protocol focuses on imaging the developing zebrafish eye and processing data from a particular imaging setup, most of the insights and troubleshooting suggestions presented here are of general use and the protocol can be adapted to a variety of light sheet microscopy experiments.

Light sheet fluorescence microscopy is an excellent tool for imaging embryonic development. It allows recording of long time-lapse movies of live embryos in near physiological conditions. We demonstrate its application for imaging zebrafish eye development across wide spatio-temporal scales and present a pipeline for fusion and deconvolution of multiview datasets.

Light sheet fluorescence microscopy (LSFM) is gaining more and more popularity as a method to image embryonic development. The main advantages of LSFM ...

Induction of Hypoxia in Living Frog and Zebrafish Embryos

Here, we introduce a novel system for hypoxia induction, which we developed to study the effects of hypoxia in aquatic organisms such as frog and zebrafish embryos. Our system comprises a chamber featuring a simple setup that is nevertheless robust to induce and maintain a specific oxygen concentration and temperature in any experimental solution of choice. The presented system is very cost-effective but highly functional, it allows induction and sustainment of hypoxia for direct experiments in vivo and for various time periods up to 48 h.
To monitor and study the effects of hypoxia, we have employed two methods - measurement of levels of hypoxia-inducible factor 1alpha (HIF-1&#945;) in whole embryos or specific tissues and determination of retinal stem cell proliferation by 5-ethynyl-2&#8242;-deoxyuridine (EdU) incorporation into the DNA. HIF-1&#945; levels can serve as a general hypoxia marker in the whole embryo or tissue of choice, here embryonic retina. EdU incorporation into the proliferating cells of embryonic retina is a specific output of hypoxia induction. Thus, we have shown that hypoxic embryonic retinal progenitors decrease proliferation within 1 h of incubation under 5% oxygen of both frog and zebrafish embryos.
Once mastered, our setup can be employed for use with small aquatic model organisms, for direct in vivo experiments, any given time period and under normal, hypoxic or hyperoxic oxygen concentration or under any other given gas mixture.

We introduce a novel hypoxic chamber system for use with aquatic organisms such as frog and zebrafish embryos. Our system is simple, robust, cost-effective and allows the induction and sustainment of hypoxia in vivo and for up to 48 h. We present 2 reproducible methods to monitor the effectiveness of hypoxia.

Here, we introduce a novel system for hypoxia induction, which we developed to study the effects of hypoxia in aquatic organisms such as frog and ...

Quantitative Whole-mount Immunofluorescence Analysis of Cardiac Progenitor Populations in Mouse Embryos

The use of ever-advancing imaging techniques has contributed broadly to our increased understanding of embryonic development. Pre-implantation development and organogenesis are two areas of research that have benefitted greatly from these advances, due to the high quality of data that can be obtained directly from imaging pre-implantation embryos or ex vivo organs. While pre-implantation embryos have yielded data with especially high spatial resolution, later stages have been less amenable to three-dimensional reconstruction. Obtaining high-quality 3D or volumetric data for known embryonic structures in combination with fate mapping or genetic lineage tracing will allow for a more comprehensive analysis of the morphogenetic events taking place during embryogenesis.
This protocol describes a whole-mount immunofluorescence approach that allows for the labeling, visualization, and quantification of progenitor cell populations within the developing cardiac crescent, a key structure formed during heart development. The approach is designed in such a way that both cell- and tissue-level information can be obtained. Using confocal microscopy and image processing, this protocol allows for three-dimensional spatial reconstruction of the cardiac crescent, thereby providing the ability to analyze the localization and organization of specific progenitor populations during this critical phase of heart development. Importantly, the use of reference antibodies allows for successive masking of the cardiac crescent and subsequent quantitative measurements of areas within the crescent. This protocol will not only enable a detailed examination of early heart development, but with adaptations should be applicable to most organ systems in the gastrula to early somite stage mouse embryo.

Here, we describe a protocol for whole mount immunofluorescence and image-based quantitative volumetric analysis of early stage mouse embryos. We present this technique as a powerful approach to qualitatively and quantitatively assess cardiac structures during development, and propose that it may be widely adaptable to other organ systems.

The use of ever-advancing imaging techniques has contributed broadly to our increased understanding of embryonic development. Pre-implantation development ...

Single-cell Photoconversion in Living Intact Zebrafish

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause disease when disrupted. Scientists have developed clever techniques to investigate characteristics and natural dynamics of these cells within intact tissue by expressing fluorescent proteins in subsets of cells. However, at times, experiments require more selected visualization of cells within the tissue, sometimes at the single-cell or population-of-cells manner. To achieve this and visualize single cells within a population of cells, scientists have utilized single-cell photoconversion of fluorescent proteins. To demonstrate this technique, we show here how to direct UV light to an Eos-expressing cell of interest in an intact, living zebrafish. We then image those photoconverted Eos+ cells 24 h later to determine how they changed in the tissue. We describe two techniques: single cell photoconversion and photoconversions of populations of cell. These techniques can be used to visualize cell-cell interactions, cell-fate and differentiation, and cell migrations, making it a technique that is applicable in numerous biological questions.

Here, we present a protocol to show how cell photoconversion is achieved through UV exposure to specific areas expressing the fluorescent protein, Eos, in living animals.

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause ...

Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D.

This protocol targets specific cells in tissue for imaging at nanoscale resolution using a scanning electron microscope (SEM). Large numbers of serial sections from resin-embedded biological material are first imaged in a light microscope to identify the target and then in a hierarchical manner in the SEM.

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a ...

Visualizing the Node and Notochordal Plate In Gastrulating Mouse Embryos Using Scanning Electron Microscopy and Whole Mount Immunofluorescence

The post-implantation mouse embryo undergoes major shape changes after the initiation of gastrulation and morphogenesis. A hallmark of morphogenesis is the formation of the transient organizers, the node and notochordal plate, from cells that have passed through the primitive streak. The proper formation of these signaling centers is essential for the development of the body plan and techniques to visualize them are of high interest to mouse developmental biologists. The node and notochordal plate lie on the ventral surface of gastrulating mouse embryos around embryonic day (E) 7.5 of development. The node is a cup-shaped structure whose cells possess a single slender cilium each. The proper subcellular localization and rotation of the cilia in the node pit determines left-right asymmetry. The notochordal plate cells also possess single cilia albeit shorter than those of the node cells. The notochordal plate forms the notochord which acts as an important signaling organizer for somitogenesis and neural patterning. Because the cells of the node and notochordal plate are transiently present on the surface and possess cilia, they can be visualized using scanning electron microscopy (SEM). Among other techniques used to visualize these structures at the cellular level is whole mount immunofluorescence (WMIF) using the antibodies against the proteins that are highly expressed in the node and notochordal plate. In this report, we describe our optimized protocols to perform SEM and WMIF of the node and notochordal plate in developing mouse embryos to help in the assessment of tissue shape and cellular organization in wild-type and gastrulation mutant embryos.

The node and notochordal plate are transient signaling organizers in developing mouse embryos that can be visualized using several techniques. Here, we describe in detail how to perform two of the techniques to study their structure and morphogenesis: 1) scanning electron microscopy (SEM); and 2) whole mount immunofluorescence (WMIF).

The post-implantation mouse embryo undergoes major shape changes after the initiation of gastrulation and morphogenesis. A hallmark of morphogenesis is ...

Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution

Caenorhabditis elegans (C. elegans) stands out as the only organism in which the challenge of understanding the cellular origins of an entire nervous system can be observed, with single cell resolution, in vivo. Here, we present an integrated protocol for the examination of neurodevelopment in C. elegans embryos. Our protocol combines imaging, lineaging and neuroanatomical tracing of single cells in developing embryos. We achieve long-term, four-dimensional (4D) imaging of living C. elegans&#160;embryos with nearly isotropic spatial resolution through the use of Dual-view Inverted Selective Plane Illumination Microscopy (diSPIM). Nuclei and neuronal structures in the nematode embryos are imaged and isotropically fused to yield images with resolution of ~330 nm in all three dimensions. These minute-by-minute high-resolution 4D data sets are then analyzed to correlate definitive cell-lineage identities with gene expression and morphological dynamics at single-cell and subcellular levels of detail. Our protocol is structured to enable modular implementation of each of the described steps and enhance studies on embryogenesis, gene expression, or neurodevelopment.

Here, we present a combinatorial approach using high-resolution microscopy, computational tools, and single-cell labeling in living C. elegans embryos to understand single cell dynamics during neurodevelopment.

Caenorhabditis elegans (C. elegans) stands out as the only organism in which the challenge of understanding the cellular origins of an entire nervous ...

Microinjection of DNA into Eyebuds in Xenopus laevis Embryos and Imaging of GFP Expressing Optic Axonal Arbors in Intact, Living Xenopus Tadpoles

The primary visual projection of tadpoles of the aquatic frog Xenopus laevis serves as an excellent model system for studying mechanisms that regulate the development of neuronal connectivity. During establishment of the retino-tectal projection, optic axons extend from the eye and navigate through distinct regions of the brain to reach their target tissue, the optic tectum. Once optic axons enter the tectum, they elaborate terminal arbors that function to increase the number of synaptic connections they can make with target interneurons in the tectum. Here, we describe a method to express DNA encoding green fluorescent protein (GFP), and gain- and loss-of-function gene constructs, in optic neurons (retinal ganglion cells) in Xenopus embryos. We explain how to microinject a combined DNA/lipofection reagent into eyebuds of one day old embryos such that exogenous genes are expressed in single or small numbers of optic neurons. By tagging genes with GFP or co-injecting with a GFP plasmid, terminal axonal arbors of individual optic neurons with altered molecular signaling can be imaged directly in brains of intact, living Xenopus tadpoles several days later, and their morphology can be quantified. This protocol allows for determination of cell-autonomous molecular mechanisms that underlie the development of optic axon arborization in vivo.

Microinjection of DNA into Eyebuds in Xenopus laevis Embryos and Imaging of GFP Expressing Optic Axonal Arbors in Intact, Living Xenopus Tadpoles

This protocol aims to demonstrate how to microinject a DNA/DOTAP mixture into eyebuds of one day old Xenopus laevis embryos, and how to image and reconstruct individual green fluorescent protein (GFP) expressing optic axonal arbors in tectal midbrains of intact, living Xenopus tadpoles.

The primary visual projection of tadpoles of the aquatic frog Xenopus laevis serves as an excellent model system for studying mechanisms that regulate the ...

Light Sheet-based Fluorescence Microscopy of Living or Fixed and Stained Tribolium castaneum Embryos

Summary

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Methods for Precisely Localized Transfer of Cells or DNA into Early Postimplantation Mouse Embryos

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Induction of Hypoxia in Living Frog and Zebrafish Embryos

Quantitative Whole-mount Immunofluorescence Analysis of Cardiac Progenitor Populations in Mouse Embryos

Single-cell Photoconversion in Living Intact Zebrafish

Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes

Visualizing the Node and Notochordal Plate In Gastrulating Mouse Embryos Using Scanning Electron Microscopy and Whole Mount Immunofluorescence

Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution

Microinjection of DNA into Eyebuds in Xenopus laevis Embryos and Imaging of GFP Expressing Optic Axonal Arbors in Intact, Living Xenopus Tadpoles