Here, we present a protocol for preparing and mounting Caenorhabditis elegans embryos, recording development under a 4D microscope and tracing cell lineage.
4D microscopy is an invaluable tool for unraveling the embryonic developmental process in different animals. Over the last decades, Caenorhabditis elegans has emerged as one of the best models for studying development. From an optical point of view, its size and transparent body make this nematode an ideal specimen for DIC (Differential Interference Contrast or Nomarski) microscopy. This article illustrates a protocol for growing C. elegans nematodes, preparing and mounting their embryos, performing 4D microscopy and cell lineage tracing. The method is based on multifocal time-lapse records of Nomarski images and analysis with specific software. This technique reveals embryonic developmental dynamics at the cellular level. Any embryonic defect in mutants, such as problems in spindle orientation, cell migration, apoptosis or cell fate specification, can be efficiently detected and scored. Virtually every single cell of the embryo can be followed up to the moment the embryo begins to move. Tracing the complete cell lineage of a C. elegans embryo by 4D DIC microscopy is laborious, but the use of specific software greatly facilitates this task. In addition, this technique is easy to implement in the lab. 4D microscopy is a versatile tool and opens the possibility of performing an unparalleled analysis of embryonic development.
4D microscopy is a multifocal time-lapse recording system that allows researchers to register and quantify the cell dynamics of a biological sample both spatially and over time. Cell cultures, yeasts or living tissues can be subjected to 4D analysis but this technique is especially suited for analyzing the development of living embryos. The resolution of this analysis reaches the level of every single cell of the embryo. Each cell division can be detected, and cell movements can be traced over time. Cell fates are assessed according to the position and shape that cells acquire. The use of Nomarski optics enhances the contrast of unstained transparent samples using orthogonally polarized light beams that interfere at the focal plane. The resulting images appear three-dimensional, illuminated on one side.
Other methods based on the use of confocal microscopy and GFP transgenic animals for automatic detection of nuclei and generation of cell lineages have been developed1,2. The advantage of those systems is obvious: the software greatly overrides the need for manually marking each nucleus over a period of time (although some manual supervision is required during the late stages). However, cellular processes involving changes in cell shape or membrane dynamics, such as those occurring during cell differentiation, migration, apoptosis or corpse engulfment, remain hidden as a black background in the fluorescent-labeled nuclei images.
In contrast, 4D Nomarski microscopy (also called DIC microscopy, Differential Interference Contrast microscopy) shows both nuclei and cell shape changes that occur during the development of wild type or mutant animals. This allows cell lineage tracing using standard microscopes, employing only transmitted light. There is no general need to use transgenic animals except to show specific expression patterns, in which case fluorescent scans can be intercalated. Therefore, this could be the optimal approach for many labs working on dynamic cell processes such as embryogenesis or apoptosis that can be highlighted under DIC microscopy3,4,5,6,7.
Several flexible and user-friendly programs are available for capturing microscopic images and reconstructing cell lineages, 3D models, cell migration paths, etc. in the recorded sample. In a standard experiment, images are acquired in a series of focal planes, at a constant distance, the number of which depends on the sample thickness. Temporal resolution of the analysis can be optimized by increasing scan frequency. There is virtually no limit for the duration of the recording other than computer storage capacity. For example, for a C. elegans embryo development analysis, we routinely acquire images on 30 focal planes (1 micron-step each), every 30 seconds for 12 hours.
These systems have been applied to the analysis of several animal embryos such as Caenorhabditis elegans8,9,10, Drosophila melanogaster11, other nematode embryos12,13, tardigrades14,15 and even early mouse embryos16. The only requirement is having a transparent embryo able to develop on the slide preparation under the microscope.
In summary, DIC based 4D microscopy is especially useful for 1) analyzing embryonic development of small, transparent animals: tracing cell lineage, cell migration paths, generating 3D models, etc; 2) defining gene expression patterns; 3) studying cell culture dynamics, from yeast to human cells; 4) analyzing tissue dynamics or embryo fragments; 5) quantifying cell death kinetics and corpse engulfment; and 6) performing comparative phylogeny analysis based on embryonic developmental characteristics. If there is interest in any of these topics (or similar ones), 4D microscopy can be used.
1. Grow C. elegans on Petri dishes
2. Prepare the 4D microscopy recording before mounting the embryos (Figure 2)
3. Prepare and mount the embryos
4. Adjust the DIC and start the 4D microscopy recording
5. Analyze the 4D-movie (Figure 4).
NOTE: Once the recording is complete, use cell lineage tracing software to reconstruct and analyze cell lineage.
Cell lineage tracing software is a powerful tool for performing detailed analyses of embryonic development or dynamics in cell cultures or tissue fragments. The program extracts and quantifies several data sets on the sample’s cellular dynamics that include generation of the complete cell lineage of each and every recorded cell, including cell divisions, cell cycle length, migration or apoptosis as well as its kinetics. In addition, cell differentiation can be scored by the cell’s morphological changes or by expression of specific markers. Basically, the software screen displays two windows: on the left window, the 4D movie can be played forward and backward or up and down to either the top or bottom levels so that each cell can be followed in time and space throughout the recording. On the right widow, the cell lineage is generated. Clicking on a cell nucleus in the 4D movie generates a point in the lineage window that stores the information of the cell name, fate and spatial coordinates. The cell lineage of a specific cell is generated by playing the 4D movie forward and clicking periodically on the nucleus to mark the mitosis of that specific cell over time. Repetition of this process for each of the recorded cells generates the complete cell lineage of the embryo or sample. The stored information for spatial coordinates of each cell is later used to reconstruct 3D embryo models and cell migration paths.
To characterize embryonic development of a C. elegans mutant for the gene gsr-1, that encodes the enzyme glutathione reductase, required to regenerate reduced glutathione (GSH) and involved in maintaining redox homeostasis in the nematode, we performed 4D microscopy of a gsr-1 (tm3574) deletion mutant that is a loss of function allele causing an early embryonic arrest phenotype18. Both WT and balanced gsr-1 (tm3574) mutant C. elegans nematodes were grown on NGM plates seeded with E. coli OP50 as the food source17. gsr-1 (tm3574) worms were grown as heterozygous at 20 °C for two generations and then segregating homozygous worms (which are able to grow up to adulthood thanks to the maternal load) were shifted to 25 °C for an overnight incubation prior to embryo analysis. Worm plates were incubated within cardboard boxes to avoid condensation (Figure 1). Gravid nematodes were cut open to extract young embryos.
To compare embryonic development of the mutant versus the stereotyped WT under identical conditions, a WT (as control) and a gsr-1 (tm3574) embryo were placed on the same preparation next to each other. 4D microscopy workflow was run on a standard motorized upright microscope outfitted with DIC optics. The selected recording parameters on the microscope control program were: z-stacks of 30 focal planes at 1 micron distance each, 30 second intervals between the beginning of each z-stack and 1500 z-stacks (12.5 hours of recording). The recording temperature was adjusted to 25 °C (both in the room and on the microscope stage) (Figure 2).
Once the recording was completed, the images file was opened, and cell lineage was reconstructed using lineage tracing software by clicking on cell nuclei shown in the video window (Figure 4). The traced gsr-1 (tm3574) mutant embryonic cell lineage was compared with the C. elegans WT lineage depicted in the background. A major result was the detection of a progressive delay of the cell cycle during embryonic development. As a consequence, mutant embryos arrested at intermediate stages whereas WT embryos progressed and finally hatched as larvae.
Preparation and direct observation of embryos under the microscope or immunostaining with antibodies against late embryonic markers could reveal the presence of a high percentage of young embryos in the mutant compared to the WT. Embryo arrest could then be inferred as the most plausible explanation. However, direct proof and exact quantification of the cell cycle delay can only be elegantly and easily shown and quantified through a 4D microscopy experiment. Other important features of embryonic development such as cell differentiation or apoptosis (Figure 5) can also be visualized in a dynamic way using 4D microscopy which offers a detailed analysis of multiple aspects of development in a single experiment.
Figure 1: C. elegans nematodes growing under laboratory conditions. Nematodes are grown on E. coli-seeded NGM plates, stored in cardboard boxes and incubated either at 15 °C, 20 °C or 25 °C. Please click here to view a larger version of this figure.
Figure 2: Screenshot of 4D microscopy recording software. Example of two different microscope control software programs (A and B). These programs create workflows to control the microscope and image capturing during 4D microscopy recording. Please click here to view a larger version of this figure.
Figure 3: Serial photographs of agar pad preparation and mounting of the C. elegans embryo showing. A. Prepared agar tubes. B-C. Preparation of the agar pad. D. Slide partially filled with water. E. Sealing the slide with petroleum jelly. F. Final preparation. Please click here to view a larger version of this figure.
Figure 4: Serial screen shots of cell lineage tracer software. The program allows reconstruction of the embryonic cell lineage of a cell cycle delay mutant (left) and a WT (right) C. elegans embryo. A. An early step of the development. B-C. Development of both embryos progresses over time. D. WT embryo develops properly and starts elongation whereas the mutant arrests. In all cases the program displays the video window and the lineage window. Please click here to view a larger version of this figure.
Figure 5: Lentil refractile shape of apoptotic cells in a C. elegans WT embryo. Cell fate, defined by morphological characteristics, can be assessed by 4D microscopy. The image shows a C. elegans embryo in the bean stage. Living cells show smooth-shaped nuclei surrounded by a granular cytoplasm. In contrast, apoptotic cells (yellow arrows) condense and adopt a lentil-like, refractile shape. Please click here to view a larger version of this figure.
One of the major challenges in modern biology is understanding the development of multicellular organisms. C. elegans has emerged as one of the best suited models for studying the fine coordination between cell proliferation and cell differentiation in the developing embryo. From an optical point of view, its transparent body and its small size make this nematode an ideal specimen for DIC microscopy. Other organisms with similar characteristics have also been subjected to 4D microscopy analysis11,12,13,14,15,16.
For those developmental studies, gene inactivation by either forward or reverse genetics provides a clue to its involvement in embryogenesis. Once a gene has been proven to play a role in development, the next step is to define its exact role in the establishment of the correct body plan. Immunostaining is the selected approach for most models. This technique elucidates problems in cell differentiation or expression of specific markers. However, a major limitation of this approach is that it only provides a static view of the expression of a single or more markers at a fixed point in development. A dynamic view of these markers throughout development can only be obtained by staining different embryos at different time points. In addition, cell lineage reconstruction is not possible in such fixed samples.
4D microscopy is a complementary approach for studying embryonic development. This technique reveals development dynamics at a cell level resolution. Any defect in the embryo such as problems in spindle orientation, cell migration, apoptosis, cell fate specification, etc. will show up in a 4D movie that can be visualized forward and backward, quantified and scored by the researcher. Using this technique, virtually each and every cell in the embryo can be followed up to the moment that the embryo begins to move. Embryos subjected to 4D microscopy with only visible light and Nomarski optics do not incur photodamage. Fluorescent scans can also be intercalated within the recording to detect when and where a gene is expressed. Embryos that suffer significant photodamage are identified by the cell cycle extension that causes strong UV irradiation compared to a standard WT lineage embryo. In that case, photodamage can be reduced by lowering the UV lamp intensity and increasing camera sensitivity or exposure time. Morphological characteristics and molecular markers can help clarify the embryonic development of any mutant.
Setting up a 4D microscopy system is easy to implement in the lab and, after some practice, enables an unmatched analysis of cell dynamics and lineage tracing of cell cultures and living transparent specimens at a resolution level of each and every cell in the microscope field. Cell lineage tracing on DIC images is still processed by hand. It is time consuming and, although the software detects lineage errors such as different lineage branches marking the same cell, mistakes are possible. While automatic detection of GFP-labeled cells is well developed2, complementary lineage tracing software based on unmarked cells and visible light images is still in the early stage and not really useful for a full embryo analysis. Without any doubt, application of image recognition systems to the field of visible light microscopy will bring about a great advance in this field.
The authors wish to acknowledge support from Rioja Salud Foundation (Fondos FEDER) and the Spanish Ministerio de Ciencia, Innovación y Universidades (MCIU) (Grant PGC2018-094276-B-I00). Cristina Romero Aranda is funded by a fellowship from the AECC (Asociación Española Contra el Cáncer).
Name | Company | Catalog Number | Comments |
Caenorhabditis elegans (N2) | GCG (Caenorhabditis Genetics Center) | N2 | WT C. elegans strain. Can be requested at GCG (Caenorhabditis Genetics Center): https://cgc.umn.edu/ |
Caenorhabditis elegans (VZ454) | GCG (Caenorhabditis Genetics Center) | VZ454 | gsr-1(tm3574) C. elegans mutant strain. Can be requested at GCG (Caenorhabditis Genetics Center): https://cgc.umn.edu/ |
Cell Lineage Tracing software | SIMI | Simi BioCell | This is the software to reconstruct the embryo cell lineage. For a detailed explanation check at: http://www.simi.com/en/products/cell-research/simi-biocell.html |
Microscope camera | Hamamatsu | Orca-R2 | Miscroscope camera for both transmitted and UV light |
Microscope control software | Caenotec | Time to Live | This software controls the microscope to perform the 4D image capture. Can be requested at: Caenotec Prof. Ralf Schnabel Kleine Dorfstr. 9 38312 Börßum, Germany, Ph: ++49 151 11653356 r.schnabel(at)tu-bs.de |
Microscope control software | Micro-manager | Micro-manager | This software controls the microscope to perform the 4D image capture. Can be downloaded at: https://micro-manager.org/ |
Motorized microscope | Leica | Leica DM6000 | Motorized upright microscope to perform 4D microscopy |
Standard equipment in a Molecular Biology lab. | |||
Stereomicroscope | Leica | MZ16FA | Steromicroscope to manipulate nematodes and prepare embryos. |
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