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Untwisting the Caenorhabditis elegans embryo.

Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H - Elife (2015)

Bottom Line: However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis.The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo.The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

No MeSH data available.


Related in: MedlinePlus

Fits used in this paper.Examples of raw, averaged data (derived from 4 to 5 embryos, blue dots) and fits (black lines). Linear, power, and three-parameter logistic curve examples were taken from the right H0 seam cell nucleus, the quartic polynomial example from AIYL, and the smoothing fits from CANR. See also Table 1. Note the different ranges in ordinate axes.DOI:http://dx.doi.org/10.7554/eLife.10070.020
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fig4s4: Fits used in this paper.Examples of raw, averaged data (derived from 4 to 5 embryos, blue dots) and fits (black lines). Linear, power, and three-parameter logistic curve examples were taken from the right H0 seam cell nucleus, the quartic polynomial example from AIYL, and the smoothing fits from CANR. See also Table 1. Note the different ranges in ordinate axes.DOI:http://dx.doi.org/10.7554/eLife.10070.020

Mentions: We applied the same time shift to the X- and Y- seam cell nuclear coordinates, finding that seam cell nuclear positions followed similar trajectories throughout elongation (average SD calculated across all 20 seam cell nuclei and all timepoints, <<σX>time>seam cell 0.8 µm, <<σY>time>seam cell 0.7 µm, <<σZ>time>seam cell 4.6 µm, see also Figure 4—figure supplement 3, Table 1, and 'Materials and methods'). After shifting, we averaged (Figure 4C) and fitted (Figure 4D, Figure 4—figure supplement 4, Table 1, Supplementary file 2) the embryo XYZ trajectories, thus generating positions representing the noise-free time evolution of seam cell nuclei. We note that the choice of fitting functions is somewhat arbitrary. For axial positions, the growth that we and others (Priess and Hirsh, 1986) have observed leads to a sigmoidal fitting function. Amongst the various three-parameter sigmoidal functions (Table 2), we found that the three-parameter logistic function gave the best qualitative and quantitative (Figure 4—figure supplement 2) agreement with the data. We fitted lateral (‘X’) seam cell nuclei positions with a two parameter power law function, and dorso-ventral (‘Y’) positions with a linear function, as empirically these functions described our data well. Despite the ad hoc nature of these fits, we found that fitted values were within 1.5 µm of the X, Y averaged data, and within 7.5 µm of the Z averaged data (Supplementary file 3). For reference, the total length of the untwisted embryo at the final time point was 162.0 ± 18.7 µm (mean ± SD, 5 embryos), measured from the nose to the last pair of seam cells, and the corresponding diameter at the last time point 16.1 ± 1.3 µm, measured at the widest cross-section in the animal.10.7554/eLife.10070.021Table 1.


Untwisting the Caenorhabditis elegans embryo.

Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H - Elife (2015)

Fits used in this paper.Examples of raw, averaged data (derived from 4 to 5 embryos, blue dots) and fits (black lines). Linear, power, and three-parameter logistic curve examples were taken from the right H0 seam cell nucleus, the quartic polynomial example from AIYL, and the smoothing fits from CANR. See also Table 1. Note the different ranges in ordinate axes.DOI:http://dx.doi.org/10.7554/eLife.10070.020
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764590&req=5

fig4s4: Fits used in this paper.Examples of raw, averaged data (derived from 4 to 5 embryos, blue dots) and fits (black lines). Linear, power, and three-parameter logistic curve examples were taken from the right H0 seam cell nucleus, the quartic polynomial example from AIYL, and the smoothing fits from CANR. See also Table 1. Note the different ranges in ordinate axes.DOI:http://dx.doi.org/10.7554/eLife.10070.020
Mentions: We applied the same time shift to the X- and Y- seam cell nuclear coordinates, finding that seam cell nuclear positions followed similar trajectories throughout elongation (average SD calculated across all 20 seam cell nuclei and all timepoints, <<σX>time>seam cell 0.8 µm, <<σY>time>seam cell 0.7 µm, <<σZ>time>seam cell 4.6 µm, see also Figure 4—figure supplement 3, Table 1, and 'Materials and methods'). After shifting, we averaged (Figure 4C) and fitted (Figure 4D, Figure 4—figure supplement 4, Table 1, Supplementary file 2) the embryo XYZ trajectories, thus generating positions representing the noise-free time evolution of seam cell nuclei. We note that the choice of fitting functions is somewhat arbitrary. For axial positions, the growth that we and others (Priess and Hirsh, 1986) have observed leads to a sigmoidal fitting function. Amongst the various three-parameter sigmoidal functions (Table 2), we found that the three-parameter logistic function gave the best qualitative and quantitative (Figure 4—figure supplement 2) agreement with the data. We fitted lateral (‘X’) seam cell nuclei positions with a two parameter power law function, and dorso-ventral (‘Y’) positions with a linear function, as empirically these functions described our data well. Despite the ad hoc nature of these fits, we found that fitted values were within 1.5 µm of the X, Y averaged data, and within 7.5 µm of the Z averaged data (Supplementary file 3). For reference, the total length of the untwisted embryo at the final time point was 162.0 ± 18.7 µm (mean ± SD, 5 embryos), measured from the nose to the last pair of seam cells, and the corresponding diameter at the last time point 16.1 ± 1.3 µm, measured at the widest cross-section in the animal.10.7554/eLife.10070.021Table 1.

Bottom Line: However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis.The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo.The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

No MeSH data available.


Related in: MedlinePlus