Limits...
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

Automatic lattice-building output.The correct lattice is listed first as it had the highest rank.DOI:http://dx.doi.org/10.7554/eLife.10070.043
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fig11: Automatic lattice-building output.The correct lattice is listed first as it had the highest rank.DOI:http://dx.doi.org/10.7554/eLife.10070.043

Mentions: As an example, the algorithm starts with a set of 20 unordered seam cell nuclei positions in 3D. Two pairs were categorized as being a possible 10th pair. For the first of the possible 10th pairs, the remaining 18 seam cell nuclei, which unconstrained would generated a set of (18!) possible pairs, instead produced 100 pairs that fell within the minimum/maximum distance threshold, of which only 31 met the mid-point test. After eliminating pairs based on the ‘essential pair’ criteria only 27 potential pairs remained. For the second of the possible 10th pairs, with 18 remaining seam cells only 104 possible pairs met the minimum/maximum distance threshold and of those only 33 pairs satisfied the mid-point test. Eliminating pairs based on the ‘essential pair’ criteria further reduced the pool of potential pairs to 28. 27 choose 9 is 4,686,825 lattices and 28 choose 9 is 6,906,900 lattices; too many to evaluate. However, automatically eliminating lattices during the building process reduced this number to 22,916 lattices that reached the target length of 10 pairs. Of those only 21 lattices passed the evaluation phase. After ranking the 21 lattices, the correct lattice was listed at the top-ranked lattice (Appendix 1—figure 5).


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)

Automatic lattice-building output.The correct lattice is listed first as it had the highest rank.DOI:http://dx.doi.org/10.7554/eLife.10070.043
© Copyright Policy
Related In: Results  -  Collection

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

fig11: Automatic lattice-building output.The correct lattice is listed first as it had the highest rank.DOI:http://dx.doi.org/10.7554/eLife.10070.043
Mentions: As an example, the algorithm starts with a set of 20 unordered seam cell nuclei positions in 3D. Two pairs were categorized as being a possible 10th pair. For the first of the possible 10th pairs, the remaining 18 seam cell nuclei, which unconstrained would generated a set of (18!) possible pairs, instead produced 100 pairs that fell within the minimum/maximum distance threshold, of which only 31 met the mid-point test. After eliminating pairs based on the ‘essential pair’ criteria only 27 potential pairs remained. For the second of the possible 10th pairs, with 18 remaining seam cells only 104 possible pairs met the minimum/maximum distance threshold and of those only 33 pairs satisfied the mid-point test. Eliminating pairs based on the ‘essential pair’ criteria further reduced the pool of potential pairs to 28. 27 choose 9 is 4,686,825 lattices and 28 choose 9 is 6,906,900 lattices; too many to evaluate. However, automatically eliminating lattices during the building process reduced this number to 22,916 lattices that reached the target length of 10 pairs. Of those only 21 lattices passed the evaluation phase. After ranking the 21 lattices, the correct lattice was listed at the top-ranked lattice (Appendix 1—figure 5).

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