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AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

Thomas J Boyle, Zhirong Bao, John I Murray, Carlos L Araya, Robert H Waterston
2006 BMC Bioinformatics  
The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns.  ...  AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data  ...  ZB is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-1813-04). JIM is a Fellow of The Jane Coffin Childs Memorial Fund for Medical Research.  ... 
doi:10.1186/1471-2105-7-275 pmid:16740163 pmcid:PMC1501046 fatcat:xlgqmwjeqvhudiluivmqe7dvvy

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

Leighton H. Duncan, Mark W. Moyle, Lin Shao, Titas Sengupta, Richard Ikegami, Abhishek Kumar, Min Guo, Ryan Christensen, Anthony Santella, Zhirong Bao, Hari Shroff, William Mohler (+1 others)
2019 Journal of Visualized Experiments  
Here, we present an integrated protocol for the examination of neurodevelopment in C. elegans embryos.  ...  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  ...  We also thank the Research Center for Minority Institutions program and the Instituto de Neurobiología Jose del Castillo (Universidad de Puerto Rico) for providing a meeting and brainstorming platform.  ... 
doi:10.3791/59533 pmid:31233035 pmcid:PMC7255390 fatcat:d3bdtwqasvd5necu7yk24nlrja

Integration of information and volume visualization for analysis of cell lineage and gene expression during embryogenesis

Andrej Cedilnik, Jeffrey Baumes, Luis Ibanez, Sean Megason, Brian Wylie, Katy Börner, Matti T. Gröhn, Jinah Park, Jonathan C. Roberts
2008 Visualization and Data Analysis 2008  
However, analyzing the wealth of resulting images requires tools capable of interactively visualizing several different types of information as well as being scalable to terabytes of data.  ...  One of the best places to start gaining insight on the mechanisms by which the genome controls an organism is the study of embryogenesis.  ...  Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04  ... 
doi:10.1117/12.768014 dblp:conf/vda/CedilnikBIMW08 fatcat:pssxclmtwnc4fgpfs6cms37b3u

Automated Lineage and Expression Profiling in LiveCaenorhabditis elegansEmbryos

John Isaac Murray, Zhirong Bao
2012 Cold Spring Harbor Protocols  
These methods can also be used for analysis of reporter expression, cell division timing, and cell position in genetically perturbed embryos.  ...  This protocol describes how to use automated lineage analysis to identify cells in Caenorhabditis elegans embryos expressing fluorescent reporters and how to quantify that expression with cellular resolution  ...  ACKNOWLEDGMENTS We thank members of the Waterston and Bao laboratories for their help in thinking about and developing these methods, especially R. Waterston and T.  ... 
doi:10.1101/pdb.prot070615 pmid:22854571 fatcat:gupj65lo65chvblcloy43fdpsm

Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans

Zhongying Zhao, Thomas J. Boyle, Zhirong Bao, John I. Murray, Barbara Mericle, Robert H. Waterston
2008 Developmental Biology  
To build a framework to address the significance of these features we determined the C. briggsae embryonic cell lineage, using the tools StarryNite and AceTree.  ...  Comparative genomic analysis of important signaling pathways in Caenorhabditis briggsae and Caenorhabditis elegans reveals both conserved features and also differences.  ...  AF16 strain is provided by the Caenorhabditis Genetics Center (CGC) which is supported by the National Institute of Health National Center for Research Resources.  ... 
doi:10.1016/j.ydbio.2007.11.015 pmid:18164284 pmcid:PMC2696483 fatcat:ykyh4cwcrnaw5m4knkxsspdffy

Comparing Cell Division- and Cell Reproduction-based Cell Lineage Analysis for Early Embryogenesis of Caenorhabditis elegans [article]

Shi V. Liu
2017 bioRxiv   pre-print
To see which reconstruction method reflects reality of early embryogenesis of Caenorhabditis elegans, a side-by-side comparison was made between two methods.  ...  A paradigm-shift from cell division- to cell reproduction-based cell lineage analysis is necessary for correct understanding of developmental biology and will lead to a revolution in cell biology and life  ...  I also thank Chang-Zucherburg Initiative for setting the creation of "human-cell atlas" as its focus ( which encouraged me to wrap up my decades-long amateur  ... 
doi:10.1101/199604 fatcat:eqflx7u7indu5dur22zv3qsmse

The AP-2 Transcription Factor APTF-2 Is Required for Neuroblast and Epidermal Morphogenesis in Caenorhabditis elegans Embryogenesis

Yemima Budirahardja, Pei Yi Tan, Thang Doan, Peter Weisdepp, Ronen Zaidel-Bar, Andrew D. Chisholm
2016 PLoS Genetics  
Here, we characterize the aptf-2 (qm27) allele in Caenorhabditis elegans, which carries a point mutation in the conserved DNA binding region of AP-2 TF.  ...  Finally, we found that another AP-2 TF, APTF-4, is also essential for epidermal morphogenesis, in a similar yet independent manner.  ...  Some deletion mutations used in this work were provided by the International C. elegans Gene Knockout Consortium C. elegans Reverse Genetics Core Facility at the University of British Columbia, which is  ... 
doi:10.1371/journal.pgen.1006048 pmid:27176626 pmcid:PMC4866721 fatcat:vrpyaan3p5htdfgugfifrbhlfm

Automated cell lineage tracing in Caenorhabditis elegans

Z. Bao, J. I. Murray, T. Boyle, S. L. Ooi, M. J. Sandel, R. H. Waterston
2006 Proceedings of the National Academy of Sciences of the United States of America  
To exploit this opportunity, we have developed a system for automated cell lineage tracing during C. elegans embryogenesis, based on 3D, time-lapse imaging and automated image analysis.  ...  The invariant cell lineage and cell fate of Caenorhabditis elegans provide a unique opportunity to decode the molecular mechanisms of animal development.  ...  T he nematode Caenorhabditis elegans offers a chance to understand development in molecular detail at the level of the individual cell with temporal resolution of a fraction of the cell cycle.  ... 
doi:10.1073/pnas.0511111103 pmid:16477039 pmcid:PMC1413828 fatcat:sur2uvg2a5cebndzpcvcj3ekwm

Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data

O. Dzyubachyk, R. Jelier, B. Lehner, W. Niessen, E. Meijering
2009 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
In this paper, we present a new algorithm for segmentation and tracking of cells in C. elegans embryogenesis image data.  ...  The nematode Caenorhabditis elegans (C. elegans) is a widely used model organism in biological investigations.  ...  A program (StarryNite [5] ) implementing the mentioned algorithm and a tool (AceTree) for analysis and editing of its results are publicly available online [1] . C.  ... 
doi:10.1109/iembs.2009.5334046 pmid:19964674 fatcat:wsbrzifnxze27ax5g5waz4kyze

Towards 3D in silico modeling of the sea urchin embryonic development

Barbara Rizzi, Nadine Peyrieras
2013 Journal of chemical biology  
for over a century.  ...  Biological circuits function over time at the level of single cells and require a precise analysis of the topology, temporality, and probability of events.  ...  We thank Paul Bourgine for helpful discussions and Yannick Kergosien for critical reading of the manuscript.  ... 
doi:10.1007/s12154-013-0101-x pmid:24386014 pmcid:PMC3877407 fatcat:bfpdzurerzebdih7cdvstnjpbm

Deterministic Nature of Cellular Position Noise During C. elegans Embryogenesis [article]

Xiaoyu Li, Zhiguang Zhao, Weina Xu, Rong Fan, Long Xiao, Xuehua Ma, Zhuo Du
2018 bioRxiv   pre-print
Here, we present a systems-level quantitative and functional analysis of noise in cellular position during embryogenesis, an important phenotype indicating differentiation and morphogenesis.  ...  Cells follow a concordant low-high-low pattern of noise dynamics, and fate specification triggers a global down-regulation of noise that provide a noise-buffering strategy.  ...  ACKNOWLEDGEMENTS This work was supported by grants from the National Natural Science Foundation of China to Z.D. DECLARATION OF INTERESTS The authors declare no competing interests.  ... 
doi:10.1101/385609 fatcat:ojsdjhwnsjcn5b6uvq7b4ylrue

A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress

Julia L. Richards, Amanda L. Zacharias, Travis Walton, Joshua T. Burdick, John Isaac Murray
2013 Developmental Biology  
The invariant lineage of Caenorhabditis elegans has powerful potential for quantifying developmental variability in normal and stressed embryos.  ...  The deep lineage tracing methods provide a powerful tool for analysis of normal development, gene expression and mutants and we provide a graphical user interface to allow other researchers to explore  ...  Acknowledgments We thank Meera Sundaram and members of the Murray laboratory for helpful comments on the manuscript, Thomas Boyle for assistance with AceTree modifications, and Anthony Santella and Zhirong  ... 
doi:10.1016/j.ydbio.2012.11.034 pmid:23220655 pmcid:PMC3548946 fatcat:5k7oid2twnbupfllasdpxoac6m

Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps

Jürgen Hench, Johan Henriksson, Martin Lüppert, Thomas R. Bürglin
2009 Developmental Biology  
The nematode Caenorhabditis elegans has been used as a model for developmental biology for decades.  ...  We find a remarkable degree of stability in the cell positions, as well as little rotational movement, which allowed us to combine the data into a single reference model of C. elegans embryogenesis.  ...  Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR).  ... 
doi:10.1016/j.ydbio.2009.06.014 pmid:19527702 fatcat:stsqrcedubegpfaa6ipqghmwua

Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colon-Ramos, H. Shroff
2011 Proceedings of the National Academy of Sciences of the United States of America  
The Caenorhabditis elegans embryo is a powerful model for studying neural development, but conventional imaging methods are either too slow or phototoxic to take full advantage of this system.  ...  Collecting ∼25,000 volumes over the entirety of embryogenesis enabled in toto visualization of positions and identities of cell nuclei.  ...  The authors declare no conflict of interest. *This Direct Submission article had a prearranged editor. 1 To whom correspondence should be addressed. E-mail:  ... 
doi:10.1073/pnas.1108494108 pmid:22006307 pmcid:PMC3203761 fatcat:cui6lb3x5vfxndwtyvz3qbkkda

System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis of Caenorhabditis elegans [article]

Guoye Guan, Ming-Kin Wong, Vincy Wing Sze Ho, Xiaomeng An, Lu-Yan Chan, Binghui Tian, Zhiyuan Li, Leihan Tang, Zhongying Zhao, Chao Tang
2019 bioRxiv   pre-print
The statistical reference permits a sensitive approach for mutant phenotype analysis, with which we phenotype a total of 1818 mutant embryos by depletion of 758 genes.  ...  To facilitate use of this quantification system, we built a software named STAR 1.0 for visualizing the wild-type reference and mutant phenotype.  ...  The strains were provided by the C. elegans Genetic Center (CGC), which is funded by National Institutes of Health, Office of Research Infrastructure Programs, Grant P40 OD010440.  ... 
doi:10.1101/776062 fatcat:rfvlu6l5cfbtdc2azymbh6mzka
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