5 Papers found (0.008 seconds)

Duncan, Leighton H. et al. (2017) International Worm Meeting "A promoter database for embryonic neurodevelopment."

Bao, Zhirong, Mohler, William, Shah, Pavak, Duncan, Leighton H., Moyle1, Mark, Kumar, Abhishek, Santella, Anthony, Ikegami, Richard, Sengupta, Titas, Christensen, Ryan, Colon-Ramos, Daniel, Shroff, Hari

[

International Worm Meeting,

2017]

WormGUIDES (Global Understanding in Dynamic Embryonic Systems) is a systems-level resource that facilitates examination of cellular decisions in the developing nervous system of C. elegans. To build this resource we have designed strategies for labeling neurons during early development. There are 198 neurons that extend processes in the C. elegans embryo, and they can be categorized into fifteen neuronal structures. By examining system-level resources such as WormBase, WormAtlas, and EPIC (Expression Patterns in Caenorhabditis) databases as a resource for this selection, we have identified a panel of 182 transcriptional promoters that are predicted to sparsely label these 198 neurons. By systematically examining this list, we have identified 28 promoters that label single neuron classes in the embryo, and 74 promoters that label two to five neuron classes each. In addition, we have implemented an imaging and cell identification pipeline that allows us to determine the dynamic expression pattern (via cell-lineaging) during the development of the embryo. We have also built a neuronal promoter database (http://promoters.wormguides.org/) to share our findings with the community. The promoter database enables researchers to submit promoters of interest, which are then imaged throughout embryogenesis and the expression patterns determined via cell-lineaging. We have combined lineaging with imaging for the precise identification of labeled neuronal classes and neurite fascicles during early nervous system development in the embryo. This service will benefit individual investigators, while providing us, and the community, with new tools to examine the nervous system during early embryonic development. In this manner our atlas builds on the C. elegans community's open-sharing of systems-level knowledge and resources and enhances the value of C. elegans as a model organism.

Sengupta, Titas et al. (2021) International Worm Meeting "A retrograde zippering mechanism regulates neurite placement in the C. elegans nerve ring"

Koonce, Noelle, Santella, Anthony, Bao, Zhirong, Wu, Yicong, Moyle, Mark, Han, Xiaofei, Fan, Li, Shroff, Hari, Mohler, William, Colon-Ramos, Daniel, Shao, Lin, Vazquez-Martinez, Nabor, Duncan, Leighton, Sengupta, Titas

[

International Worm Meeting,

2021]

A fundamental design principle of nervous systems is the grouping of neuronal contacts into layers within nerve bundles. The layered arrangement of neurites requires nanoscale precision in their placement within bundles, and this precision, which cannot be exclusively explained by simple tip-directed outgrowth dynamics, underpins synaptic specificity and circuit architecture. Here we implement novel imaging methods to document the specific placement of single neurites during the assembly of the C. elegans nerve ring. We uncover a retrograde zippering mechanism that controls precise placement of neurites along specific layers. Nanoscale precision in neurite placement is orchestrated via temporally-regulated expression of Ig adhesion molecule SYG-1. SYG-1 acts as an instructive signal, defining layer boundaries and guiding neurite zippering onto target neurons. SYG-1 acts through its canonical ligand SYG-2 and SYG-1 extracellular domains are sufficient for instructing neurite placement. Our study suggests that adhesion-mediated retrograde zippering might be an important developmental mechanism that coordinates neurite placement and synaptic connectivity within brain neuropil bundles in vivo.

Santella, Anthony et al. (2017) International Worm Meeting "WormGUIDES: Assembling and Accessing an Integrated Record of Neural Development."

[

International Worm Meeting,

2017]

WormGUIDES is an interactive 4D atlas of C. elegans embryogenesis. Its goals are to (1) provide a model of neural development based on detailed time lapse measurements of nuclear positions and neurite outgrowth; (2) cross reference worm community data with the 4D model and (3) provide an easy to use visualization platform for exploring, understanding and annotating the model and sharing insights. The major tracts of the adult nervous system are laid out early and added to over time. By the 1.5 fold stage many major structures are established. The nerve ring (NR) forms a complete loop that includes dorsal and ventral cells. Sensory nerves have extended to the dent, and the amphid commissure is established. Motor neurons in the VNC have intercalated and others have extended into the VNC and toward the NR. The early emergence of tracts motivates a hierarchal approach to modeling and measuring neural development. Our model contains three levels of structure: (1) Tracts, major nerve tracts; (2) Multi-cellular structures, small groups of co-labeled neurons; and (3) Individual cells. The latter two include cell bodies as well as fascicules or individual neurites. Neurites are threaded through the tracts based on measured lengths and tip positions to minimize noise in alignment and maximize legibility. The current model contains 9 tracts representing the amphid sensory nerves, amphid commissures, NR, VNC and connections, 21 neurons (5 single cell) and nuclear positions up to twitching. We have mapped 6 groups of neurites in the NR with stereotypical positions involving 30 neurons, and sorted the 38 ventral-going amphid commissure axons into 4 temporal groups. 182 markers slated for analysis cover almost all neurons. Stochastic labeling by heat shock, mosaicism of reporter arrays and single cell photo conversion are being pursued to distinguish intertwined neurons. Additional imaging and analysis tools are being developed to push our model to hatching. The wormguides.org website provides comprehensive information on the project, access to our reagents and image data, and a download of the latest atlas. We accept nomination of markers and cells as priorities, and promote sharing of user-driven annotations of developmental processes.

Christensen, Ryan et al. (2021) International Worm Meeting "A partial nuclear atlas of the post-twitching Caenorhabditis elegans embryo"

[

International Worm Meeting,

2021]

The limited number of cells and invariant cell lineage of the Caenorhabditis elegans embryo make it an excellent system for examining complex developmental events, such as tissue movement and neurodevelopment. Prior work from the WormGUIDES project has digitized the position of all nuclei for the first half of embryogenesis, creating a computational map of the embryo that can be used to overlay developmentally relevant information like gene expression or neurite outgrowth. Creating a similar map for the second half of embryogenesis is difficult due to embryo elongation and movement. We have developed software to computationally untwist the moving embryo, allowing for analysis of cell position during this period of development, and have begun expanding our computational map into the second half of embryogenesis. Our current map includes 202 nuclei across the embryo, including 32 neuronal nuclei, 81 body wall muscle nuclei, 20 intestinal, and 20 seam cell nuclei. We also include a tract-based model of the nerve ring, showing how it is positioned relative to neuronal and body wall muscle nuclei as the embryo elongates. In addition to our partial nuclear atlas, we describe improvements to our untwisting and tracking workflow, including a deep-learning image restoration capability which improves image quality during rapid embryo movements, and a semi-automated tracking upgrade to our untwisting software which improves tracking throughput. As we continue to add nuclei and neuronal morphology to the atlas, we plan to integrate our post twitching model with previous pre-twitching work to develop a digital atlas spanning the entirety of embryogenesis.

Pourkarimi, Ehsan et al. (2017) International Worm Meeting "Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans."

Pourkarimi, Ehsan, Whitehouse , Iestyn, Bellush, James

[

International Worm Meeting,

2017]

During DNA replication Half of the genome is duplicated discontinuously on the lagging strand in the form of Okazaki Fragments (OFs). Despite many years of research, the precise location of replication origins, efficiency, and abundance in metazoa remains elusive. We have recently isolated and sequenced OFs from C. elegans embryos and developing larva, and have generated a first comprehensive genome wide map of DNA replication in multi cellular organism1. Aligning sequence reads of OFs to the C. elegans genome reveals the complementary enrichment of Okazaki fragments to either the Watson or Crick strands, which is the hallmark of a replication origin1,2. Importantly, we found that replication origins are associated with transcriptionally active regions of chromatin and replication start sites are strongly associated with histone modifications that define genetic enhancers such as H3K27 acetylation. By mapping DNA replication origins in various embryonic stages, we have demonstrated that origins are pre-defined prior to the onset of zygotic transcription. However, at the time of gastrulation, when zygotic transcription initiates, it does so in proximity of pre- defined replication origins. Replication origins and transcription are correlated until the last wave of embryonic cell division. When cell division ceases, this association breaks down and transcription shifts away from replication initiation sites and anti-correlates with replication origins in differentiated cells. Whilst majority of embryonic cells are terminally differentiated at the time of hatching, 53 somatic blast cells in newly hatched L1 larvae divide post embryonically to generate additional 403 cells in C. elegans hermaphrodites. The majority of the somatic blast cell lineage generate vulva, muscle, hypodermal, and neuronal cells. We have shown that the position and the efficiency of somatic replication origins are distinguishable from the embryonic origins yet remain associated with somatic H3K27 acetylation. Interestingly, genes located in proximity of somatic replication start sites are functionally related to vulva, muscle, hypodermal and neuronal cells. Our data strongly suggest that in rapidly dividing embryonic cells, replication is a fundamental regulator of gene activity, while during notably slower post embryonic cell division, transcriptional activity shapes the DNA replication profile. Currently we are investigating the causal link between transcription and somatic replication. 1.Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans. Ehsan Pourkarimi, James M Bellush, Iestyn Whitehouse. eLIFE, 2016. 2. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Duncan J. Smith & Iestyn Whitehouse. Nature, 2012