Rogers, Anthony S. (2009) International Worm Meeting "WormBase or WormSBase?"

Rogers, Anthony S.

[International Worm Meeting, 2009]

The scale of data produced from biological experiments has grown enormously over recent years. Genome-wide experiments are common and the capacity to sequence whole worm genomes widespread. Both of these provide huge challenges to data providers like WormBase. We have already incorporated the genomes of the five sequenced Caenorhabditis species into WormBase and provide a synteny viewer for visualising regions of genome similarity. We plan to expand this list by adding more distantly related nematode species as they are sequenced allowing a wider community to benefit from the vast amount of knowledge on C. elegans. The addition of data from OMIM about worm orthologs of human disease-associated genes has already made WormBase useful to a wider audience. Researchers working on nematodes of medical or economical importance will also benefit from the infrastructure that WormBase can provide. Working closely with the modENCODE project WormBase will continue integrating large studies such as transcriptome sequencing and CHiP-seq experiments and to develop improved ways to present this to users. Alongside these developments WormBase continues the curation of published scientific literature describing detailed functioning of individual genes. We have developed novel ontologies to describe the anatomy and phenotypes of C. elegans and its mutants and are working to update these to accommodate the other species included in the database.

Anthony Rogers (2008) European Worm Meeting "WormBase Keeps Growing - in all Directions"

Anthony Rogers

[European Worm Meeting, 2008]

WormBase remains the foremost repository for C. elegans research data.. We aim to continue making improvements to the site by maintaining high. quality, manual curation of the literature, incorporating new data types. derived from technological advances and including more comparative species.. Next generation sequencing and genome wide tiling arrays produce vast. quantities of data. WormBase is developing methods to make this data. available to our users through familiar tools such as the Gbrowse based. genome browser.. We will use our existing infrastructure and technologies to provide. consistent access to the other nematode species for which genome sequencing. projects are planned. Providing an environment where easy comparison. between multiple species will be one of the major challenges for WormBase. in the future. We will be including species whose main usefulness will be. as comparators for C. elegans along with species of agricultural and. medical importance.. Many of the species being added will have little or no manual annotation.. WormBase will provide several mechanisms to allow community annotation.. Do not add objects such as pictures, boxes, headers, footers, footnotes,. etc.

Anthony S Rogers (2005) International Worm Meeting "Full Length Transcripts in WormBase"

Anthony S Rogers

[International Worm Meeting, 2005]

UnTranslated Regions (UTRs) of messenger RNAs have been shown to be important in the regulation of several C.elegans genes such as tra-2(1) and fem-3(2). To give an improved representation of UTR regions in WormBase predicted full length transcripts are now generated each release. These are built up automatically from the available transcript data and the current CDS structure. Non-genomic transcript sequence such as Trans-spliced leaders and polyA tails are masked before aligning the transcript to the genome using BLAT(3). Identifying TSL and polyA sequences prior to genome alignment helps to prevent misalignments and means individual features can be made to represent these sequences. UTR structures are built from the subset of transcripts which have been computationally shown to agree with the CDS prediction. This new method of representing full length transcripts allows us to build objects that more closely resemble their biological reality with trans-spliced leader sequence and polyadenylation information included where applicable. It is also possible to show where there is evidence of multiple UTRs for a single CDS.As of WS140 there are 25869 transcripts derived from 22410 CDSs representing the 19735 protein coding genes. 1) Translational regulation of tra-2 by its 3' untranslated region controls sexual identity in C.elegans Goodwin EB, Okkema PG, Evans TC and Kimble J. Cell, 1993 75:329-339 2) Control of the sperm-oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3' untranslated region. Ahringer JA, Kimble JE Nature, 1991 349:346-348 3) BLAT The BLAST-Like Alignment Tool W. James Kent. Genome Research (2002) Vol. 12, Issue 4, 656-664

Anthony Otsuka et al. (2007) International Worm Meeting "Analysis of C. elegans CLASP2."

Anthony Otsuka, Myeongwoo Lee, Jeong Ahn, Catherine McDonald, Gamuchirainyasha Machekanyanga, Stephanie Burge

[International Worm Meeting, 2007]

CLASP2 is a member of the +TIP group of proteins that are found at the plus-ends of growing microtubules. Plus TIPs include such proteins as CLIP, APC, and EB1. CLASP2 is involved in chromosome capture by growing spindle microtubules and in the directional movement of cell edges in migration and growth cone extension. We have found that CLASP2 interacts with UNC-44 AO13 ankyrin in yeast two hybrids. To study the function of CLASP2 in C. elegans, GFP fusions were created with either the CLASP2 (cls-2) promoter (pAO402) or with the full-length cls-2 coding region (pAO398). The patterns of CLASP2 antibody staining and CLASP2 transgene expression differed. Antibody staining occurred throughout the animal, but was strong in the gonad, several lateral cells, and structures in the head. Transgenic CLASP2-GFP animals showed strong expression in several cells, including posterior intestinal cells, nerves in the pharynx, and nerves in the anterior and posterior of the worm, but low levels of expression in the gonad. In dividing cells, CLASP2-GFP is localized to mitotic structures, including chromosomes and spindles. CLASP2-GFP did not interfere with cell division and may be a useful tool for real time analysis of mitosis.

Anthony Rogers et al. (2006) European Worm Meeting "WormBase: Recent and Future Developments"

Anthony Rogers, The WormBase Consortium

[European Worm Meeting, 2006]

Anthony Rogers1, The WormBase Consortium1234. WormBase is a database concerned primarily with providing current and comprehensive information on the genome and genetics of Caenorhabditis elegans. As more nematode worm genomes are being sequenced WormBase attempts to make this data available to the scientific community in a convenient and familiar fashion. We are constantly developing and evaluating new analyses and tools to help users make the most of this wealth of data. Recent developments have included the incorporation of external data sets such as InParanoid, COGS and TreeFam, Vancouver fosmid mappings and nematode EST clusters from NEMBASE and Nematode Net, amongst others.. As well as adding new data and features, our recent user survey indicated that some of the things weve been doing for a long time are still important. Correct gene structures were a high priority for the majority of respondents. We constantly review these in light of new data and user submissions. As more worm genome sequences become available they will give us more valuable comparative data for determining gene structures and other genomic sequence features. WormBase will play a central role in making the new genome data available in a timely manner. We will also be taking advantage of the COMPARA system developed for EnsEMBL to analyse and display this multispecies data.. To increase the accessibility of this data we have developed WormMart, a BioMart based data-warehouse including an easy-to-use wizard style query tool. The functionality of GBrowse has been enhanced, giving the ability to create genetic and physical maps. Web site speed has been an issue in the past and we have addressed this by restructuring the web site code, hardware and data management strategies. The establishment of a second European mirror in the UK should be of particular help to conference delegates.

Anthony Otsuka et al. (2008) C.elegans Neuronal Development Meeting "Localization of CLASP2 in C. elegans"

Catherine MacDonald, Anthony Otsuka, Stephanie Burge, Gamuchirainyasha Machekanyanga, Myeongwoo Lee, Ping Gong, Jeong Ahn

[C.elegans Neuronal Development Meeting, 2008]

CLASP2 is a +TIP protein that is found at the leading edges of growth cones and migrating cells. It also plays an important role in mitosis. We have characterized CLASP2 by confocal microscopy using either CLASP2 antibodies (kind gift of A. Desai and K. Oegema) or transgenic CLASP2-GFP protein fusions. There are similarities and differences between endogenous and transgenic CLASP localization. For example, in cells of transgenic embryos, there are peripheral loops of bundled microtubules that are not seen in non-transgenic animals. High levels of CLASP2 are known to cause such loops in other systems. By confocal microscopy, it was possible to observe the details of CLASP2 antibody staining in many cells. While phalloidin-FITC did not strongly stain the cell periphery, CLASP2 staining was observed at the cell cortex. The pattern of CLASP2 staining changed from cytoplasmic in interphase cells to parachromosomal in dividing cells. The centrosomes also stained in many cells. In the hermaphrodite gonad, there was CLASP2 staining of material in the rachis and ring-like structures around the developing germinal vesicles. In newly fertilized eggs, there were peripheral wisps of CLASP2. In addition, there was a CLASP2-labeled terminal plaque containing several DNA molecules which may be an intermediate accompanying fertilization. In larval stages, there was strong CLASP2 staining at the apical junctions of intestinal cells, a few somatic cells, and at the nerve ring. For transgenic animals, CLASP2-GFP expressed from the CLASP2 promoter was found in several cell types, including neurons, muscle, and intestinal cells. CLASP2-GFP was strongly expressed in gland cells, such as pharyngeal g1 and g2, posterior glands, and the excretory canal cell.

Santella, Anthony et al. (2013) International Worm Meeting "Towards the Complete Embryonic Cell Lineage."

Bao, Zhirong, Santella, Anthony, Yu, Zidong, Shroff, Hari, Wu, Yicong, Du, Zhuo

[International Worm Meeting, 2013]

The invariant lineage has been a cornerstone of C. elegans biology. John Sulston's initial lineage 30 years ago used multiple embryos to assemble the invariant pattern. Complete continuous lineaging has never been performed for a single animal. While image analysis software has facilitated lineage creation during early embryogenesis, embryo movement at later stages has hampered the analysis of later development. We have made progress towards lineage tracing during this developmental period through a combination of innovative computational and imaging methods. Our efforts on image analysis are focused on the challenge of reliably following small and crowded nuclei over long periods of time in under sampled images. Our nuclear detection method uses per slice segmentation and a learned shape model to robustly detect and segment nuclei in crowded configurations. The detection results are merged into a cell lineage using multiple linking steps, which select from a set of possible causes and actions, including cell movements, divisions, or detection errors. This is based on probabilistic models of nuclear appearance and local spatial configuration. These computational improvements are bolstered by a qualitative improvement in image quality through the dual-view inverted Selective Plane Illumination Microscope (diSPIM), which captures isotropically sampled volumes at speeds that largely eliminate motion artifacts even through the final stage of embryogenesis. We anticipate that our combined effort will allow not just lineage tracing, but that the detailed dynamics of development (including cell positions and expression patterns) can be followed at high spatiotemporal resolution to build a quantitative model of development. A long term application is the production of WormGUIDES, a 4D atlas tracking both cell positions and neuronal outgrowth.

Santella, Anthony et al. (2015) International Worm Meeting "WormGUIDES: The Making of the Worm's Nervous System."

Wu, Yicong, Shroff, Hari, Catena, Raul, Kovacevic, Ismar, Christensen, Ryan, Marquina-Solis, Javier, Santella, Anthony, Mohler, William A., Kumar, Abhishek, Bao, Zhirong, Moyle, Mark, Colon-Ramos, Daniel

[International Worm Meeting, 2015]

WormGUIDES is a 4D interactive atlas of C. elegans embryogenesis. Its purpose is to support the exploration and analysis of embryogenesis at the molecular, cellular, tissue and organism levels. The current WormGUIDES release contains a minute-by-minute record of nuclear positions for all cells until twitching. Current efforts focus on adding records of 3D cell morphology to reconstruct neural morphogenesis and the dynamics of neurite outgrowth. Our strategy consists of acquiring 3D time-lapse images of embryogenesis using promoter-driven fluorescent markers to sparsely label subsets of neurons. Ubiquitous histone markers enable automated lineaging to identify cells and align datasets acquired from different embryos into a digital composite record.Data from our initial set of markers reveals dynamic processes that contribute to the architecture of the major neural organs such as the nerve ring, ventral nerve cord and the head nerve bundles. Much of this morphogenesis occurs before twitching. Surprisingly, some morphogenetic modules are formed in neural progenitors and maintained through two cell cycles. Perturbations suggest novel collective cell behaviors and unexpected roles for surrounding tissue in shaping the nervous system.Lineage-based cell identification has yielded a list of approximately 50 neurons that are currently being tracked and segmented. These cells account for about a quarter of embryonic neurons and include critical components of the major neural structures. To support the throughput needed for systematic reconstruction, we have developed computational pipelines for semi-automated segmentation and alignment of cell shapes from multiple embryos and markers. In addition, we have developed computational tools to untwist the elongating embryo and trace post-twitching events. We are making additional markers, and developing a desktop application extending the current mobile app. Ultimately, the goal is to produce a complete, dynamic record of the assembly of the C. elegans connectome.

Anthony J Flemming et al. (2001) International C. elegans Meeting "Nuclear Powered Growth in Nematodes."

Anthony J Flemming, Scott W Emmons, Armand M Leroi, Zai-Zhong Shen, Ana Cunha

[International C. elegans Meeting, 2001]

Most of the hypodermis of a Rhabditid nematode such as Caenorhabditis elegans is a single syncitium. The size of this syncitium (as measured by body size) has evolved repeatedly in the Rhabditid nematodes. Two cellular mechanisms are important in the evolution of body size: changes in the numbers of cells that fuse with the syncitium, and syncitial growth that is independent of cell division. Thus nematodes differ from mammals and other invertebrates in which body size evolution is caused by changes in cell number alone. The evolution of syncitial growth without cell division in nematodes is associated with changes in the ploidy of hypodermal nuclei. These nuclei are polyploid as a consequence of iterative rounds of endoreduplication, and the extent of polyploidy has evolved repeatedly. The association between syncitial growth and endoreduplication is not only seen among species, but also within species with the smaller males of sexual taxa being hypo-endoreduplicated relative to the female or hermaphrodite. Furthermore, this association is also seen in C. elegans with mutations which interrupt TGF-beta signalling and which result in dwarfism and deficiencies in hypodermal ploidy. The TGF-beta pathway is a candidate for being involved in nematode body size evolution.

Santella, Anthony et al. (2011) International Worm Meeting "Cell lineaging for single cell, high throughput analysis."

Bao, Zhirong, Santella, Anthony

[International Worm Meeting, 2011]

The study of embryonic phenotypes at high detail and large scale requires accurate and fast assembly of detected nuclei into a cell lineage. Accuracy is essential. Every error limits analysis, requiring either manual correction or a retreat from the goal of single cell tracking. In addition, high throughput work limits the effort that can be spent on correction and quality control of results. The time it would take to confirm, unguided, the correctness of even a perfectly accurate cell lineage may be unsupportable. As such, a measure of the local reliability of results is just as important as low error. Existing methods do not to provide this combination of features. Common, simple methods such as nearest neighbor association across time are error prone and lack a model that can provide confidence in results. More sophisticated general tracking methods such as particle filters lack an explicit model of cell division, a key source of ambiguity and error. These requirements lead to an approach that scores lineage configurations against a learned model. The key design decision is what aspects of the lineage, as revealed via imaging and cell detection, to include in the model used to judge alternative tree configurations. Our desire is for a general method applicable to any embryo capable of normal cell division. As such, we model key local behaviors of nuclei, firstly their individual change over time (in appearance and position), and secondly the correlation in these measures expected between daughter cells at division. We also model two key aspects of the detection method that provides the raw nuclear positions for lineage assembly, firstly the relationship between nuclear appearance and the probability of a detection being a false positive and secondly the probability of a hypothesized series of detection failures. This model, which can be learned from a set of corrected lineages, is relatively simple but sufficient to produce accurate results and to highlight ambiguous areas for human inspection.