Wolkow, C.A. et al. (2015) International Worm Meeting "What's new with WormAtlas?"

Altun, Z.F., Herndon, L.A., Wolkow, C.A., Fisher, K., Hall, D.H., Crocker, C.

[International Worm Meeting, 2015]

Over the past two years WormAtlas has added new content and many new features. 1) The Dauer Handbook has doubled in size and is now complete. This Handbook offers 12 chapters describing the basics of dauer anatomy, organized by tissue type. We also continue to curate and update the Adult Hermaphrodite and Male Handbooks. 2) The Individual Neuron pages have been extensively updated to include information on neurotransmitter and receptor specificity. To better convey the developmental dynamics in the origins of individual neurons, videos illustrating neuronal development and patterning in the embryo have been added for many of the C. elegans neurons. Videos were created by Anthony Santella & Zhirong Bao. 3) SlidableWorm has been expanded to include head and tail sections of the adult male. Currently, SlidableWorm offers over 100 annotated sections from the adult hermaphrodite. Work continues towards greater coverage of the hermaphrodite and male bodies. 4) An extensive collection of micrographs from aging adults has been added to WormImage. This collection describes adults at young, middle and old age and is annotated with locomotory data and aging class for each adult (Herndon et al., 2002). WormImage welcomes further contributions to the EM archive. 5) WormAtlas has expanded its collection of archived papers and has reformatted the HTML version of classic C. elegans publications, including doctoral theses, to make them more accessible to users. 6) WormAtlas continues to make the handbook content accessible to mobile devices for the ease and convenience of all users. We are grateful to continued funding from NIH OD 010943.

Herndon, L.A. et al. (2011) International Worm Meeting "New and Improved: WormImage 2.0 and WormAtlas Mobile."

Herndon, L.A., Hall, D.H., Altun, Z.F., Xu, M., Stephney, T., Wolkow, C.A., Crocker, C., Fisher, K.

[International Worm Meeting, 2011]

We announce the release of WormImage 2.0. The WormImage database houses over 55,000 unpublished electron micrographs and their related metadata. This new version of WormImage still includes access to this enormous collection of C. elegans micrographs, but now features a new look and a new search interface making the data more easily accessible to users. To streamline the website, users can now search directly from the front page. As before, search criteria allow users to narrow results by sex, genotype, age, body portion and tissue type of the animal, but now this is found all on one page. Additionally, with new expandable menu options, one can now select a single tissue or multiple tissue types with just a few clicks. Search results are presented in a new format that is simpler, making it easier to screen through and navigate among all the images. The dataset offered by WormImage continues to expand and welcomes all laboratories to share their best archival TEM and SEM images so that this resource can continue to grow and serve the C. elegans community. The WormAtlas website is also growing and changing. To adapt to the increased demand for mobile-ready content, WormAtlas is now available in a format optimized for access from mobile devices. This allows for users to quickly navigate through the handbook chapters without worrying about zooming in on small icons and menu bars. We are also pleased to announce that WormAtlas will soon feature a new handbook section on the Dauer Larva. Sections for this new handbook will be posted as they become available. In addition to adding new content, we are also continually updating material on WormAtlas to keep the information available to users current. As such, the Individual Neuron pages are being revised and feature new images and data. Slidable Worm is expanding as well, with the ongoing addition of new slices. This work is supported by NIHRR 12596 to DHH.

Herndon, L. A. et al. (2013) International Worm Meeting "WormAtlas Update."

Wolkow, C. A., Altun, Z. F., Hall, D. H., Crocker, C., Fisher, K., Herndon, L. A.

[International Worm Meeting, 2013]

Since its inception in 2001, WormAtlas has added new features and become more user friendly each year. New additions since the last International Meeting include: 1) A new Handbook on the anatomy of the Dauer Larva consisting of 6 chapters, with more on the way. Many Handbook chapters for the adult Hermaphrodite have been updated to include recent findings, new references, illustrative movies, and more links. For the future, we are planning new Handbooks that will feature the anatomy of the Embryo and of Aging worms. 2) An updated version of the Pharynx Atlas uses a rollover cell identification function to allow users to link to pages with detailed descriptions of each pharyngeal cell in the terminal bulb. New movies have been added to illustrate patterning during embryonic pharynx development. 3) Many Individual Neuron pages have been added or substantially revised, adding more recent data on gene expression patterns. 4) The Neurons and Circuits section is expanding, with a comprehensive new Table of Neurotransmitter and Neuropeptide Receptors for C. elegans, plus links to new initiatives such as the WormWiring website. 5) The Anatomical Methods section has been updated and now includes new techniques and detailed protocols for high resolution EM studies and "connectomics". 6) SlidableWorm has a new interface and has many more sections available. Users can now access transverse cross-sections of C. elegans by moving a cursor along the length of the worm to select which slice to visualize. There are four different ways to view the electron micrograph sections: with no annotation, with labels and with tissue highlighting displayed as either a transparent or an opaque overlay. 7) WormImage 2.0 has a new look and new search interface making data more easily accessible, first introduced at the last meeting. WormImage now includes virtually every well-annotated animal received from the MRC EM archive of Brenner, White and colleagues. We welcome further contributions from the community to this archive. 8) WormAtlas offers mobile users better access to its content. All Handbooks are now available in a format optimized for browsing from mobile devices. This work is supported by NIH OD 010943 to DHH.

Nelson, Matthew et al. (2013) International Worm Meeting "NLP-22 is a Neuromedin S-like neuropeptide which regulates behavioral quiescence."

Raizen, David, Nelson, Matthew

[International Worm Meeting, 2013]

Sleep behavior in C. elegans occurs in association with larval molts during the four lethargus stages. Neuropeptides are small centrally secreted signaling molecules which play a central role during the regulation of sleep in mammals and flies (Crocker and Sehgal, 2010). However, roles for neuropeptide signaling during C. elegans sleep regulation are just beginning to be identified. We have found that nlp-22 regulates sleep during lethargus and has both structural and functional similarities with the human neuropeptide neuromedin S (NMS). NMS is an anorexigenic neuropeptide, which shows a circadian pattern of expression and is expressed in a small subset of neurons in the brain, specifically in the superchiasmatic nucleus, a master circadian regulatory region (Ida et al, 2005; Mori et al, 2005). Both NMS and nlp-22 have a FRP motif at or near their C-terminus. Simliar to NMS, nlp-22 over-expression during normally active stages causes locomotion and feeding cessation. nlp-22 mRNA shows cyclical expression in synchrony with the molting/lethargus cycle. NLP-22 signals downstream of LIN-42/PER. We find that nlp-22 is expressed in a single pair of head interneurons, the RIAs. In addition, we find that reduction of nlp-22 function results in reduced sleep during lethargus. The similar structure, relationship to a PER/LIN-42 based clock, restricted nature of expression and anorexigenic effects of NLP-22 and NMS, suggest that FRP neuropeptides serve an ancient role in the regulation of feeding and sleep.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Antika TR et al. (2023) J Biol Chem "Sequence-specific targeting of C. elegans C-Ala to the D-loop of tRNAAla."

Horng JC, Hsu HL, Nazilah KR, Wang CC, Wang TL, Wang SC, Antika TR, Chuang TH, Chrestella DJ, Wang SW, Tseng YK, Pan HC

[J Biol Chem, 2023]

Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Ala_c) robustly binds both ligands. How Ce-C-Ala_c targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Ala_c are responsible for DNA and tRNA binding, respectively. Ce-C-Ala_c specifically recognized the conserved invariant base G¹⁸ in the D-loop of tRNA^Ala through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala (Ce-C-Ala_m) robustly bound both tRNA^Ala and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNA^Ala.

Blumenthal TE et al. (1994) Worm Breeder's Gazette "C. elegans U2AF 65."

Zorio DAR, Lea K, Blumenthal TE

[Worm Breeder's Gazette, 1994]

C. elegans U2AF65

Oomura, S. et al. (2019) International Worm Meeting "Early embryogenesis of C. inopinata, a sibling species of C.elegans."

Matsumura, Y., Haruta, N., Hoshi, Y., Sugimoto, A., Oomura, S.

[International Worm Meeting, 2019]

C. inopinata is a newly discovered sibling species of C. elegans. Despite their phylogenetic closeness, they have many differences in morphology and ecology. For example, while C. elegans is hermaphroditic, C. inopinata is gonochoristic; C. inopinata is nearly twice as long as C. elegans. A comparative analysis of C. elegans and C. inopinata enables us to study how genomic changes cause these phenotypic differences. In this study, we focused on early embryogenesis of C. inopinata. First, by the microparticle bombardment method we made a C. inopinata line that express GFP::histone in whole body, and compared the early embryogenesis with C. elegans by DIC and fluorescent live imaging. We found that the position of pronuclei and polar bodies were different between these two species. In C. elegans, the female and male pronuclei first become visible in anterior and posterior sides, respectively, then they meet at the center of embryo. On the other hand, the initial position of pronuclei were more closely located in C. inopinata. Also, the polar bodies usually appear in the anterior side of embryo in C. elegans, but they appeared at random positions in C. inopinata. Therefore, we infer that C. inopinata may have a different polarity formation mechanism from that in C. elegans. We are also analyzing temperature dependency of embryogenesis in C. inopinata, whose optimal temperature is ~7 degree higher than that in C. elegans.

Guven K (1995) Journal of Thermal Biology "Differential expression of hsp70 proteins in response to heat and cadmium in Caenorhabditis elegans."

Guven K

[Journal of Thermal Biology, 1995]

1. The patterns of HSP70 expression induced in Caenorhabditis elegans by mild (31 degrees C) or severe (34 degrees C) heat shock, and by cadmium ions at 31 degrees C, have been compared with those expressed constitutively ill 20 degrees C controls by 1- and a-dimensional immunoblotting. 2. The 2D spot patterns become more complex with increasing severity of stress (34 degrees C > 31 degrees C + Cd > 31 degrees C > 20 degrees C). 3. A stress-inducible transgene construct is minimally active at 31 degrees C, but is abundantly expressed in the presence of cadmium or at 34 degrees C. 4. Differing degrees or types of stress may differentially induce available hsp70