Huawei Weng et al. (2005) International Worm Meeting "A web-based searchable image database for C.elegans anatomy."

Huawei Weng, Toni Long, Tylon Stephney, Erik Hyrkas, David H Hall

[International Worm Meeting, 2005]

The Center for C. elegans Anatomy holds an archive of over 200,000 electron micrographs generated by the C. elegans community over the last 30 years including those used in such landmark studies as the reconstruction of the hermaphrodite *(White et al., 1986; Hall et al., 1991). We have been developing a digital image database that will make this material readily available to the community at large. This web-based searchable database will allow C.elegans researchers to efficiently retrieve high resolution TEM images (and later, images from other types of microscopy) over internet. We are using MySQL as a relational database management system, and JAVA, Java Server Page (JSP) and Java Database Connectivity(JDBC) technology to develop the data access and web interface layers. We are scanning archival prints and negatives for wild type and mutants at various magnifications and covering most tissues. Image database features include: 1.Advanced search tools let the user choose an image by creating a query to the database according to sex, age, genotype, body region and tissue type. 2. A browse list that sorts the retrieved images by age, body region and worm name. 3. For each image there are three sizes and associated archival data such as source, age, genotype, fixation method, microscopy method, tissue type, color code etc. stored in the database. Thus the user can scan thumbnails, inspect a medium resolution view, or assess the archival data before downloading the highest resolution image. 4. Data sharing function: an online feedback form allows the user to add their own comments for an individual image; if the user chooses to make it public, comments will be posted as added archival data for that image; alternately they can save it as private with limited access to a selected audience. The project is part of Wormatlas: http://www.wormatlas.org and is supported by NIH RR 12596. *We are grateful for donation of many images from MRC/LMB, U. Wisconsin, U. Missouri, Mt. Sinai Res. Institute, Caltech and others. We welcome further donations of EM images from wild type and mutant studies to our collection.

Robyn Lints et al. (2005) International Worm Meeting "WormAtlas Update"

Zeynep F Altun, Gloria Stephney, David H Hall, Huawei Weng, Robyn Lints, Maurice Volaski, Tylon Stephney

[International Worm Meeting, 2005]

WormAtlas (www.wormatlas.org) is a web site for C. elegans anatomy that uses illustrations, various modes of microscopy and computer models to describe the animals anatomy. As part of our long-term goal to describe C. elegans developmental stages and sexes, we are nearing the completion of the adult hermaphrodite handbook. Recently posted is an informative description of the animals muscle system including a 3D model based on serial section electron micrograph (EM) data that shows the physical relationship between muscle arms and motor neurons. During 2004 we began a handbook dedicated to the male starting with an overview of sexually dimorphic tissues and guides to gender identification. More recent additions include a description of the male musculature containing substantial unpublished data from MRC archives. Working closely with the Male Wiring Project (see Xu et al., this meeting) we have also been posting new male connectivity data as it emerges. Even at this early stage of its description, it is evident that male cell biology differs in a number of ways: some tail neurons are much more branched than is typically observed in C. elegans, many sensory neurons are also motor neurons, and muscles are not necessarily innervated via arms. Our most recent and exciting development is the launch of The Worm Image Database (see Weng et al., this meeting). This database will provide the community with online access to more than 200,000 EM images in our archives, generated by the community over the past 30 years and now housed at the Center for C. elegans Anatomy. This collection includes the MRC series used to reconstruct the hermaphrodite nervous system and the N2Y series currently being used by the Male Wiring Project to reconstruct the male connectivity. This searchable database will later be extended to include light microscopy images. Archival descriptors such as source, stage, gender and preparation method will automatically be retrieved with the images. In future, users will be able to add annotations to the descriptors that may be shared privately among a work group, or publicly with the community at large. The database will not only give users ready access to irreplaceable community resources, but also provide a powerful mechanism for knowledge and data sharing. Our thanks to community members who have generously shared data with our Center.

Zeynep Altun et al. (2006) Neuronal Development, Synaptic Function, and Behavior Meeting "Studying Worm Anatomy Online: WormAtlas And WormImage"

Laura Herndon, Robyn Lints, Zeynep Altun, Huawei Weng, David Hall

[Neuronal Development, Synaptic Function, and Behavior Meeting, 2006]

We have developed two online resources to allow users to learn the anatomy of C. elegans based upon electron microscopic images of the animal, and light micrographs of gfp-labelled animals to illustrate all tissues and cell types. WormAtlas (www.wormatlas.org) is a text-based website that offers several means to study the animal, including on a tissue-based Handbook, a wholistic approach (Slideable Worm), a comprehensive Glossary, and online access to key anatomical publications. One can also explore the cell lineages, the neuronal wiring diagram, and individual pages for each neuron that summarize their anatomy, synaptic interactions and receptors. Most portions of the website have direct links to relevant portions of WormBase (www.wormbase.org) so that one can quickly compare anatomical, molecular and genetic information about a particular cell or tissue. New in 2006 is an improved search function covering the whole website. WormImage (www.wormimage.org) is an online database that can retrieve archival electron microscope data from several laboratories. Many key thin section series are available from the MRC, Missouri and AECOM collections, including male and hermaphrodites, embryos, adults dauer, and larval stages. The site has more than 5000 digital images, most with hand annotations to mark identified cell types. More images are added weekly. The user can search this database by animal name, age, sex, or by regional information (head, midbody, tail) or by tissue types to identify potential images of interest. The program first presents small thumbnail versions so that one can quickly sort among more interesting choices. By clicking on a thumbnail, larger thumbnail versions are quickly retrieved, along with information explaining the source of the image and how the specimen was prepared. Click again on this image, and a still larger image can be retrieved. Full size digital scans are also available on request. We are very grateful to many laboratories that have contributed data to our collections for presentation on these two websites, and to peer reviewers who have helped to check them for accuracy. We welcome your comments on how to improve these resources. We especially thank Igor Antoshechkin (WormBase, Caltech) for his help in upgrading the search function on WormAtlas. This work is funded by NIH RR 12596

Zeynep Altun et al. (2006) Development & Evolution Meeting "Studying Worm Anatomy Online: WormAtlas And WormImage"

Laura Herndon, Huawei Weng, Zeynep Altun, David Hall, Robyn Lints

[Development & Evolution Meeting, 2006]

We have developed two online resources to allow users to learn the anatomy of C. elegans based upon electron microscopic images of the animal, and light micrographs of gfp-labelled animals to illustrate all tissues and cell types. WormAtlas (www.wormatlas.org) is a text-based website that offers several means to study the animal, including on a tissue-based Handbook, a wholistic approach (Slideable Worm), a comprehensive Glossary, and online access to key anatomical publications. One can also explore the cell lineages, the neuronal wiring diagram, and individual pages for each neuron that summarize their anatomy, synaptic interactions and receptors. Most portions of the website have direct links to relevant portions of WormBase (www.wormbase.org) so that one can quickly compare anatomical, molecular and genetic information about a particular cell or tissue. New in 2006 is an improved search function covering the whole website. WormImage (www.wormimage.org) is an online database that can retrieve archival electron microscope data from several laboratories. Many key thin section series are available from the MRC, Missouri and AECOM collections, including male and hermaphrodites, embryos, adults dauer, and larval stages. The site has more than 5000 digital images, most with hand annotations to mark identified cell types. More images are added weekly. The user can search this database by animal name, age, sex, or by regional information (head, midbody, tail) or by tissue types to identify potential images of interest. The program first presents small thumbnail versions so that one can quickly sort among more interesting choices. By clicking on a thumbnail, larger thumbnail versions are quickly retrieved, along with information explaining the source of the image and how the specimen was prepared. Click again on this image, and a still larger image can be retrieved. Full size digital scans are also available on request. We are very grateful to many laboratories that have contributed data to our collections for presentation on these two websites, and to peer reviewers who have helped to check them for accuracy. We welcome your comments on how to improve these resources. This work is funded by NIH RR 12596.

Robyn Lints et al. (2004) East Coast Worm Meeting "Frogs and snails and puppy dog tails? Wormatlas launches a guide to what boy worms are made of."

Robyn Lints, Zeynep F Altun, Huawei Weng, David H Hall, Maurice Volaski, Gloria Stephney

[East Coast Worm Meeting, 2004]

C. elegans is sexually dimorphic, producing hermaphrodite and male sexes that differ from one another in both their morphology and behavior. The hermaphrodite has been studied extensively and over the past three years we have developed a web-based guide to its anatomy (www.wormatlas.org) designed to assist researchers with interests ranging from gene characterization to computational modeling. In addition, The Handbook, Glossary and selected Slideable Worm electron micrographs (EMs) from the site are to be published as a laboratory handbook in the coming year (Cold Spring Harbor Laboratory Press, NY). As part of our long-term objective to describe C. elegans developmental stages and sexes, we are now embarking on a description of the male anatomy. Males differ from hermaphrodites primarily in the reproductive tract and in the tail, which bears the male copulatory apparatus (1, 2). The male has a single-armed gonad containing a germ line that produces only sperm. The tract opens to the exterior at the male anus (cloaca) via a modified rectal epithelial chamber called the proctodeum. The tail copulatory apparatus is organized around this opening and consists of the copulatory spicules, several types of male-specific external sensory organs, interneurons, motor neurons and muscles. Most male-specific cells arise post-embryonically through sex-specific division of precursors common to both sexes. Thus, establishing the adult male form involves the generation and organization of a large number of male-specific cells and their integration into an existing framework of non-sex-specific tissues. Several studies have assigned roles for male-specific cells in fascinating sex-specific behaviors such as mate-searching (3) and copulation (4). However, a full understanding of these behaviors requires a detailed knowledge of the cellular substrates underlying their expression, both at the level of individual cells and the functional units they form through their interconnection. In contrast to the hermaphrodite, the male anatomy is only partially described and, in particular, the connectivity of many male neurons is still unknown. To resolve this problem, we are currently collaborating with the Emmons lab to describe the fine structure and connectivity of individual neurons and other cell types in the male. This project resumes the effort initiated by the MRC in the 1970s to reconstruct the male posterior nervous system from the N2Y EM series. Emerging connectivity data will be incorporated into a web-based guide to the male anatomy. The male anatomy will be presented in a format similar to that used for the hermaphrodite. Additional features we hope to incorporate in the future include a Slideable Male Worm, 3D models of cell shapes generated from EM serial reconstructions and quick-time movies of those important events in a male's life. We anticipate that the male web pages will provide a comparative basis for gene expression or developmental studies and represent a significant advancement on current descriptions of this sex. It is our hope that, through this multi-tiered web-based description and an accompanying handbook, the workings of at least this male sex will become less of a mystery. 1. Horvitz and Sulston (1977) Dev. Biol. 56, 110-156. 2. Sulston et al. (1980) Dev. Biol. 78, 542-576. 3. Lipton and Emmons (2003) J. Neurobiol 54: 93-110. 4. Sternberg and Emmons (1997). In C. elegans II (Eds. Riddle et al., CSHL Press, NY), pp. 295-334.

Robyn Lints et al. (2004) West Coast Worm Meeting "Frogs and snails and puppy dog tails? Wormatlas launches a guide to what boy worms are made of."

Zeynep F Altun, Huawei Weng, Maurice Volaski, Gloria Stephney, Robyn Lints, David H Hall

[West Coast Worm Meeting, 2004]

C. elegans is sexually dimorphic, producing hermaphrodite and male sexes that differ from one another in both their morphology and behavior. The hermaphrodite has been studied extensively and over the past three years we have developed a web-based guide to its anatomy (www.wormatlas.org) designed to assist researchers with interests ranging from gene characterization to computational modeling. In addition, The Handbook, Glossary and selected Slideable Worm electron micrographs (EMs) from the site are to be published as a laboratory handbook in the coming year (with Cold Spring Harbor Laboratory Press, NY). As part of our long-term objective to describe C. elegans developmental stages and sexes, we are now embarking on a description of the male anatomy. Males differ from hermaphrodites primarily in the reproductive tract and in the tail, which bears the male copulatory apparatus (1, 2). The male has a single-armed gonad containing a germ line that produces only sperm. The tract opens to the exterior at the male anus (cloaca) via a modified rectal epithelial chamber called the proctodeum. The tail copulatory apparatus is organized around this opening and consists of the copulatory spicules, several types of male-specific external sensory organs, interneurons, motor neurons and muscles. Most male-specific cells arise post-embryonically through sex-specific division of precursors common to both sexes. Thus, establishing the adult male form involves the generation and organization of a large number of male-specific cells and their integration into an existing framework of non-sex-specific tissues. Several studies have assigned roles for male-specific cells in such fascinating sex-specific behaviors as mate-searching (3) and copulation (4). However, a full understanding of these behaviors requires a detailed knowledge of the cellular substrates underlying their expression, both at the level of individual cells and the functional units they form through their interconnection. In contrast to the hermaphrodite, the male anatomy is only partially described and, in particular, the connectivity of many male neurons is still unknown. To resolve this problem, we are currently collaborating with the Emmons lab to describe the fine structure and connectivity of individual neurons and other cell types in the male. This project resumes the effort initiated by the MRC in the 1970s to reconstruct the male posterior nervous system from the N2Y EM series. Emerging connectivity data will be incorporated into a web-based guide to the male anatomy. The male anatomy will be presented in a format similar to that used for the hermaphrodite. Additional features we hope to incorporate in the future include a Slideable Male Worm, 3D models of cell shapes generated from EM serial reconstructions and quick-time movies of those important events in a male's life. We anticipate that the male web pages will provide a comparative basis for gene expression or developmental studies and represent a significant advancement on current descriptions of this sex. It is our hope that, through this multi-tiered web-based description and an accompanying handbook, the workings of at least this male sex will become less of a mystery. 1. Horvitz and Sulston (1977) Dev. Biol. 56, 110-156. 2. Sulston et al. (1980) Dev. Biol. 78, 542-576. 3. Lipton and Emmons (2003) J. Neurobiol 54: 93-110. 4. Sternberg and Emmons (1997) In C. elegans II (Eds. Riddle et al., CSHL Press, NY), pp. 295-334.

Tylon Stephney et al. (2007) International Worm Meeting "WormImage: An online photo album for C. elegans electron microscopy."

Huawei Weng, Maurice Volaski, David H. Hall, Toni Long, Kevin Fisher, Meng Xu, Tylon Stephney

[International Worm Meeting, 2007]

The Hall lab is the home for the physical EM data for C. elegans that was collected by many scientists working at several key laboratories over the past 40 years. We have almost all of the annotated prints, negatives, data notebooks and often the original thin sections and blocks from the MRC, Missouri, Caltech and AECOM collections, including the work of John White, John Sulston, Sam Ward, and many others. This archive includes wild type and mutant data, and covers both males and hermaphrodites, and all ages from embryo to adulthood, and some aging animals. We are scanning much of this physical print data to produce a digital archive of C. elegans anatomy. We have generated about 3 terabytes of digital images, and there is much more scanning to be done. We have designed a simple online photo album, WormImage, to share some of this archive as small thumbnail versions that can quickly transit across the Internet to all users, for free. Bandwidth issues limit our ability to ship full size scans electronically, but we also supply users with higher resolution scans upon request, by ftp or on DVDs. WormImage (www.wormimage.org) is an online database developed for remote retrieval of this digitized microscopy data. Currently this database contains about 20,000 different digital images. Most scans have been taken from the workprints, to preserve original hand annotations which mark identified cell types. The WormImage database is updated weekly to provide more images. The user can search this database by animal name, age, sex, or by regional information (head, midbody, tail) or by tissue types to identify potential images of interest. The user can quickly survey many animals in small thumbnail images, or concentrate on details of a few images expanded to larger size. The program was recently revised to make it easy for the user to click through all the thumbnails for one animal in serial order. Hall has been reviewing the original annotations and writing brief summaries for each animal, also offered on the website. These Color Code summaries help to translate the shorthand markings on the original prints into the familiar cell names for many structures. During 2007, WormImage will begin showing images of key mutant phenotypes and aging animals. We are grateful to Demian Nave and Art Wetzel at the Pittsburgh Supercomputing Center for their help in providing a mirror site. This work is funded by NIH RR 12596.

Haskell, D. et al. (2017) International Worm Meeting "Forward genetic screen to identify regulators of microRNA strand choice."

Haskell, D., Zinovyeva, A., Li, L.

[International Worm Meeting, 2017]

Precisely controlled gene regulation is essential for proper organism development and homeostasis. A species of small non-coding RNAs called microRNAs (miRNAs) play a critical role in post-transcriptional regulation of gene expression. miRNAs regulate gene expression by binding to partially complementary sites in mRNA targets, repressing their translation, or targeting the mRNA for degradation through recruitment of miRNA induced silencing complex (miRISC) components. One of the key steps in miRNA biogenesis is Dicer-mediated processing of the hairpin precursor miRNA to generate a double stranded miR::miR* duplex. As the miRNA duplex loads into Argonaute, the orientation of the duplex loading dictates which miRNA strand will become the more abundant, mature miRNA. Most of the time, this process of miRNA strand selection is highly asymmetric, with one miRNA strand dominantly selected. It is known that 5' nucleotide (nt) identity and thermodynamic stabilities of the miRNA duplex ends are important determinants of small RNA strand selection in vitro1,2. Interestingly, evidence recently emerged that miRNA strand choice may be regulated in vivo, with miR and miR* levels changing in response to physiological or environmental cues, suggesting the miRNA duplex extrinsic factors may play a role in miRNA strand selection. We have generated a sensor that is designed to differentially express fluorescent proteins based on the relative abundance of miR and miR* strands of a given miRNA. We will use this sensor to conduct a forward genetic screen to identify factors that may be important for miRNA strand selection in vivo. 1 Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43-56 (2010). 2 Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).