-
[
Microsc Microanal,
2005]
Extended abstract of a paper presented at Microscopy and Microanalysis 2005 in Honolulu, Hawaii, USA, July 31--August 4, 2005.
-
[
Japanese Worm Meeting,
2002]
The synaptic connectivity of C. elegans is well known from observations of the somatic system by White et al. and those of the pharyngeal system by Albertson et al. So far, three databases were constructed for computational usage by Achacoso et al. and Durbin, and recently in WormBase. However, they lack some data such as those in tables of White's paper and those in figures of Albertson's book. Our database (K. Oshio, S. Morita, Y. Osana and K. Oka: Technical Report of CCEP, Keio Future No.1, 1998) includes all data described in White's paper and Albertson's book. Unfortunately, some mistakes were found in the database through private communications with John White who is the author of White's paper and with the users of the database. Thus we have been proceeding with the revision to make it perfect one. We are planning to complete the revision in September 2002. The database should be worthwhile not only for neurophysiological studies, but also for post-genomic interests mediating genomes and behavior.
-
[
International Worm Meeting,
2005]
We have developed a computational model of vulval precursor cell (VPC) fate specification. This model is capable of reproducing essentially all of the experimental observations reported in a subset of papers that form the basis of our initial understanding of this process. Since this model is mechanism-based, it is also capable of predicting outcomes of new experiments. Our results demonstrate that the development of such computational models can be helpful in integrating the complex, dynamic behaviors of biological systems. The generic nature of the tool and methodologies used for this project enables the natural extension of our model to other aspects of C. elegans biology. We used the language of LSCs and the Play-Engine tool to build a model that dynamically recapitulates the experiments presented in three seminal papers [Sternberg and Horvitz (1986); Sternberg (1988); Sternberg and Horvitz (1989)]. Our model is driven by biological mechanisms inferred from results reported in these papers as well as several more recent papers. The Play-Engine allows both experiments and mechanistic hypotheses to be entered in a user-friendly manner via the manipulation of a graphical user interface (GUI). The GUI also reflects the dynamic representation of the computer-executed simulations. In constructing the model, we represented all of the biological behaviors and phenomena referred to in these papers including developmental time, cell movements, gradient formation, cell fate assumption, variable biological outcomes, and inter- and intra-cellular signaling. The model enables the user to perform all experimental perturbations described in these papers, including cell ablations and genetic manipulations. The construction and analysis of our model of VPC fate specification enhanced our understanding of this biological process in several ways. First, we identified mechanistic gaps that have not been investigated. One such mechanism governs the movements of the VPCs that allow them to replace one another according to their developmental hierarchy. Second, constructing the model provided unexpected insights into the biology of this system, such as the dynamics and prioritization of fate assumption. These insights have instigated a number of experiments whose results will further enhance the model and our understanding of this process.
-
[
International C. elegans Meeting,
1999]
We use worms as teaching models in labs and lectures for our courses in Developmental Genetics, Molecular Genetics, Advanced Genetics, Cell Biology, and Principles of Evolution. In the laboratory component of Developmental Genetics, students test hypotheses and gain hands-on experience with models systems to reinforce lecture topics. In a demonstration of the "forward" approach to identify genes, students test for linkage with a cross between wild type males and hermaphrodites homozygous for 3 markers. Students use germline transformation with dominant markers or RNAi to demonstrate "reverse" approaches to understanding gene function. To test the functions of the distal tip cell, students perform laser ablations, replicating the classic experiments of Kimble and White (1981). The utility of GFP as a marker is demonstrated as students use epifluorecence microscopy to examine axon guidance mutants and mosaic animals. In the graduate genetics courses, we use primary worm literature for small-group discussions to explore topics as basic as 3-factor mapping and as complex as integration of multiple signaling pathways. Formal debates are used to augment students' skills in presentation and persuasion. Primary research papers are discussed in depth to understand current biological questions and approaches as well as how to design control experiments, discriminate among alternative hypotheses, uncover assumptions, and write papers and proposals. In Molecular Genetics, students write mock grant proposals about problems of their choice, incorporating approaches covered in the course; in Advanced Genetics, students write in-depth reviews of a "heavy" genetics paper. Worm literature is also used to illustrate principles and experimental approaches in the Cell Biology and Evolution courses (open to undergraduates). In Cell Biology, worms are used almost exclusively as a model for understanding mechanisms of programmed cell death. In the Evolution course, heterochronic mutants are discussed for their relevance to macroevolutionary changes. Papers by Sommer et al. (1994-1995) are used to illustrate how model systems may be applied to address important evolutionary principles such as canalization and co-option.
-
[
East Asia Worm Meeting,
2004]
The anatomical data of synaptic connectivity of C. elegans has been degitized for research with computers. The set of files are entitled 'The database of Synaptic Connectivity of C. elegans for Computaiton' and electronicaly delivered to request. The data files describe all items involved in the paper of Albertson and Thomson (1976) and that of White et al. (1986). The policy we empolyed on creating the data base was that diagrams and tables in the original paper can be reconstructed uniquely up to topology from the degitized data. Since our database is equivalent to the anatomical data, quality of the latter can be investigated on analysing the former by computer. It has been found that the anatomical data is almost perfectly self-contained except a few inconsistent descriptions such that the neuron class PDE sends 61 synapses to the class DVA while the latter receives only 36 synapses from the former. This is an exceptionally extreme case of inconsistency and number of erroneously described synaptic contacts are several hundred among eight thousand contacts. In addition, it has been found that several inconsistent description can be corrected from consideration of topological nature of processes in a three dimensional space, which is also suggested by the database.
-
[
International Worm Meeting,
2011]
As a supplement to traditional physiology laboratory exercises, I require my comparative physiology students to design and implement physiology research projects involving C. elegans. Although I tend to guide the student's projects as little as possible, the level of instructor involvement is be quite variable. By requiring students to write a research proposal prior to initiating their experiments, they can be directed towards realistic projects likely to succeed. The only stipulations are that 1. the research investigate some area of physiology and 2. they not reproduce published data or experiments. At the first laboratory meeting, I introduce C. elegans as a research organism and ask them to consider their favorite area of physiology. From this interest, I guide them towards the relevant C. elegans literature and ultimately to a research plan. Prior to spring break, the students have formulated a research plan that includes a hypothesis, a detailed experimental design, and identification of the relevant controls. This way, during the break, I can gather the required reagents, strains, and supplies. As the groups begin their experimentation, it is important to regularly check their progress in the event that experimental design troubleshooting is required. Ultimately, the students are responsible for initiating the experiments, experiment troubleshooting, data collection, and assembly of the data into a research paper. I required that the research papers adhere to a specific journal format, typically one that is readily available for examples, such as Current Biology. This way, they experience the many steps in the process of converting great research ideas into meaningful publications. At the end of the semester, student groups present their hypothesis, experimental design, data, and conclusions to their colleagues in order to gain experience in oral research presentations and expose all the students to the various research projects. This presentation, along with the paper, is reviewed by other research teams as a mechanism to introduce them to peer review. Here, I present some recent examples of these projects.
-
[
International Worm Meeting,
2003]
A major challenge facing researchers in biomedical sciences is extracting the vast amount of information available only in biological literature, most of it contained in individual papers. Manual extraction of information from scientific papers is tedious and slow. We therefore seek to design a web-based system that aids the C. elegans researcher and professional curator in retrieving and efficiently extracting information from papers and abstracts. We have started to devise an information extraction system, which consists of several elements. A preprocessing unit prepares and formats plain text files from the corpus of currently 1880 pdf-files of C. elegans articles and 15000 abstracts. The text is then tagged semantically according to an ontology we have developed. This ontology contains thirty three categories. They can be summarized as classes of biological interest (such as gene, phenotype and cell), of actions, facts or circumstances that relate two (biological) entities or describe one (such as physical association, regulation, and effect), as well as other (auxiliary) classes that are useful for the information extraction process. The ontology includes all terms from the Gene Ontology (GO) Consortium. The semantically marked-up text is presented in XML format, making it available to XML-processing software tools. The marked-up text will then be used for the retrieval and fact extraction of pre-specified types of relationships, events or entities, such as gene-gene interactions or GO-gene associations. A web-based user interface (www.textpresso.org) allows the researcher to formulate queries in a variety of ways: simple keyword searches, searches for a set of occurrences of categories in a sentence or publication as well as the extraction of specified facts. The researcher is able to view sentences, paragraphs and whole articles as well as bibliographical information to verify the returned output. The project currently focuses on C. elegans literature, however, an expansion to the literature of other model organisms should be straightforward. The project is part of WormBase (www.wormbase.org).
-
[
International C. elegans Meeting,
1995]
The Caenorhabditis Genetics Center (CGC), supported by NIH NCRR, supplies Caenorhabditis strains and information to researchers. The St. Paul team is responsible for acquiring, maintaining and distributing worm stocks, generating and maintaining a C. elegans bibliography, and publishing the Worm Breeder's Gazette (WBG). The Cambridge team acts as a clearing house for C. elegans genetic nomenclature and maintains the genetic map. The CGC now has over 2150 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. In addition, we have several strains of species closely related to C. elegans. Strains are available upon written request, which should include a brief statement of the intended use of the strains. Email requests (to stier@molbio.cbs.umn.edu) are satisfactory. The CGC bibliography currently includes over 2025 research articles and book chapters. The WBG is published 3 times each year and currently has over 675 subscribers. Various types of information from the CGC are available electronically. By gopher you can get current strain lists, the WBG subscriber directory, WBG Tables of Contents and the CGC bibliography. We can also email files to you. We like to be acknowledged in papers for providing strains. We also like to receive reprints of worm papers.
-
[
Proceedings of the Seventh IASTED International Conference on Computer Graphics and Imaging,
2004]
Egg-laying is an important phase of the life cycle of the nematode Caenorhabditis elegans (C. elegans). Previous studies examined egg-laying events manually. This paper presents a method for automatic detection of egg-laying onset using deformable template matching and other morphological image analysis techniques. Some behavioral changes surrounding egg-laying events are also studied. The results demonstrate that the computer vision tools and algorithm developed here can be effectively used to study C. elegans egg-laying behaviors. The algorithm developed will be an essential part of a machine vision system for C. elegans tracking and behavioral analysis.
-
[
International Worm Meeting,
2009]
The Caenorhabditis Genetics Center (CGC), supported by the National Institutes of Health - National Center for Research Resources (NIH-NCRR), supplies Caenorhabditis strains and information to researchers throughout the world. The CGC continues to be housed at the University of Minnesota, but will see changes in the next year as Theresa Stiernagle retires as Curator and pursues other interests. The CGC will continue its duties of acquiring, maintaining and distributing worm stocks. The CGC now has over 11,499 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. Selected multiple-mutant stocks and transgenic strains are also available including strains that express various green fluorescent protein (GFP) reporter fusions. The CGC also has stocks of nematode species closely related to C. elegans and bacterial strains necessary for nematode growth. A searchable strains list, including information about CGC stocks, is accessible either through the CGC website (www.cbs.umn.edu/CGC/) or through WormBase. Requests for strains should be made via the on-line ordering system available through our website. As mandated by NIH-NCRR, a small yearly user fee and charge per strain is assessed with each order. The CGC strongly encourages use of credit cards for these charges. We provide quarterly reports to the NIH with statistics that reflect our services to the worm community. We especially like to be acknowledged in papers for providing strains. We also like to receive pdf files of such papers, copies of which we provide to NIH.