Townsend SR et al. (1994) Worm Breeder's Gazette "C. elegans Molecular Genetics and Long PCR."

Finelli AL, Savage C, Xie T, Padgett RW, Townsend SR

[Worm Breeder's Gazette, 1994]

C. elegans Molecular Genetics and Long PCR Scott R. Townsend, Cathy Savage, Alyce L. Finelli, Ting Xie, and Richard W. Padgett, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08855

Martinelli SD et al. (1995) International C. elegans Meeting "ACEDB"

Durbin RM, Martinelli SD

[International C. elegans Meeting, 1995]

We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.

(2024) Development "The people behind the papers - Thomas Mullan and Richard Poole."

[Development, 2024]

Asymmetric cell divisions can produce daughter cells of different sizes, but it is unclear whether unequal cell cleavage is important for cell fate decisions. A new paper in Development explores the role of unequal cleavages in Caenorhabditis elegans embryos. To learn more about the story behind the paper, we caught up with first author Thomas Mullan and corresponding author Richard Poole, Associate Professor of Developmental Biology at University College London, UK.

Arthur Wetzel et al. (2008) C.elegans Neuronal Development Meeting "Large-scale Automated Alignment of C. elegans TEM Serial Section Volumes"

Arthur Wetzel, Richard Fetter, David Hall, Greg Hood

[C.elegans Neuronal Development Meeting, 2008]

The understanding of anatomical structure and function is is based on accurate knowledge of 3D relationships typically derived from2D images.Studies of cell biology, morphogenesis, neural connectionsand other research use large numbers of optical or TEM serial images.Although many useful relationships are visible in specific 2D images abroader more rapid understanding can be obtained from 3D representationsthat preserve geometry over a large volume. A number of web resources,including WormAtlas and WormImage, provide searchable access to 2D images, depictions of surface models, and other C. elegans reference materials. We have been working to develop a next generation web framework for distributing C. elegans and other anatomical datasets in 3D volumetric formats that enable interactive viewing and analysis from any orientation rather than just original image planes. The core user interface, the PSC Volume Broswer, provides graphical controls designed for interactive manipulation of 3D models and volumes. Users work from their own Mac or PC computers to interactively view and analyse datasets up to terabyte scales that are stored on remote volume servers or work with local datasets up to ~2 GBytes. The system is designed to support multiple data modalities which will eventually allow integration of optical and gene expression data. This poster and associated computer demonstration show the current state of our prototype applied to a C. elegans embryo and larval TEMimage sets captured by Richard Fetter while working in the Bargmannlab at The Rockefeller University. The greatest technical challenge in using TEM data is the lack ofregistration between slices rather than the overall size of the data.To provide useful views of TEM datasets from arbitrary orientations andsimplify the processes of 3D segmentation and model construction data mustbe volumetrically coregistered. This process must cope with large nonlineardeformations between slices, artifacts, missing slices, intensityvariations and other issues. This is a computationally demandingtask. Our current alignment code, used to align the Fetter data,runs on amid-size 32 processor system at the Pittsburgh Supercomputing Center and produces quality 3D alignment of 700 sections in a few hours. We are working to improve thespeed and quality of this process to test it on portions of the AECOMimage collection and make the process available to the research community.

Herman RK et al. (1997) Worm Breeder's Gazette "STATUS OF THE CAENORHABDITIS GENETICS CENTER (CGC)"

Herman RK, Stiernagle TL

[Worm Breeder's Gazette, 1997]

May 31, 1997 will mark the end of our current five-year contract with the NIH National Center for Research Resources, which supports the activities of the CGC. The activities in St. Paul have involved primarily the acquisition, maintenance and distribution of stocks and information about stocks, acquisition and maintenance of the C. elegans bibliography, and publication and distribution of The Worm Breeder's Gazette (WBG) and WBG Subscriber Directory. Genetic nomenclature and the genetic map have been managed for the period 1992-1997 by Jonathan Hodgkin (CGC Map Curator) on a subcontract. Currently, the subcontract provides half of Sylvia Martinelli's salary, plus travel and minor expenses. Additional support from within the MRC Laboratory of Molecular Biology and the Sanger Centre has been used to fund other essential resources such as computer equipment, as well as Jonathan's and Richard Durbin's time. Richard has been involved in mapkeeping through his work on ACeDB. We are pleased that Jonathan, Richard and Sylvia agreed to continue their work for another five years. We have submitted an application for a new five year contract that would include a subcontract for nomenclature and mapkeeping on essentially the same terms as before. A description of the nomenclature and mapkeeping activities is given in the following abstract. We are grateful to Leon Avery for setting up our CGC gopher server and also for arranging for the electronic submission of WBG abstracts (as well as abstracts for various C. elegans meetings). His C. elegans WWW server has become an essential resource for the worm community. We were therefore pleased to include Leon (only 5% effort) in a second subcontract as part of our new CGC application. We welcome comments and suggestions about any of the CGC activities.

Liang, Xing et al. (2021) International Worm Meeting "Growth Cone-Localized Microtubule Organizing Center Establishes Microtubule Orientation in Dendrites"

Feldman, Jessica, Fetter, Richard, Kokes, Marcela, Liang, Xing, Shen, Kang, Sallee, Maria, Moore, Adrian

[International Worm Meeting, 2021]

A polarized arrangement of neuronal microtubule arrays is the foundation of membrane trafficking and subcellular compartmentalization. Conserved among both invertebrates and vertebrates, axons contain exclusively "plus-end-out" microtubules while dendrites contain a high percentage of "minus-end-out" microtubules, the origins of which have been a mystery. Here we show that in Caenorhabditis elegans the dendritic growth cone contains a non-centrosomal microtubule organizing center, which generates minus-end-out microtubules along outgrowing dendrites and plus-end-out microtubules in the growth cone. RAB-11-positive endosomes accumulate in this region and co-migrate with the microtubule nucleation complex gamma-TuRC. The MTOC tracks the extending growth cone by kinesin-1/UNC-116-mediated endosome movements on distal plus-end-out microtubules and dynein clusters this advancing MTOC. Critically, perturbation of the function or localization of the MTOC causes reversed microtubule polarity in dendrites. These findings unveil the endosome-localized dendritic MTOC as a critical organelle for establishing axon-dendrite polarity.

Kelley S (2000) Brief Bioinform "Getting started with Acedb."

Kelley S

[Brief Bioinform, 2000]

Acedb is one of the more venerable pieces of Genomics software. Acedb was originally created in 1992 by Richard Durbin and Jean Thierry-Mieg to manage the data from the Caenorhabditis elegans mapping project and subsequently the C. elegans sequencing project. From beginnings as a C. elegans-specific tool, it has been continuously developed into a flexible suite of data management, display and scripting tools providing facilities for managing and annotation mapping information and DNA and peptide sequences.This paper gives a basic overview of the Acedb suite, and step-by-step guidance on how to download and install Acedb. It is intended to take an Acedb novice to stage where they can begin to experiment and explore the facilities that are available.

Arthur Wetzel et al. (2006) Neuronal Development, Synaptic Function, and Behavior Meeting "PSC-VB: A System for the Assembly, Visualization, Analysis and Sharing of Large Serial Section Datasets"

Richard Fetter, Cornelia Bargmann, Arthur Wetzel, David Deerfield, David Hall, Demian Nave, Stuart Pomerantz, Greg Hood

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

Serial section electron microscopy is an essential source of image data for building 3D models of C. elegans anatomy with sufficient resolution to map neuronal development and synaptic connections. Despite continued advances in computing speed and capacity it is still difficult to store, visualize, and distribute large stacks of TEM images on PC and workstation computers. Achieving the proper mutual alignment and warping of image slices to simplify the segmentation and tracing of neuronal conections continues to be both computationally intensive and manually tedious. Developers at the Pittsburgh Supercomputing Center (PSC) have been working to extend the PSC Volume Browser (PSC-VB) to address these problems. PSC-VB is a networked client server system to interactively link users PC and Mac computers, running the PSC-VB graphical user interface, to high performance servers that provide large scale computing resources where the actual data storage and manipulation is done. The PSC-VB system, developed for use with the NLM Visible Human datasets and large MRI and CT time series studies of mouse cardiac function, was built to handle datasets to ~100 GBytes and is being extended to TByte scales. The system includes image processing toolkits, data upload services and the ability to import and export data volumes for use with other tools such as ImageJ. This poster describes the PSC-VB system and shows its use with original data from the MRC archives curated by David Hall and with a complete 3-fold embryo volume built from ~24 GBytes of TEM imagery captured by Richard Fetter in the Bargmann lab. A significant aim in both cases is to improve the speed and accuracy of segmentation and model construction by performing complete automated nonlinear slice alignment with minimal human intervention. We are working to extend the system to include additional data modalities and means for remote data sharing and collaborative multi-user work sessions.

Sommer RJ (2008) Bioessays "Homology and the hierarchy of biological systems."

Sommer RJ

[Bioessays, 2008]

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.

Arthur W. Wetzel et al. (2007) International Worm Meeting "Computational assembly, analysis and distribution of C. elegans volumetric anatomy."

Stuart M. Pomerantz, Greg Hood, Richard D. Fetter, Demian Nave, David H. Hall, Arthur W. Wetzel

[International Worm Meeting, 2007]

Understanding of anatomical structure and function is based on 3D relationships typically derived from 2D images. Studies of cell biology, morphogenesis, neural connectivity, etc. build 3D models from optical and TEM serial sections. A number of web resources, including WormAtlas and WormImage, provide searchable 2D reference images, depictions of surfaces, and other instructional materials. Broader, more rapid understanding may come from volumetric representations that preserve geometry over large 3D regions. We are working to develop next generation services to distribute C. elegans and other anatomical data in 3D volumetric formats to enable interactive viewing and analysis from any orientation rather than just image capture planes. Our user interface, the PSC Volume Browser, provides graphical controls for interactive manipulation of 3D models and volumes. Users work from their own Mac or PC computers to interactively view and analyze datasets up to terabyte scales that are stored on remote volume servers or work with local volumes up to ~2 GBytes. The system is designed to support multiple data modalities and will eventually allow integration of optical and gene expression data. This poster and associated computer demonstration show our current prototype applied to a complete 24 GByte C. elegans embryo volume built from TEM images captured by Richard Fetter in the Bargmann lab at The Rockefeller University. The greatest technical challenge of TEM data is lack of registration rather than the size of the data. To provide useful views of TEM datasets from arbitrary orientations and simplify processes for 3D segmentation and model construction data must be aligned. This process must cope with large nonlinear deformations between slices, artifacts, missing slices, intensity variations, nonisotropic voxels and other issues. This is a computationally demanding task. Our current registration code, used to align the embryo data, runs on a mid-size 32-processor system at the Pittsburgh Supercomputing Center and produces good alignment quality in a few hours. We are working to improve the speed and quality of this process in order to process portions of the AECOM image collection and make the Volume Browser service and resulting datasets available to the research community.