Hall David H et al. (2008) "C. elegans Atlas"

Altun Zeynep F, Hall David H

[2008]

Hall, David H. et al. (2009) International Worm Meeting "Electron tomography: a new tool for exploring C. elegans cellular anatomy."

Fisher, Kevin, Nguyen, Ken C.Q., Hall, David H., Crocker, Chris, Derr, KD, Rice, William J., Politi, Kristin A., Gunther, Leslie

[International Worm Meeting, 2009]

C. elegans has been studied intensively using serial section reconstruction for several decades, so that every cell type is now known in considerable detail. Nevertheless, limitations of the serial section technique (notably the poor resolution of detail within the depth of each 50 nm "thin" section) have made it difficult to model the shapes of fine details in many organelles, such as the cristae of a mitochondrion, the canaliculi of the excretory canal, membrane ruffles in many cell types, or the constituents at a chemical synapse. High pressure freeze fixation and freeze substitution (1) are a required element in preserving smaller structures that generally escaped our notice in conventional TEM imaging. Modern electron microscopes using higher energy electrons now offer much better resolution by collecting multiple images in a tilting series through comparatively thick sections (150 nm) using the SerialEM program (2). The Protomo software package (3) is used to compute a 3D tomographic reconstruction that offers the same level of detail in any dimension (roughly 2 nm resolution). Annotation and modeling is done using IMOD (4) and/or Amira. This permits us to take a new look at many familiar objects in the anatomy of C. elegans, to identify missing parts of the whole anatomy, and potentially, to detect smaller anatomical defects in a variety of mutant backgrounds. Here we will introduce the tomographic procedure, and share finished 3D models of some typical intracellular organelles at high resolution. Supported by NIH RR 12596 to DHH. 1.Weimer, R.M. (2006) Methods Mol. Biol. 351: 203-221. 2.Mastronarde, D.N. (2005) J. Struct. Biol. 152: 36-51 3.Winkler, H. and Taylor, K.A. (2006) Ultramicroscopy 106: 240-254. 4.Kremer, J.R., Mastronarde, D.N. and McIntosh, J.R. (1996) J. Struct. Biol. 116: 71-76.

David Hall (2006) Development & Evolution Meeting "TEM Anatomy of the Worm: Then and Now"

David Hall

[Development & Evolution Meeting, 2006]

In the beginning, rather little was known about what types of cells, tissues or organelles might lie within the nematode C. elegans. The very small size of the animal pushed us to begin exploring the anatomy using the electron microscope. Most tissue types and cell types in the worm emerged gradually after 1968, when Sydney Brenner, John White, and Nichol Thomson first began to study the animal in depth by serial thin sections. They were soon joined by a host of others in Cambridge and Pasadena, and eventually in many more labs. By 1980, most of this TEM work was completed, and the community moved on to biochemical, molecular and genomic studies, and relied more heavily on other modalities of microscopy. Exact characterization of all individual neurons and their synapses by TEM took still longer (1986), and a few cell types were still a mystery into the 21st century. Similarly, many familiar organelles and cell junctions were quickly identified by TEM in virtually all cells. Indeed the nematode is made up of simple cells that share many common features with higher animals. To a lesser extent, morphogenesis in the embryo and the larval stages has also been characterized by TEM. Since 1980, TEM has also been used to explore the pathology of cells gone wrong in the worm: in developmental mutants, under toxic conditions, in aging, and during key events such as cell death. Even given the advent of GFP probes, FRET, confocal imaging, and laser ablations, we continue to lean on TEM techniques to answer certain questions. I will briefly survey some of the events, cells and organelles whose anatomy remains mysterious, and the techniques that show promise to reveal them at high resolution.

David Hall et al. (2008) Development & Evolution Meeting "What's New on WormAtlas and WormImage?"

Tylon Stephney, Chris Crocker, Zeynep Altun, David Hall, Carolyn Norris, Laura Herndon

[Development & Evolution Meeting, 2008]

The pages of WormAtlas are getting a fresh look and organization.These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website.Here we will explain the principles of the new organization, and show you how to find your favorite features.This is the first major revamping of WormAtlas since its launch in 2002.We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners.As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages.Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo.Third will be the addition of more data to Slidable Worm.Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily.It now presents much more mutant data, particularly for genes affecting the nervous system.As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files.We encourage more laboratories to share your own best archival TEM and SEM images for this purpose.We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites.This work is supported by NIH RR12596.

David Hall (2001) Worm Breeder's Gazette "Center For C. elegans Anatomy Expands its Archives"

David Hall

[Worm Breeder's Gazette, 2001]

David Hall et al. (2008) C.elegans Neuronal Development Meeting "What's New on WormAtlas and WormImage?"

Laura Herndon, David Hall, Carolyn Norris, Zeynep Altun, Chris Crocker, Tylon Stephney

[C.elegans Neuronal Development Meeting, 2008]

The pages of WormAtlas are getting a fresh look and organization. These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website. Here we will explain the principles of the new organization, and show you how to find your favorite features. This is the first major revamping of WormAtlas since its launch in 2002. We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners. As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages. Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo. Third will be the addition of more data to Slidable Worm. Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily. It now presents much more mutant data, particularly for genes affecting the nervous system. As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files. We encourage more laboratories to share your own best archival TEM and SEM images for this purpose. We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites. This work is supported by NIH RR12596.

David H Hall et al. (2001) International C. elegans Meeting "New! Improved! Fixation protocols for TEM"

David H Hall, Tylon Stephney, Gloria Stephney, Ya Chen, Frank Macaluso

[International C. elegans Meeting, 2001]

We continue to test alternate methods for preparing worms for transmission electron microscopy. We will describe new protocols, and will demonstrate what makes them better [or different] in comparison to previous methods (Hall, 1995). We still like simple immersion fixation and chopping open the animals by knife blade, and have made minor changes in the starting solutions to get optimum results. For early larval stages, which have never fixed well by immersion, and which are too little to chop open easily, we have adapted a new microwave protocol which gives very good results on intact worms. The resulting fixation looks equivalent to our immersion preparations of adults. Microwave fixation is proving very useful in the analysis of arrested animals from RNAi preparations, and should be excellent for looking at late embryos or dauers. Fast freezing methods offer a quite different approach, and the quality of tissue preservation can be superb. Both metal mirror freezing and high pressure freezing can produce excellent results, and they are achieving wider use over the past few years (Mohler et al., 1998; Rappleye et al., 1999). The inherent contrast after freeze substitution is often much greater, in part because the primary fixation contains only osmium, or a combination of osmium and aldehyde together. These methods allow much more rapid fixation. We can capture more "life-like" views of biological events in action, particularly for events such as vesicle fusions at the plasma membrane. Delicate cytoskeletal elements such as microtubules are also well preserved. We continue to try new combinations of fixatives and solvents to improve the appearance of nerve processes and synapses by fast freezing. Kent McDonald has been very helpful in suggesting improvements to these protocols. Laserhole fixations of embryos are technically rather difficult to accomplish, but can facilitate the passage of fixatives and embedding resins through the eggshell. We are continuing to use the protocol worked out by Carolyn Norris. See our website for details.

David H Hall et al. (2003) International Worm Meeting "Synapses in decline: age-related deterioration in neuronal anatomy"

David H Hall, Peter J Schmeissner, Laura A Herndon, Gloria Stephney, Monica Driscoll

[International Worm Meeting, 2003]

As nematodes age, various tissue-specific changes occur that coincide with the deterioration of the animal. We characterized the general appearance and the locomotory behavior of wild type adults over time and found that we could distinguish three classes (A, B and C) of behavioral types in the same-age population. By following individuals throughout their lifetime, we determined that decline is progressive. However, we also established that individual time of onset and rate of decline are strikingly variable suggesting aging in C. elegans has a stochastic component. We have used GFP-tagged proteins that highlight the morphologies of specific tissues, cells and subcellular structures in conjunction with electron microscopy to give a detailed histological description of aging in C. elegans. Initial studies indicate that the nervous system remains remarkably intact in old animals while other tissues, such as muscle and intestine, undergo dramatic deterioration (Herndon et al., 2002). While the nervous system appears intact in aged nematoes, we are now trying to determine whether the neurons undergo more modest changes during the aging process. Measures of synapse numbers using snb-1::GFP demonstrate that they remain relatively constant over the adult lifespan. Similar studies of the GABAergic receptor found them present in both neuromuscular junctions and in neurons of old nematodes. However, electron microscopy studies in 18-day-old adults indicate that synaptic vesicle number decreases as the animals progress from A to B to C class. Although synapses can still be recognized, neuronal processes are markedly thinner, their plasma membranes more electron dense, and pre-synaptic densities at active zones are smaller. The terminal volume at individual synapses is reduced, contains fewer vesicles, and has fewer docked vesicles per active zone. Changes are evident when class A animals are compared to young adults, but the decline is more severe in all respects in B and C class animals. Thus, the age-related decline of the nervous system is subtle, with virtually no cell loss and little loss in synapse number. However, the reduction in the pool of releasable synaptic vesicles may play a significant role in the behavioral changes of B and C class animals.

David H Hall et al. (2003) International Worm Meeting "Wormatlas: A comprehensive online reference of C. elegans anatomy"

David H Hall, Zeynep F Altun

[International Worm Meeting, 2003]

David H Hall et al. (2002) West Coast Worm Meeting "Wormatlas: A web-based behavioral and structural atlas of C. elegans"

Thomas Boulin, Zeynep F Altun, Michael Zhang, Maurice Volaski, Constantinos Polydorou, David H Hall

[West Coast Worm Meeting, 2002]

We have recently launched the prototype of Wormatlas (www.wormatlas.org). This atlas is designed to serve the scientific community with the main goal of bringing all the anatomical information pertinent to C. elegans within one readily accessible and easy to use web site. By creating extensive links to the WormBase as well as the C. elegans WWW server, we are aiming to provide users with seamless links between these databases. We hope to create the most comprehensive and complete online anatomy atlas for any genetic model organism.