Large-scale biomedical image analysis in grid environments.

This paper presents the application of a component-based Grid middleware system for processing extremely large images obtained from digital microscopy devices. We have developed parallel, out-of-core techniques for different classes of data processing operations employed on images from confocal microscopy scanners. These techniques are combined into a data preprocessing and analysis pipeline using the component-based middleware system. The experimental results show that: 1) our implementation achieves good performance and can handle very large datasets on high-performance Grid nodes, consisting of computation and/or storage clusters and 2) it can take advantage of Grid nodes connected over high-bandwidth wide-area networks by combining task and data parallelism.

The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.

Evidence for ectopic neurotransmission at a neuronal synapse.

Neurotransmitter release is well known to occur at specialized synaptic regions that include presynaptic active zones and postsynaptic densities. At cholinergic synapses in the chick ciliary ganglion, however, membrane formations and physiological measurements suggest that release distant from postsynaptic densities can activate the predominantly extrasynaptic alpha7 nicotinic receptor subtype. We explored such ectopic neurotransmission with a novel model synapse that combines Monte Carlo simulations with high-resolution serial electron microscopic tomography. Simulated synaptic activity is consistent with experimental recordings of miniature excitatory postsynaptic currents only when ectopic transmission is included in the model, broadening the possibilities for mechanisms of neuronal communication.

New oral linguiform projections and their associated neurons in the third-stage infective larva of the parasitic nematode Oesophagostomum dentatum.

The infective larvae (L3i) of the nematode parasite of swine, Oesophagostomum dentatum, are passively ingested by their hosts. The L3i exhibit certain behaviors that are probably selected to increase the likelihood of ingestion, by strategic positioning in the environment. The larvae show positive geotactic behavior and respond to temperature variations in their environment, as shown by their behavior on a thermal gradient. To investigate neuronal control of this behavior, we initiated a study of the structure of the amphidial neurons of this parasite. The same number and types of neuronal dendritic processes are found in the amphids of the O. dentatum L3i as in those of its close relatives Haemonchus contortus and Ancylostoma caninum. Well-developed dendritic processes of wing cells are located in the amphidial sheath cells, these being similar to wing cells AWA in the free-living nematode Caenorhabditis elegans but actually more extensive. Similar to its close relatives just mentioned, and C. elegans as well, O. dentatum L3i has prominent finger cell processes, the finger cell neurons being the thermoreceptors in all 3 of the preceding species. However, unlike the arrangement seen in H. contortus and A. caninum, where the microvilli-like "fingers" of these neurons lie dorsal to the amphidial channel and occupy a very large portion (>50%) of the anterior end of the larva, the dendritic process of the finger cells in O. dentatum extends into unusual linguiform projections that, in turn, extend into the lumen of the mouth tube, a complex structural arrangement that has not been described for any other nematode.