A system for scalable 3D visualization and editing of connectomic data

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 57-58).The new field of connectomics is using technological advances in microscopy and neural computation to form a detailed understanding of structure and connectivity of neurons. Using the vast amounts of imagery generated by light and electron microscopes, connectomic analysis segments the image data to define 3D regions, forming neural-networks called connectomes. Yet as the dimensions of these volumes grow from hundreds to thousands of pixels or more, connectomics is pushing the computational limits of what can be interactively displayed and manipulated in a 3D environment. The computational cost of rendering in 3D is compounded by the vast size and number of segmented regions that can be formed from segmentation analysis. As a result, most neural data sets are too large and complex to be handled by conventional hardware using standard rendering techniques. This thesis describes a scalable system for visualizing large connectomic data using multiple resolution meshes for performance while providing focused voxel rendering when editing for precision. After pre-processing a given set of data, users of the system are able to visualize neural data in real-time while having the ability to make detailed adjustments at the single voxel scale. The design and implementation of the system are discussed and evaluated.by Brett M. Warne.M.Eng

Microbial ecology of chlorinated solvent biodegradation

International audienceThis study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials

Structure-based reassessment of the caveolin signalling model: Do caveolae regulate signaling through caveolin-protein interactions

Caveolin proteins drive formation of caveolae, specialized cell-surface microdomains that influence cell signaling. Signaling proteins are proposed to use conserved caveolin-binding motifs (CBMs) to associate with caveolae via the caveolin scaffolding domain (CSD). However, structural and bioinformatic analyses argue against such direct physical interactions: in the majority of signaling proteins, the CBM is buried and inaccessible. Putative CBMs do not form a common structure for caveolin recognition, are not enriched among caveolin-binding proteins, and are even more common in yeast, which lack caveolae. We propose that CBM/CSD-dependent interactions are unlikely to mediate caveolar signaling, and the basis for signaling effects should therefore be reassessed

Proceedings of the 4th World Conference on Research Integrity

CITATION: O’Brien, S. P., et al. 2016. Proceedings of the 4th World Conference on Research Integrity. Research Integrity and Peer Review, 1:9, doi:10.1186/s41073-016-0012-9.The original publication is available at https://researchintegrityjournal.biomedcentral.comThese Proceedings contain the abstracts of the presentations given at the 4th World Conference in concurrent sessions, partner symposia, and poster sessions. Also included are summaries of the discussions in three focus tracks, which allowed delegates to consider and work on questions about the roles of funders, institutions, and countries in improving research systems and strengthening research integrity. Videos of the plenary presentations are available at the conference website (www.wcri2015.org).https://researchintegrityjournal.biomedcentral.com/articles/10.1186/s41073-016-0012-