Mount Desert Island Biological Laboratory

About: Mount Desert Island Biological Laboratory is a nonprofit organization based out in Bar Harbor, Maine, United States. It is known for research contribution in the topics: Squalus acanthias & Spiny dogfish. The organization has 898 authors who have published 819 publications receiving 34283 citations.

Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence

Abstract: Computational inference of putative functional elements in noncoding DNA sequence can significantly hasten the search for verified functional elements, such as transcription factor binding sites. However, while computational methods are able to identify promising putative elements, the number of regions of interest may remain unrealistic for experimental validation. Visualization of putative functional elements can assist tremendously in identifying the regions of greatest interest; interactive vizualization allows researchers additional means of asking and answering questions about putative elements. For example, interactive visualizations allow one to look at motifs in the context of verified functional elements or other putative elements, interactively altering the amount of information displayed and the level of resolution at which it is displayed. The work presented here describes initial efforts toward interactive visualization of putative functional elements specifically for our work with conserved elements.

AMP-activated protein kinase and adenosine are both metabolic modulators that regulate chloride secretion in the shark rectal gland ( Squalus acanthias).

Abstract: The production of endogenous adenosine during secretagogue stimulation of CFTR leads to feedback inhibition limiting further chloride secretion in the rectal gland of the dogfish shark (Squalus aca...

Visualizing minute details in light-sheet and confocal microscopy data by combining 3D rolling ball filtering and deconvolution.

Abstract: We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction in three directions with deconvolution using a synthetic or measured point spread function. Via automatic block-wise processing image stacks of virtually unlimited size can be deconvolved even on small computers with 8 or 16 GB RAM. By parallelization and optional GPU-acceleration, the software works with high speed: On a PC equipped with a state-of-the-art NVidia graphic board a three dimensional (3D)-stack of about 1 billion voxels can be deconvolved within 5 to 10 minutes. The implemented variation of the Richardson-Lucy deconvolution algorithm preserves the photogrammetry of the image data by using flux-preserving regularization, an approach that to our knowledge has not been applied for deconvolving microscopy data before.