Department of Biomedical Engineering http://hdl.handle.net/2144/974 2013-05-19T19:45:09Z 2013-05-19T19:45:09Z Hayete, Boris Gardner, Timothy S Collins, James J http://hdl.handle.net/2144/3065 2012-01-11T07:00:43Z 2007-02-13T00:00:00Z

Size Matters: Network Inference Tackles the Genome Scale Hayete, Boris; Gardner, Timothy S; Collins, James J

2007-02-13T00:00:00Z Ahmad, Q Rushdy Nguyen, Dat H Wingerd, Mark A Church, George M Steffen, Martin A http://hdl.handle.net/2144/3063 2012-01-11T07:00:41Z 2005-06-08T00:00:00Z

Molecular Weight Assessment of Proteins in Total Proteome Profiles using 1D-PAGE and LC/MS/MS Ahmad, Q Rushdy; Nguyen, Dat H; Wingerd, Mark A; Church, George M; Steffen, Martin A BACKGROUND. The observed molecular weight of a protein on a 1D polyacrylamide gel can provide meaningful insight into its biological function. Differences between a protein's observed molecular weight and that predicted by its full length amino acid sequence can be the result of different types of post-translational events, such as alternative splicing (AS), endoproteolytic processing (EPP), and post-translational modifications (PTMs). The characterization of these events is one of the important goals of total proteome profiling (TPP). LC/MS/MS has emerged as one of the primary tools for TPP, but since this method identifies tryptic fragments of proteins, it has not generally been used for large-scale determination of the molecular weight of intact proteins in complex mixtures. RESULTS. We have developed a set of computational tools for extracting molecular weight information of intact proteins from total proteome profiles in a high throughput manner using 1D-PAGE and LC/MS/MS. We have applied this technology to the proteome profile of a human lymphoblastoid cell line under standard culture conditions. From a total of 1×107 cells, we identified 821 proteins by at least two tryptic peptides. Additionally, these 821 proteins are well-localized on the 1D-SDS gel. 656 proteins (80%) occur in gel slices in which the observed molecular weight of the protein is consistent with its predicted full-length sequence. A total of 165 proteins (20%) are observed to have molecular weights that differ from their predicted full-length sequence. We explore these molecular-weight differences based on existing protein annotation. CONCLUSION. We demonstrate that the determination of intact protein molecular weight can be achieved in a high-throughput manner using 1D-PAGE and LC/MS/MS. The ability to determine the molecular weight of intact proteins represents a further step in our ability to characterize gene expression at the protein level. The identification of 165 proteins whose observed molecular weight differs from the molecular weight of the predicted full-length sequence provides another entry point into the high-throughput characterization of protein modification.

2005-06-08T00:00:00Z Peterson, Matthew W Colosimo, Marc E http://hdl.handle.net/2144/3064 2012-01-11T07:00:41Z 2007-10-31T00:00:00Z

TreeViewJ: An Application for Viewing and Analyzing Phylogenetic Trees Peterson, Matthew W; Colosimo, Marc E BACKGROUND. Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images. RESULTS. We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order. CONCLUSION. TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net.

2007-10-31T00:00:00Z Jain, Abhishek Munn, Lance L. http://hdl.handle.net/2144/3058 2012-01-11T07:00:38Z 2009-09-21T00:00:00Z

Determinants of Leukocyte Margination in Rectangular Microchannels Jain, Abhishek; Munn, Lance L. Microfabrication of polydimethylsiloxane (PDMS) devices has provided a new set of tools for studying fluid dynamics of blood at the scale of real microvessels. However, we are only starting to understand the power and limitations of this technology. To determine the applicability of PDMS microchannels for blood flow analysis, we studied white blood cell (WBC) margination in channels of various geometries and blood compositions. We found that WBCs prefer to marginate downstream of sudden expansions, and that red blood cell (RBC) aggregation facilitates the process. In contrast to tubes, WBC margination was restricted to the sidewalls in our low aspect ratio, pseudo-2D rectangular channels and consequently, margination efficiencies of more than 95% were achieved in a variety of channel geometries. In these pseudo-2D channels blood rheology and cell integrity were preserved over a range of flow rates, with the upper range limited by the shear in the vertical direction. We conclude that, with certain limitations, rectangular PDMS microfluidic channels are useful tools for quantitative studies of blood rheology.

2009-09-21T00:00:00Z