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Seattle, WA, United States

Deng W.,University of Washington | Maust B.S.,University of Washington | Nickle D.C.,University of Washington | Nickle D.C.,Rosetta Inpharmatics LLC | And 6 more authors.
BioTechniques | Year: 2010

DIVEIN is a web interface that performs automated phylogenetic and other analyses of nucleotide and amino acid sequences. Starting with a set of aligned sequences, DIVEIN estimates evolutionary parameters and phylogenetic trees while allowing the user to choose from a variety of evolutionary models; it then reconstructs the consensus (CON), most recent common ancestor (MRCA), and center of tree (COT) sequences. DIVEIN also provides tools for further analyses, including condensing sequence alignments to show only informative sites or private mutations; computing phylogenetic or pairwise divergence from any user-specified sequence (CON, MRCA, COT, or existing sequence from the alignment); computing and outputting all genetic distances in column format; calculating summary statistics of diversity and divergence from pairwise distances; and graphically representing the inferred tree and plots of divergence, diversity, and distance distribution histograms. DIVEIN is available at http://indra.mullins.microbiol.washington.edu/DIVEIN.

Lee S.-Y.,Fox Chase Cancer Center | Coffey F.,Fox Chase Cancer Center | Fahl S.P.,Fox Chase Cancer Center | Peri S.,Fox Chase Cancer Center Philadelphia | And 9 more authors.
Immunity | Year: 2014

Gradations in extracellular regulated kinase (ERK) signaling have been implicated in essentially every developmental checkpoint or differentiation process encountered by lymphocytes. Yet, despite intensive effort, the molecular basis by which differences in ERK activation specify alternative cell fates remains poorly understood. We report here that differential ERK signaling controls lymphoid-fate specification through an alternative mode of action. While ERK phosphorylates most substrates, such as RSK, by targeting them through its D-domain, this well-studied mode of ERK action was dispensable for development of γδ Tcells. Instead, development of γδ Tcells was dependent upon an alternative mode of action mediated by the DEF-binding pocket (DBP) of ERK. This domain enabled ERK to bind a distinct and select set of proteins required for specification of the γδ fate. These data provide the first invivo demonstration for the role of DBP-mediated interactions in orchestrating alternate ERK-dependent developmental outcomes. © 2014 Elsevier Inc.

Microsoft and Rosetta Inpharmatics LLC | Date: 2008-06-17

Computer software that validates mass spectrometry search results for improved peptide identification in experiments using mass spectrometer.

Microsoft and Rosetta Inpharmatics LLC | Date: 2009-01-06

Data management analysis system comprised of software designed for use in genetic studies.

Sundaram P.,Childrens Hospital of Philadelphia | Hultine S.,Childrens Hospital of Philadelphia | Smith L.M.,University of Pennsylvania | Dews M.,Childrens Hospital of Philadelphia | And 10 more authors.
Cancer Research | Year: 2011

Thrombospondin-1 (TSP-1) is an endogenous inhibitor of angiogenesis encoded by the THBS1 gene, whose promoter is activated by p53. In advanced colorectal cancers (CRC), its expression is sustained or even slightly increased despite frequent loss of p53. Here, we determined that in HCT116 CRC cells, p53 activates the THBS1 primary transcript, but fails to boost THBS1 mRNA or protein levels, implying posttranscriptional regulation by microRNAs (miRNA). In a global miRNA gain-of-function screen done in the Dicer-deficient HCT116 variant, several miRNAs negatively regulated THBS1 mRNA and protein levels, one of them being miR-194. Notably, in agreement with published data, p53 upregulated miR-194 expression in THBS1 retrovirus-transduced HCT116 cells, leading to decreased TSP-1 levels. This negative effect was mediated by a single miR-194 complementary site in the THBS1 3′-untranslated region, and its elimination resulted in TSP-1 reactivation, impaired angiogenesis in Matrigel plugs, and reduced growth of HCT116 xenografts. Conversely, transient overexpression of miR-194 in HCT116/THBS1 cells boosted Matrigel angiogenesis, and its stable overexpression in Ras-induced murine colon carcinomas increased microvascular densities and vessel sizes. Although the overall contribution of miR-194 to neoplastic growth is context dependent, p53-induced activation of this GI tract-specific miRNA during ischemia could promote angiogenesis and facilitate tissue repair. ©2011 AACR.

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