Project description:Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer world wide, and survival rates range from 40-80% depending on subsite. As novel treatment strategies are investigated, comprehensively characterized cell lines representative of the diversity seen in patients will be crucial to correlating genetic and phenotypic features with therapeutic response. The University of Michigan has generated a large panel of HNSCC cell lines that are utilized in laboratories worldwide. Here, we performed Oncoscan array analysis for 33 of these cell lines along with 2 HNSCC lines derived elsewhere to inform selection of model systems for future studies.
Project description:The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae we provide novel insights into the evolution of gbM and its underlying mechanism. The angiosperm- and eudicot-specific whole genome duplication events gave rise to what are now referred to as CMT1, 2 and 3 lineages. CMTε, which includes the eudicot-specific CMT1 and 3, and orthologous angiosperm clades, is essential for the perpetuation of gbM in angiosperms, implying that gbM evolved at least 236 MYA. Independent losses of CMT1, 2 and 3 in eudicots, and CMT2 and CMTmonocot+magnoliid in monocots suggests overlapping or fluid functional evolution. The resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation.
Project description:Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus. In order to generate the Salvia Subtracted Diversity Array (SDA), a Suppression Subtractive Hybridization (SSH) was performed between a pool of ten Salvia species and a pool of non-angiosperm and angiosperms (excluding the Lamiaceae) to selectively isolate Salvia-specific sequences. A total of 285 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating closely related species of S. officinalis and S. miltiorrhiza and was also able to reveal genetic relationships consistent with geographical origins. Species-specific features were also found for S. elegans, S. officinalis, S. sclarea, S. przewalskii and S. runcinata.
