Project description:Migratory birds use protein as a fuel source during flight, but the mechanisms and benefits of protein catabolism during migration are poorly understood. The tissue-specific turnover rate hypothesis proposes that lean mass loss depends solely on the constitutive rate of protein degradation for a given tissue, and is therefore independent of metabolic rate or environmental stimuli. However, it has been demonstrated that environmental stressors such as humidity affect the rate of lean mass catabolism during flight, a finding that seemingly contradicts the tissue-specific turnover rate hypothesis. In order to resolve this, we placed migratory Swainson's thrushes in either high (HEWL) or low (LEWL) evaporative water loss conditions at rest and while undergoing simulated migratory flight at 8 m s-1 in a wind tunnel to test the impact of both environmental stressors and metabolic rate on the rate of protein breakdown. The total quantity and rate of lean mass loss was not different between flight and rest birds, but was affected by humidity condition, with HEWL losing significantly more lean mass. These results show that the rate of protein breakdown in migratory birds is independent of metabolic rate, but it can be augmented in response to environmental stressors.
Project description:As the cost of DNA sequencing decreases, association studies based on whole genome sequencing are now becoming feasible. It is still unclear, however, how much more we could gain from whole genome sequencing compared to exome sequencing, which has been widely used to study a variety of diseases. In this project, we performed a comparison between whole genome sequencing and exome sequencing for family-based association analysis using data from Genetic Analysis Workshop 18. Whole genome sequencing was able to identify several significant hits within intergenic regions. However, the increased cost of multiple testing counteracted the benefits and resulted in a higher false discovery rate. Our results suggest that exome sequencing is a cost-effective way to identify disease-related variants. With the decreasing sequencing cost and accumulating knowledge of the human genome, whole genome sequencing has the potential to identify important variants in regulatory regions typically inaccessible for exome sequencing.
Project description:Comparative population genomics of cryptic speciation and adaptive divergence in Bicknell's and Gray-cheeked Thrushes (Aves: Catharus bicknelli and C. minimus) Journal: Genome Biology and Evolution
Project description:We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14?000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.
Project description:BACKGROUND:Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered telomere content and aberrations in telomere composition. To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets. RESULTS:We here present TelomereHunter, a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. A novel key feature is the extraction of singleton telomere variant repeats, which improves the identification and subclassification of the alternative lengthening of telomeres phenotype. We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r?=?0.94). For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r?=?0.78). An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r?=?0.79). However, this is considerably improved by normalization with matched controls (r?=?0.91). CONCLUSIONS:TelomereHunter provides new functionality for the analysis of the footprints of telomere maintenance mechanisms in cancer genomes. Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. The software runs under a GPL license and is available at https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html .