Project description:Cardiomyopathy is a heart muscle disease and diagnosis relies on radiography and echocardiography, while blood-based markers are lacking. Development of a non-invasive test would be useful when imaging is not possible (e.g., prenatal diagnosis). In southern sea otters (Enhydra lutris nereis), cardiomyopathy is a prevalent cause of mortality and antemortem diagnosis is challenging. Sea otters requiring clinical care are at significant anesthetic risk if cardiomyopathy is present. A blood-based assay would improve triage decisions, case management, and treatment protocols to safeguard against co-morbidities. With support from the Oiled Wildlife Care Network, we analyzed undepleted sea otter serum using mass spectrometry-based proteomics. Though the larger sample set included 63 sera (that included a validation set of 22 sera with class labels blinded to the data collector), we a priori compared only samples from wild otters. Additionally, we generated proteomic data for four heat tissues with paired sera. These results demonstrate the utility of proteomic analysis, offer a glimpse into the sea otter proteome, and serve as a reference data set for relative protein abundance in sera and cardiac tissue.
Project description:This GEO submission includes RNAseq raw data (fastq) and processed data (using ASpli 1.6.0) from samples obtained in the wild type and the single prefoldin4 and lsm8 mutants in three different environmental conditions as well as in the triple prefoldin2 prefoldin4 prefoldin6 mutant growth in standard conditions.
Project description:Ancient protein analysis provides clues to human life and diseases from ancient times. Paleoproteomics has the potential to give a better understanding of the modes of fabrication of ancient materials, their composition, and pathways of degradation, as well as the development of animal fibers through domestication and breeding. Thus, this study aimed at providing guidance for choosing proteomics workflows to analyze leather samples and their capacity to distinguish between unknown archeological species. Here, we performed shotgun proteomics of archeological animal skin for the first time. The raw output data were analyzed using three different software (Proteome Discoverer, Protein Pilot, and Peptide Shaker) with their impeded algorithms. The study found that the best species identification percentage was obtained using protein piolet with protein database. Particularly prevalent and relatively high collagen expression suggests its resistance to degradation, despite the samples’ exposure to environmental and chemical alterations. The success of this case study indicates that further analyses could assist in reworking historical baseline data for putative identification of unknown archeological samples.
Project description:The aim of this study is to investigate the effects of dietary plant and animal proteins on gut metabolism and markers for colorectal cancer as well as blood protein metabolites and markers for type 2 diabetes in healthy adults. The study participants will be stratified into three groups with different protein composition in diets: 1) animal 70%/plant 30%; 2) animal 50%/plant 50% and 3) animal 30%/plant 70%. The participants will get part of their diet as ready foods or raw material to promote their compliance. The participants will also get personal advice for their diets. Blood, stool and urine samples will be collected in the beginning and in the end of the 12 week intervention, as well as phenotype measures like BMI, blood pressure and body composition. The participants will also fill food diary before and in the end of the intervention.
