ABSTRACT: Health Status, Infection and Disease in California Sea Lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches
Project description:This data is a re-analysis of samples used in a prior study (doi:10.1371/journal.pone.0123295) evaluating plasma candidate biomarkers of chronic domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus). The previous study used 2D-gel electrophoresis to analyze plasma from a training (n = 32; 12 DAT and 20 non-DAT) and validation set (n = 20; 7 DAT and 13 non-DAT). Using spot intensity followed by in-gel digestion and LC-MS/MS, decreased ApoE was identified and qualified as a classifier of chronic DAT. The current analysis is from 31 of these samples (14 DAT and 17 non-DAT), since some samples were no longer available or had been through too many freeze/thaw cycles and were no longer suitable for robust analysis. This subset of 31 undepleted plasma samples was analyzed using shotgun proteomics with a tribrid mass spectrometer, and searching was performed with the recently completed California sea lion genome (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Zalophus_californianus/100/). Using MS1-based label-free methods we were able to identify candidate markers of chronic DAT, such as decreasing ApoE, ApoC-III and ApoB-100. We expect other analytical pipelines could be used to analyze this data, and we deliberately collected the MS1 and MS2 at high resolution to enable spectral library creation for approaches such as data-independent acquisition, which may be used in follow-up studies.
Project description:In this study we assessed the utility of a microarray to identify changes in gene expression predictive of health status by interrogating blood samples from California sea lions in rehabilitation.
Project description:Transcriptional analysis of the effects of natural environmental variation across the latitudinal range of Mytilus californianus Keywords: Environmental response
Project description:Domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus) is caused by exposure to the marine biotoxin domoic acid and has been linked to massive stranding events and mortality. Diagnosis is based on clinical signs in addition to the presence of domoic acid in body fluids. Chronic DAT further is characterized by reoccurring seizures progressing to status epilepticus. Diagnosis of chronic DAT is often slow and problematic, and minimally invasive tests for DAT have been the focus of numerous recent biomarker studies. The goal of this study was to retrospectively profile plasma proteins in a population of sea lions with chronic DAT and those without DAT using two dimensional gel electrophoresis in an effort to discover whether individual, multiple, or combinations of protein and clinical data could be utilized to identify sea lions with DAT. 49 spots were excised, digested and analyzed by MS/MS. These are the data.
