Project description:Using WGBS we investigated blood DNA methylation profiles of Canis lupus basenji and determined putative regulatory elements (unmethlated regions, UMRs, and lowly methylated regions, LMRs).
Project description:Using WGBS we investigated blood DNA methylation profiles of Canis lupus dingo and determined putative regulatory elements (unmethlated regions (UMRs) and lowly methylated regions (LMRs).
Project description:Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily
Project description:Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq proved more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with literature describing successful use of drugs targeting this pathway in lymphomas.
Project description:This paper presents the earliest documented evidence for the presence and consumption of horse meat in Early Bronze Age Sicily, significantly revising previous understandings of equid use on the island. Multidisciplinary analyses involving proteomics and lipidomics were performed on ceramic vessels from the Castelluccian settlement at Polizzello Mountain (Caltanissetta), revealing residues consistent with equine-derived substances. Proteomic data unequivocally identified equine serum albumin in multiple pottery fragments, demonstrating active consumption or processing of horse-derived substances within a ceremonial or dietary context. Lipid residues further supported this interpretation, indicating the presence of animal fats and vegetable-derived substances within the pottery. These findings substantially alter existing models of horse domestication, utilization, and dietary practices in prehistoric Sicily, suggesting a far earlier and more complex human-equid relationship. Furthermore, the integration of biomolecular data enhances our understanding of intercultural interactions, ritual behaviors, and economic strategies in the central Mediterranean during the third millennium BCE.
