Project description:A custome-made 8x15k oligonucleotide limanda limanda microarray (Agilent) comprised of 14919 experimental probes, was used to characterize gene expression profiles of dab hepatocellular adenoma tumours from sites of different pollution status in Irish Sea.
Project description:We report the application of DNA methylation immunoprecipitation coupled with de novo high throughput sequencing for profiling and identifying methylation alterations in liver tumours of un-sequenced flatfish dab (Limanda limanda). We achieved approximately 90 million and 88 million paired-end reads for hepatocellular adenoma (HCA) and corresponding healthy surrounding tissue (S.T) respectively, of which 47,052,820 and 45,008,483 were uniquely mapped. By calculating the fold changes observed between HCA and S.T we identified 1693 CpG island containing regions that are differentially methylated in HCA compared to S.T (fold change >1.5). The identified genes were further annotated for gene name and biological functions. Ingenuity Pathway Analysis demonstrated enrichment of networks and top functions, such as cell-to-cell signalling, cell cycle, DNA replication, cellular assembly and organisation as well as canonical pathways including Wnt/β-catenin signalling, growth hormone signalling and apoptosis signalling associated with the differentially methylated genes in HCA compared to S.T. Finally, our data showed that MeDIP-HTP sequencing achieves substantial overlapping reads for construction of contigs and annotation of the based on closely related species for studying DNA methylation in un-sequenced species.
Project description:Electrical stimulation is known to promote bone regeneration, but conventional systems often require wired connections or implanted power sources and provide limited stimulation to deep tissues. To address this, a dual-amplified body-coupled (DAB) electrostimulation approach was developed, enabling wireless deep-tissue stimulation by harvesting ambient low-frequency electrical fields. A conductive membrane electrode was chosen to focus electrical potentials at the bone-defect site, and both simulations and ex vivo measurements confirmed enhanced electric field intensity within bone tissue under DAB stimulation. To figure out the mechanistic insights, bulk RNA-seq analysis was conducted on DAB-stimulated human bone marrow mesenchymal stromal cells (hBMSCs) and their corresponding controls across multiple time points (Days 2, 4, 7, and 14). Differentially expressed gene (DEG) analysis revealed that by Day 14 of DAB treatment, osteogenic markers including BMP2, BMP6, and SPP1 were significantly upregulated, suggesting enhanced osteogenic differentiation, as these genes are integral to bone formation and mineralization processes.
