Application of high-throughput sequencing technology in HIV drug resistance detection

Sequencing-based network analysis provides a core set of genes for understanding hemolymph immune response mechanisms against Poly I:C stimulation in Amphioctopus fangsiao

Aquatic viruses can spread rapidly and widely in seawater for their high infective ability. Polyinosinic-polycytidylic acid (Poly I:C), a viral dsRNA analog, is an immunostimulant that has been proved to activate various immune responses of immune cells in invertebrate. Hemolymph is a critical site that host immune response in invertebrates, and its transcriptome information obtained from Amphioctopus fangsiao stimulated by Poly I:C is crucial for understanding the antiviral molecular mechanisms of this species. In this study, we analyzed gene expression data in A. fangsiao hemolymph tissue within 24 h under Poly I:C stimulation and found 1082 and 299 differentially expressed genes (DEGs) at 6 and 24 h, respectively. Union set (1,369) DEGs were selected for subsequent analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were carried out for identifying DEGs related to immunity. Several significant immune-related terms and pathways, such as toll-like receptor signaling pathways term, inflammatory response term, TNF signaling pathway, and chemokine signaling pathway were identified. A protein-protein interaction (PPI) network was constructed for examining the relationships among immune-related genes. Finally, 12 hub genes, including EGFR, ACTG1, MAP2K1, and other nine hub genes, were identified based on the KEGG enrichment analysis and PPI network. The quantitative RT-PCR (qRT-PCR) was used to verify the expression profile of 12 hub genes. This research provides a reference for solving the problem of high mortality of A. fangsiao and other mollusks and provides a reference for the future production of some disease-resistant A. fangsiao.

Transcriptome profiling based on protein-protein networks provides a core set of genes for understanding blood immune response mechanisms against LPS stress in Amphioctopus fangsiao

Gram-negative bacteria are significant pathogens in the ocean, posing serious threats to marine organisms. Lipopolysaccharide (LPS) is a characteristic chemical constituent in Gram-negative bacteria that can be recognized by the pattern recognition receptor (PRR) of immune cells. This system is often used to simulate the invasion of bacteria. Blood is a transport channel for immune cells, and its transcriptome information obtained from Amphioctopus fangsiao stimulated by LPS is essential for understanding the antibacterial biological mechanisms of this species. In this study, we analyzed the gene expression profiles of A. fangsiao blood within 24h under LPS stress and found 778 and 561 differentially expressed genes (DEGs) at 6 and 24h, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were performed to search for immune-related DEGs. The relationships among immune genes were examined by constructing a protein-protein interaction (PPI) network. Finally, 16 hub genes were identified based on the PPI network and KEGG enrichment analysis. The expression profiles of these genes were verified using quantitative RT-PCR (qRT-PCR). This research provides valuable resources for the healthy culture of A. fangsiao and helps us understand the molecular mechanisms of innate immunity.