Genes

Background/Objectives: The elongated egg is a morphological mutant of silkworm (Bombyx mori) eggs, yet the biochemical processes and molecular mechanisms underlying this trait remain unclear. Methods: In this study, we performed transcriptome sequencing on the ovaries of female pupae from the Nistari silkworm strain (comparing normal and elongated eggs) during the first three days post-pupation using high-throughput sequencing. Results: A total of 153.56 Gb of filtered data was obtained, identifying 23,366 genes and 35,798 mRNAs. Comparative analysis across three control groups revealed 374 differentially expressed genes (DEGs), with 131 upregulated and 243 downregulated genes in the elongated egg group. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were primarily associated with protein hydrolysis, DNA metabolic processes, and euchromatin/heterochromatin organization. Trend expression analysis revealed that transcriptional activity in elongated eggs was significantly higher than in normal eggs, particularly on day 3 of the pupal stage. Conclusions: Weighted gene co-expression network analysis (WGCNA) classified gene expression patterns into twelve modules, with two modules showing specificity. Thirteen hub genes were identified, which are functionally linked to translation initiation, protein density regulation, post-translational modification, and protein turnover. These findings provide foundational insights into the molecular mechanisms driving the formation of the elongated egg in silkworms.

Background: Viburnum (Adoxaceae) is a species-rich woody genus whose taxonomy is complicated by morphological convergence and hybridization. Methods: We assembled complete plastomes of eight species representing five sections and analyzed their structural variation, sequence divergence, and molecular evolution. Results: All plastomes displayed the conserved quadripartite structure typical of angiosperms, with limited size variation attributable primarily to intergenic spacer-length polymorphisms. Sequence divergence was unevenly distributed, with single-copy regions exhibiting substantially higher nucleotide diversity than inverted repeat regions. We identified multiple hypervariable intergenic spacers such as the region trnK-UUU–rps16, suitable as molecular markers for population genetics and species identification. Selection pressure analysis revealed that while most protein-coding genes evolved under strong purifying selection, three genes involved in fatty acid biosynthesis and protein import—accD, ycf1, and ycf2—showed significantly relaxed constraints, suggesting ongoing functional divergence. Phylogenetic analysis recovered well-supported relationships consistent with previous classifications, while clarifying the positions of Viburnum amplificatum and Viburnum tinus. Conclusions: These findings provide molecular resources for Viburnum systematics and offer insights into the evolutionary dynamics of plastome genes with non-photosynthetic functions.

Background/Objectives. Oxidative stress is a key contributor to HIV-associated neurocognitive disorders (HANDs), yet the regional organization and functional engagement of the NRF2 antioxidant pathway in the human brain remain incompletely defined. This study aimed to characterize NRF2 pathway architecture, baseline brain expression, and disease-associated transcriptional and coexpression remodeling across HAND stages. Methods. The NRF2 signaling network was reconstructed using curated pathway data and protein–protein interaction analysis to identify central hub genes. Baseline expression in the normal human cortex was assessed using the Human Protein Atlas. Transcriptomic profiling of postmortem brain samples from individuals with HAND (GSE35864) was performed using differential expression, hierarchical clustering, and region-specific coexpression analyses across white matter, frontal cortex, and basal ganglia. Results. Low-to-medium baseline expression of NRF2-related genes was observed in the normal cortex. Bulk differential expression revealed minimal NRF2 pathway modulation in the frontal cortex and basal ganglia. On the other hand, white matter exhibited robust NRF2 transcriptional activation specifically in HIV encephalitis (HIVE). Coexpression analysis performed specifically within HAND samples revealed a highly coordinated transcriptional organization of the NRF2 signaling network across all analyzed brain regions. Conclusions. NRF2 signaling in HAND is preserved as a coordinated transcriptional network but is selectively activated in white matter during encephalitic disease, highlighting region- and cell-type-targeted therapeutic opportunities.