Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus

Bioaccumulation and biochemical impact of polyethylene terephthalate microplastics in Cipangopaludina chinensis: Tissue-specific analysis and homeostasis disruption

Microplastics are a novel pollutant that adversely affect freshwater benthic organisms. However, few studies have investigated the mechanism underlying the bioaccumulation and the toxicity of microplastics. In this study, microplastics bioaccumulation of wild Cipangopaludina chinensis in the Songhua River were utilized, and a 28-day aquatic toxicity test was performed to determine the effects of exposure to polyethylene terephthalate (PET), the bioaccumulation of PET, and changes in multiple biomarkers in the muscle, gill, and kidney tissues. The concentration pattern of microplastics was as follows: kidney tissue > muscle tissue > gill tissue. Microplastic ingestion caused AChE inhibition led to significant increases in redox and energy metabolism indicators. Furthermore, the IBR analysis presented a "response-resistance-breakdown" process, indicating that Cipangopaludina chinensis possessed resistance with time (D14 and D21) and concentration (0.10 mg/L and 1.00 mg/L) thresholds. Tissue sensitivity to microplastics was ranked as gill > muscle > kidney, which was the opposite order of microplastic accumulation. These findings implied that less sensitive tissues stored a larger amount of pollutants, suggesting a reduction in tissue sensitivity to microplastics with higher microplastic occurrence rates. This study provides new insights into biological resistance to pollutant stress, warranting further investigation into the underlying mechanisms.

Time-dependent changes in genome-wide gene expression and post-transcriptional regulation across the post-death process in silkworm

Despite death marking the end of life, several gene expression and miRNA-mediated post-transcriptional regulation events may persist or be initiated. The silkworm (Bombyx mori) is a valuable model for exploring life processes, including death. In this study, we combined transcriptomics and miRNAomics analyses of young, old, and post-mortem silkworms across the entire process after death to unravel the dynamics of gene expression and miRNA-mediated post-transcriptional regulation. In total, 171 genes exhibited sustained differential expression in post-mortem silkworms compared to the pre-death state, which are primarily involved in nerve signalling, transport, and immune response. Post-mortem time-specific genes were associated with cell cycle regulation, thermogenesis, immunity, and zinc ion homeostasis. We found that the down-regulated expression of 36 genes related to transcription, epigenetic modification, and homeostasis resulted in a significant shift in global gene expression patterns at 2 h post-death. We also identified 5 mRNA-miRNA pairs (i.e. bmo-miR-2795-mhca, 2784-achi, 2762-oa1, 277-5p-creb, and 1000-tcb1) associated with stress hormone regulation, transcription activity, and signal transduction. The roles of these pairs were validated through in vivo experiments using miRNA mimics in silkworms. The findings provide valuable insights into the intricate mechanisms underlying the transcriptional and miRNA-mediated post-transcriptional regulation events in animals after death.

Combined analysis of transcriptomics and metabolomics provide insights into the antibacterial mechanism of bacteriocin XJS01 against multidrug-resistant Staphylococcus aureus

Multidrug-resistant (MDR) bacteria are widespread in the environment and pose a serious threat to public health. It has been shown that bacteriocins have a great potential in controlling MDR pathogens, including Staphylococcus aureus. A previously reported Lactobacillus salivarius bacteriocin XJS01 exhibited good antibacterial activity against MDR S. aureus 2612:1606BL1486 (henceforth referred to as S. aureus_26), but its molecular mechanism remains unknown. Herein, we investigated the antibacterial mechanism of XJS01 on S. aureus_26 using an approach combining transcriptomics and metabolomics. The results showed that XJS01 induced significant changes at both transcriptional and metabolic levels in S. aureus_26. In total, 231 differentially expressed genes (DEGs) and 206 differentially abundance metabolites (DAMs) were identified in S. aureus_26 treated with 1 × MIC (minimum inhibition concentration) XJS01 compared with untreated (XJS01-free) cells (control). Functional analysis revealed that these DEGs and DAMs, alone with the related pathways and biological processes, were typically involved in stress response, being primarily related to metal uptake, cell virulence, self-help mechanism, amino acid and energy metabolism, bacterial stress response (e.g., two-component system), and membrane transport (e.g., phosphotransferase system). Overall, this study uncovered the multi-target effects of bacteriocins against MDR S. aureus at the genome-wide transcriptional and metabolic levels. These findings might be useful in the development of bacteriocins for the control of MDR S. aureus and other drug-resistant bacteria.