Advanced biotechnology最新文献

Microplastics (MPs) and bisphenol A (BPA) frequently co-occur in freshwater ecosystems, yet their combined impacts on host-pathogen interactions remain poorly understood. Here, we exposed juvenile largemouth bass (Micropterus salmoides) to environmentally relevant concentrations of MPs, BPA, and their mixture. Co-exposure markedly inhibited NRF2-mediated antioxidant signaling, leading to downregulation of antioxidant enzymes (SOD1, CAT, GPx), elevated hepatic reactive oxygen species and malondialdehyde, and depletion of ATP. These redox disturbances were accompanied by mitochondrial damage, increased expression of pro-apoptotic genes (Bax, Caspase-3), and accumulation of TUNEL-positive nuclei, indicative of apoptosis. Strikingly, only co-exposed fish exhibited enhanced replication of nervous necrosis virus (NNV), a response absent under single exposures. Our findings demonstrate that MPs and BPA act synergistically to disrupt redox homeostasis and compromise antiviral defense, thereby heightening viral susceptibility in a freshwater aquaculture species. This study highlights the overlooked infection risks posed by pollutant mixtures and emphasizes the need to incorporate mixture toxicity into freshwater ecotoxicological risk assessments.

Amphioxus, a basal chordate with highly heterozygous genomes (3.2 ~ 4.2% in sequenced species), represents a key model for understanding vertebrate origins. However, the extreme heterozygosity poses challenges for many genomic analyses, including studying meiotic recombination. Here, we present a novel bioinformatic pipeline that enables direct detection of crossover (CO) and non-crossover (NCO) recombination events using short-read whole-genome sequencing of a two-generation pedigree (two parents and 104 F1 offspring) of the amphioxus Branchiostoma floridae. Using parental assemblies generated by Platanus-allee as a custom reference for read alignment, we tracked inheritance patterns in offspring and phased contig-level haplotypes in parents, allowing us to detect recombination events. We identified 2,329 paternal and 2,288 maternal COs, yielding recombination rates of 4.66 cM/Mb and 4.57 cM/Mb, respectively. We found CO coldspots spanning > 140 Mb in each parent and these are likely associated with large-scale heterozygous inversions. CO rates were positively correlated with transposable element and gene density in both sexes, but showed weak or no correlation with GC content. We further identified ~ 10,000 paternal and ~ 5,800 maternal NCO events, predominantly shorter than 200 bp in tract length, and found evidence of GC-biased gene conversion. This work provides the first direct and genome-wide measurement of recombination in amphioxus and demonstrates how high heterozygosity, often considered a barrier, can be leveraged for fine-scale recombination mapping. Our findings illuminate conserved and divergent features of recombination in chordates and establish a framework for studying recombination in other highly heterozygous organisms.

Skeletal muscle serves as a valuable source of nutrition, with distinct muscle fiber types exhibiting different physicochemical properties that influence both meat quality and muscle function. Bama miniature pigs (BM) are recognized for their superior meat quality and their relevance as models for human medical research. Therefore, investigating the differences between slow and fast muscles at various developmental stages (from 57 days post-fertilization to 120 days postnatally) in BM is crucial for both the pork industry and biomedical studies. In this study, we employed a non-targeted data-independent acquisition (nDIA) -based proteomic approach for the first time to porcine embryonic skeletal muscle fibers. A total of 616 differentially expressed genes (DEGs) and 272 differentially abundant proteins (DAPs) were identified in the fast-twitch longissimus dorsi (LD) and slow-twitch semitendinosus (SD) muscles of BM. Domain enrichment analysis and in vitro experiments demonstrated that the NEK3 gene, containing the S_TKc domain, inhibits fast-twitch muscle fiber differentiation postnatally. Additionally, cross-species analysis showed upregulation of skeletal muscle development organ genes in pigs at postnatal day 28. In summary, our results provide both fundamental data and novel insights to further uncover the mechanisms underlying pig skeletal muscle development and muscle fiber transition.

Trypanosoma brucei, the causative agent of African trypanosomiasis, develops from the long slender (LS) to the short stumpy (SS) form in the mammalian host. The SS trypanosomes are critical for transmission to the insect vector but face significant challenges within the vertebrate host. The role of the immune response in controlling the parasitaemia is well studied, however, the mechanism underpinning the rapid degeneration of SS trypanosomes during the first parasitaemic peak in mice remains somewhat elusive. We demonstrate that fever is a critical yet underexplored factor in facilitating the clearance of SS trypanosomes, suggesting that temperature may play a critical role in regulating the natural turnover of SS trypanosomes. The elevated body temperature correlates with the parasitaemic dynamics, accelerating SS trypanosome elimination in the mammalian host. The SS trypanosomes exhibited high thermo-sensitivity to elevated temperatures, accompanied with apoptosis-like events, mitochondrial damage and oxidative stress. Metabolomic profiling also revealed disruptions in glycolysis and the TCA cycle, shedding light on the processes in compromising the SS trypanosomes. Interestingly, antibodies during the acute phase did not directly cause SS trypanosomes death, but the combination of elevated temperature and antibodies enhanced the clearance of SS trypanosomes, highlighting the critical role of fever in eliminating the first parasitaemic peak. Our findings detail the mechanism of vulnerability of SS trypanosome to elevated temperatures and suggest that host fever serves as a neglected, but critical mechanism, for T. brucei SS trypanosome clearance.

Approximately 75% of the human genome is transcribed into RNA, yet less than 5% encodes proteins, with the majority producing non-coding RNAs (ncRNAs). Among them, long non-coding RNAs (lncRNAs) represent a major class that exerts broad regulatory influence across cellular processes, disease contexts, and developmental stages. Despite their potential as biomarkers and therapeutic targets, their low sequence conservation, limited abundance, and structural complexity present significant challenges for functional characterization. Traditional RNA interference and CRISPR-Cas9-based methods have offered partial insights but remain limited in efficiency, specificity, and scalability. To address these barriers, Neville E. Sanjana's team developed CaRPool-seq, a transcriptome-scale CRISPR-Cas13 screening platform that directly targets RNA. Applying this approach across diverse human cell lines, they identified 778 essential lncRNAs, including 46 universally required for survival, with distinctive structural features and functional independence from neighboring protein-coding genes. Integration with single-cell transcriptomics revealed their critical roles in cell-cycle regulation, apoptosis, and developmental gene expression, as well as aberrant expression patterns in cancer linked to patient outcomes. This study establishes CRISPR-Cas13 as a precise and scalable strategy for lncRNA functional discovery, expanding opportunities for biomarker identification, therapeutic development, and precision medicine.

Trichomes are crucial for plant defense and secondary metabolite biosynthesis. In Artemisia argyi, T-shaped non-glandular trichomes (TSTs) are a defining morphological feature and the primary structural component of moxa floss. We observed pronounced TST accumulation on the lower leaf surfaces. To elucidate the genetic regulation of TST development, we performed comparative transcriptomics of TSTs and non-TST tissues. This identified several MIXTA-like transcription factors (named AarMIXTAs) as key regulators of TST differentiation. Phylogenetic analyses revealed gene expansion and functional divergence between the AarMIXTAs and their homologs in Artemisia annua. Heterologous overexpression of AarMIXTA1.2 in Arabidopsis significantly increased TST density, demonstrating its positive regulatory role via transcriptional activation of downstream targets. These findings elucidate molecular mechanisms underlying TST morphogenesis and provide a genetic framework for enhancing moxa floss yield in A. argyi cultivars.

In plants, autophagy is a conserved recycling system essential for development and stress responses by targeting cellular components for massive degradation in the vacuole. Our previous work suggested that autophagy contributes to Arabidopsis (Arabidopsis thaliana) stress responses by modulating NADPH-oxidase-mediated reactive oxygen species (ROS) homeostasis; however, the molecular link between extracellular ROS and autophagy remains unknown. We performed a yeast two-hybrid screen to identify components involved in autophagy, using the central autophagy component ATG8e as a bait. We identified MEMBRANE ATTACK COMPLEX/PERFORIN-LIKE 2 (MACP2) as an interactor of ATG8e via its the ATG8-interacting motif and confirmed this interaction by co-immunoprecipitation and bimolecular fluorescence complementation assays. MACP2-overexpressing lines showed enhanced sensitivity to nutritional starvation, accelerated leaf senescence, and increased hydrogen peroxide (H₂O₂) levels, resembling the phenotypes of atg mutants defective in autophagy. Conversely, macp2 knockouts exhibited diminished starvation-induced H₂O₂ accumulation and attenuated autophagosome formation and fully suppressed the starvation-hypersensitive phenotypes of the atg5-1 mutant. In particular, MACP2 was degraded through the autophagy machinery during prolonged starvation, suggesting a feedback regulatory mechanism for maintaining MACP2 homeostasis. Our findings suggest that MACP2 acts as a key regulator in autophagy induction by controlling influx of extracellular H₂O₂ in Arabidopsis.

The mannose receptor (MR) is a member of the C-type lectin superfamily and a type I transmembrane protein that functions as a pattern recognition receptor (PRR) in immune responses. In this study, we identified 13 MR genes (RpMR1-13) in the genome of Ruditapes philippinarum and investigated their expression profiles following Vibrio anguillarum challenge. Notably, RpMR1, RpMR2, RpMR3, and RpMR4 exhibited peak expression at 72 h post-infection. We successfully purified the recombinant RpMR1 protein and demonstrated its antibacterial activity against three Gram-negative bacteria (V. splendidus, V. alginolyticus, and V. anguillarum), though it had no effect on Gram-positive bacteria. Furthermore, in vivo injection of RpMR1 significantly reduced mortality in R. philippinarum following V. anguillarum infection. To explore role of RpMR1 in immune signaling, we performed RNA interference (dsRNA-RpMR1) and observed successful gene silencing. Subsequent qRT-PCR analysis revealed that RpMR1 knockdown significantly suppressed TLR4 expression (P< 0.05) under V. anguillarum stress, confirming an interaction between RpMR1 and TLR4 in the immune response. This study provides the first functional evidence of mannose receptor-mediated immunity in mollusks, offering new insights into the molecular defense mechanisms of R. philippinarum against bacterial infection.

Arbuscular mycorrhizal fungi (AMF) have the potential to enhance plant tolerance to abiotic stresses. However, the impact of AMF on the rhizosphere bacterial community of tobacco under conditions of low nutrient availability remains unclear. This study investigated the influence of inoculating Claroideoglomus etunicatum on the tobacco rhizosphere bacterial community and the microbial mechanisms by which AMF enhanced plants antioxidant capacity, employing Illumina MiSeq high-throughput sequencing. The findings indicated that AMF significantly increased both the aboveground and belowground fresh weight, as well as the plant height of tobacco. AMF inoculation led to elevated activities of catalase (CAT) and superoxide dismutase (SOD), a reduction in malondialdehyde (MDA) content, and an overall enhancement of the plants antioxidant capacity. Phylogenetic analysis demonstrated that AMF modified the bacterial community structure and significantly enriched beneficial rhizosphere bacteria, predominantly from the phyla Proteobacteria, Chloroflexi, Actinobacteriota, and Myxococcota, thereby facilitating tobacco growth. The network analysis revealed that the incorporation of arbuscular mycorrhizal fungi (AMF) contributed to increased stability within the bacterial community, enriched species diversity, and more intricate ecological networks. AMF enhanced interactions and positive correlations among bacterial species, indicating that heightened microbial synergy is associated with improved symbiotic relationships. Furthermore, the structural equation model demonstrated that AMF bolstered the plants antioxidant capacity by modulating the rhizosphere bacterial community. This study elucidates the impact of AMF on the tobacco rhizosphere bacterial community, providing a theoretical basis for promoting tobacco growth.