Identification and functional analysis of a serine protease inhibitor using machine learning strategy.

In the intricate realm of animal biology, a multitude of vital processes heavily rely on precisely orchestrated proteinase cascades, but the potential for havoc makes proteinase inhibitors indispensable, with serine proteinase inhibitors (serpins) at the forefront, serving as custodians of homeostasis and participating in various critical biological processes. Importantly, there are still many unexplored facets of serpin functionality. In this study, we focused on the serpin family proteins from Marsupenaeus japonicus, utilizing a fine-tuned pretrained protein language model. This approach led to the identification and evolutionary validation of 28 serpins, one of which, referred to as Mjserpin-1, was both computationally and experimentally demonstrated to show potential as an antiviral and apoptosis inhibitor. Our research unveils exciting prospects for the fusion of state-of-the-art artificial intelligence and rich bioinformatics, holding the promise of significant discoveries that could pave the way for future therapeutic advancements.

Generation and application of a novel transgenic zebrafish line Tg(GAcyp1a:eGFP/Luc) as an in vivo assay to sensitive and specific monitoring of DLCs in the environment.

CYP1A is the most commonly used biomarker and transgenic fish which carrying a cyp1a promoter to drive a reporter gene can be used as reliable way to monitor dioxin/dioxin-like compounds (DLCs) in the environment. Here, we cloned the cyp1a promoter of Gambusia affinis and this promoter showed stronger transcriptional activity than that of zebrafish. Then, a Tg(GAcyp1a:eGFP/Luc) transgenic zebrafish line was first constructed with the G. affinis cyp1a promoter driving eGFP expression using meganuclease I-SceI mediated transgenesis technology. The Tg(GAcyp1a:eGFP/Luc) larvae at 72 h post-fertilization (hpf) were tested by exposing to TCDD for 72 h, and induced GFP was mainly expressed in the liver with low background. The Tg(GAcyp1a:eGFP/Luc) zebrafish showed high sensitivity (limit of detection of 0.322 ng/L TCDD and 0.7 TEQ-ng/L PCDD/Fs) and specificity (insensitive to responses to PAHs and PCBs). In addition, the transgenic line showed a low detection concentration of the DLCs contaminated environmental samples (as low as 1.8 TEQ-ng/L), and the eGFP fluorescence intensity and the chemical-TEQ values were closely correlated. In conclusion, a sensitively and specifically transgenic zebrafish line was established to convenient and effective to detect DLCs in the environment.

The impact of deleting the mitfa gene in zebrafish on the intestinal microbiota community.

To explore the relationship between the mitfa gene and intestinal microbiota, the 16S rRNA gene amplicon sequencing was performed to compare the intestinal microbiota composition of the mitfa knockout zebrafish line (CKO group) and the wild-type zebrafish (WT group) in this study. The results showed that the Fusobacteria and Firmicutes were significantly decreased and the Dependentiae and Patescibacteria were significantly increased in the CKO group at the phylum level. Furthermore, the relative abundance of Citrobacter, Gordonia, Mesorhizobium, Legionella, and Bradyrhizobium were extremely higher in the CKO group, whereas the other four genera Nocardia, Pannonibacter, Shinella, and Cetobacterium were significantly declined in the CKO group at the genus level. Due to these changed intestinal microbiota appear to be related to lipid metabolism and immunity, eight lipid metabolism-related genes and nine inflammation-related genes were detected in the intestinal. The results showed that the expression levels of these genes were significant differences between the CKO and WT group. These results indicated that the deletion of mitfa can affect the expression levels of immune and metabolism-related genes, and causing changes in the composition of the intestinal microbiota.