The zebrafish intestine and liver, as in other vertebrates, are derived from the endoderm. Great effort has been devoted to deciphering the molecular mechanisms controlling the specification and development of the zebrafish intestine and liver; however, genome-wide comparison of the transcriptomes between these two organs at the larval stage remains unexplored. There is a lack of extensive identification of feature genes marking specific cell types in the zebrafish intestine and liver at 5 days post-fertilization, when the larval fish starts food intake. In this report, through RNA sequencing and single-cell RNA sequencing of intestines and livers separately dissected from wild-type zebrafish larvae at 5 days post-fertilization, together with the experimental validation of 47 genes through RNA whole-mount in situ hybridization, we identified not only distinctive transcriptomes for the larval intestine and liver, but also a considerable number of feature genes for marking the intestinal bulb, mid-intestine and hindgut, and for marking hepatocytes and cholangiocytes. Meanwhile, we identified 135 intestine- and 97 liver-enriched transcription factor genes in zebrafish larvae at 5 days post-fertilization. Our findings provide rich molecular and cellular resources for studying cell patterning and specification during the early development of the zebrafish intestine and liver.

The ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. Whilst the biochemical mechanisms of the SSU processome in 18S rRNA processing and maturation have been extensively studied, how SSU processome components enter the nucleolus has yet to be systematically investigated. Here, in examining the nucleolar localization of 50 human SSU processome components, we found that UTP3, together with another 24 proteins, enter the nucleolus autonomously. For the remaining 25 proteins we found that UTP3/SAS10 assists the nucleolar localization of five proteins (MPP10, UTP25, EMG1 and the two UTP-B components UTP12 and UTP13), likely through its interaction with nuclear importin α. This ‘ferrying’ function of UTP3 was then confirmed as conserved in the zebrafish. We also found that knockdown of human UTP3 impairs cleavage at the A₀-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes the accumulation of aberrantly processed 5′ETS products, which highlights the crucial role of UTP3 in mediating 5′ETS processing. Mechanistically, we found that UTP3 facilitates the degradation of processed 5′ETS by recruiting the RNA exosome component EXOSC10 to the nucleolus. These findings lay the groundwork for studying the mechanism of cytoplasm-to-nucleolus trafficking of SSU processome components.

Skin defects are one of the primary problems that occur in post-harvest grading and processing of loquats. The loquats with skin defects will lead to the loquat being easily destroyed during transportation and storage, which will cause the risk of other loquats being infected, affecting the selling price of loquat. In this paper, a method combining band radio image with improved three-phase level set segmentation algorithm (ITPLSSM) is proposed to achieve high accuracy, rapid, and non-destructive detection of skin defects of loquats. Principal component analysis (PCA) was used to find the characteristic wavelength and PC images to distinguish between four types of skin defects. Determine the best band ratio image based on characteristic wavelength. The band ratio image (Q_782/944) based on PC2 image is the best segmented image. Based on Pseudo-color image enhancement, morphological processing, and local clustering criteria, the band ratio image (Q_782/944) has better contrast between defective area and normal area in loquat. Finally, the ITPLSSM was used to segment the processing band ratio image (Q_782/944), with the accuracy is 95.28 %. The proposed ITPLSSM method is effective in distinguishing with four types of skin defects. Meanwhile, it also effectively segments the images with intensity inhomogeneities.

Xeroderma pigmentosum complementation group C (XPC) protein recognizes bulky DNA adducts to initiate global genomic nucleotide excision repair (GG-NER). Humans carrying germline mutations in the XPC gene display strong susceptibility to skin and certain internal cancers. In addition to its role in NER, recent studies have indicated that XPC is also involved in other DNA damage repair pathways and transcription regulation. In this report, we generated a zebrafish xpc knockout mutant. Zebrafish xpc^−/− mutant fish develop relative normally and are fertile. However, the mutant embryos were more sensitive to ultraviolet (UV) irradiation. Upon UV irradiation, compared with the wild type embryos, mutant embryos accumulated significantly higher levels of unrepaired DNA damages and apoptotic cells, which led to more severe abnormal development. Transcriptome analysis showed that the p53 signal pathway and apoptosis were enriched in the over upregulated genes in UV-irradiated mutant embryos, suggesting that high levels of unrepaired DNA lesions activated p53 to trigger apoptotic activity in mutant embryos. More interestingly, up to 972 genes in the untreated mutant embryos were differentially expressed, compared with those in the untreated WT. Among these differentially expressed genes (DEGs), 379 genes did not respond to UV irradiation, indicating that Xpc plays a role in addition of DNA damage repair. Our results demonstrate that Xpc is an evolutionally conserved factor in NER repair. Zebrafish xpc^−/− mutant also provides a platform to study other functions of Xpc beyond the DNA damage repair.

Insect wing polyphenism enables a single genome to produce distinct wing morphs in response to environmental cues, yet its underlying cellular determinants remain elusive. Here, we perform single-cell RNA sequencing of long-winged- and short-winged-destined wing buds of Pyrrhocoris apterus and Nilaparvata lugens, identifying six conserved cell types with comparable proportions between the two morphs. RNA interference-mediated silencing of 51 marker genes indicates that wing-patterning genes En (epithelial-like cells) and bs (tracheal cells), and cell-cycle genes Anln, CycB3, and cdk1 (neuron cells), are essential for long-winged development, among which En exhibits a specific temporal requirement. Flow cytometry analysis shows that long-winged formation mainly relies on an extended duration of cell proliferation. Cross-species comparisons indicate shared wing cell identities. Our findings indicate that hemipteran short-winged morphs may evolve from ancestral long-winged forms via precise regulation of wing-patterning and cell-cycle gene expression in epithelial‑like, tracheal, and neuron cells. This provides insights into the developmental plasticity of insect tissues at single‑cell resolution.

Adult zebrafish and neonatal mice can fully regenerate their hearts after partial amputation through the proliferation of preexisting cardiomyocytes (CMs). However, the adult mammalian heart has limited regenerative capability following cardiac damage. The reason for this phenomenon remains elusive. Here, we find that docosahexaenoic acid (DHA) is accumulated only in the injured hearts of zebrafish and neonatal mice, but not of adult mice, which coincides with the upregulation of DHA synthesis genes in CMs, fibroblasts, and macrophages near the injury areas. Inhibition of Fads2, a DHA synthesis enzyme, impairs heart regeneration in both zebrafish and neonatal mice. Injection of DHA remodels the transcriptome from injury response to regeneration response and improves cardiac function in adult mice after myocardial infarction. Interestingly, DHA facilitates CM proliferation but inhibits fibrosis and inflammation. Mechanistically, only DHA, but not oleic acid (OA), can trigger the peroxisome proliferator-activated receptor d (PPARD) to bind to the promoter regions of heart regeneration-related genes, such as Mef2d, Phlda3, and Txndc5, to regulate their expression. Molecular docking, molecular dynamics simulations, and mutagenesis experiments suggest that DHA binds to PPARD in a distinct manner compared to OA, which may help explain their differing abilities to influence the expression of heart regeneration genes. Our findings demonstrate that the DHA signal plays an essential and evolutionarily conserved role in heart regeneration and provide a therapeutic potential for myocardial infarction.