Carboxyl ester lipase is highly conserved in utilizing maternal supplied lipids during early development of zebrafish and human

Transcriptomics and Phenotypic Analysis of gpr56 Knockout in Zebrafish

The adhesion G-protein-coupled receptor is a seven-transmembrane receptor protein with a complex structure. Impaired GPR56 has been found to cause developmental damage to the human brain, resulting in intellectual disability and motor dysfunction. To date, studies on gpr56 deficiency in zebrafish have been limited to the nervous system, and there have been no reports of its systemic effects on juvenile fish at developmental stages. In order to explore the function of gpr56 in zebrafish, the CRISPR/Cas9 gene-editing system was used to construct a gpr56-knockout zebrafish. Subsequently, the differentially expressed genes (DEGs) at the transcriptional level between the 3 days post fertilization (dpf) homozygotes of the gpr56 mutation and the wildtype zebrafish were analyzed via RNA-seq. The results of the clustering analysis, quantitative PCR (qPCR), and in situ hybridization demonstrated that the expression of innate immunity-related genes in the mutant was disordered, and multiple genes encoding digestive enzymes of the pancreatic exocrine glands were significantly downregulated in the mutant. Motor ability tests demonstrated that the gpr56^-/- zebrafish were more active, and this change was more pronounced in the presence of cold and additional stimuli. In conclusion, our results revealed the effect of gpr56 deletion on the gene expression of juvenile zebrafish and found that the gpr56 mutant was extremely active, providing an important clue for studying the mechanism of gpr56 in the development of juvenile zebrafish.

Comparative Study of the Molecular Characterization, Evolution, and Structure Modeling of Digestive Lipase Genes Reveals the Different Evolutionary Selection Between Mammals and Fishes

Vertebrates need suitable lipases to digest lipids for the requirement of energy and essential nutrients; however, the main digestive lipase genes of fishes have certain controversies. In this study, two types of digestive lipase genes (pancreatic lipase (pl) and bile salt-activated lipase (bsal)) were identified in mammals and fishes. The neighborhood genes and key active sites of the two lipase genes were conserved in mammals and fishes. Three copies of PL genes were found in mammals, but only one copy of the pl gene was found in most of the fish species, and the pl gene was even completely absent in some fish species (e.g., zebrafish, medaka, and common carp). Additionally, the hydrophobic amino acid residues (Ile and Leu) which are important to pancreatic lipase activity were also absent in most of the fish species. The PL was the main digestive lipase gene in mammals, but the pl gene seemed not to be the main digestive lipase gene in fish due to the absence of the pl gene sequence and the important amino acid residues. In contrast, the bsal gene existed in all fish species, even two to five copies of bsal genes were found in most of the fishes, but only one copy of the BSAL gene was found in mammals. The amino acid residues of bile salt-binding sites and the three-dimensional (3D) structure modeling of Bsal proteins were conserved in most of the fish species, so bsal might be the main digestive lipase gene in fish. The phylogenetic analysis also indicated that pl or bsal showed an independent evolution between mammals and fishes. Therefore, we inferred that the evolutionary selection of the main digestive lipase genes diverged into two types between mammals and fishes. These findings will provide valuable evidence for the study of lipid digestion in fish.

Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits

BACKGROUND

Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits.

RESULTS

Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits.

CONCLUSIONS

The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.

Photoaging enhanced the adverse effects of polyamide microplastics on the growth, intestinal health, and lipid absorption in developing zebrafish

The safety of microplastics (MPs) and associated health effects has been one of the major concerns worldwide. However, the role of photoaging toward the risk of MPs in water ecosystems remains inconclusive yet. In this study, the size of polyamide (PA, ∼32.50 μm) MPs was obviously decreased after photoaging in water containing fulvic acid (FA) and humic acid (HA) (∼19.75 and ∼24.30 μm, respectively). Nanoplastics were formed (4.65% and 2.03%, respectively) and hydrophilia and colloidal stability was improved due to the formation of oxygen-containing functional groups. FA-aged PA exhibited higher inhibition on body length and weight of developing zebrafish than HA-aged and pristine PA. Photoaged MPs in intestine were more difficult to be depurated by zebrafish, leading to the disappearance of intestinal folding, shedding of more enterocytes, and emaciation of intestinal microvilli. Dietary lipid digestion in larvae was inhibited by aged PA due to oxidative stress-triggered lipid peroxidation and inhibition of lipase activities and bile acids secretion. Exposure of photoaged MPs down-regulated genes (cd36, dgat1a, dgat2, mttp, etc.) associated with triglyceride resynthesis and transportation, resulting in lipid maladsorption and growth inhibition. Our findings highlight the potential negative effects of environmentally aged MPs on diet digestion and nutrient assimilation in fish.

Association Analysis of Variants of DSCAM and BACE2 With Hirschsprung Disease Susceptibility in Han Chinese and Functional Evaluation in Zebrafish

Hirschsprung disease (HSCR) has a higher incidence in children with Down syndrome (DS), which makes trisomy 21 a predisposing factor to HSCR. DSCAM and BACE2 are close together on the HSCR-associated critical region of chromosome 21. Common variants of DSCAM and rare variants of BACE2 were implicated to be associated with sporadic HSCR. However, the submucosal neuron defect of DS mouse model could not be rescued by normalization of Dscam. We aimed to explore the contribution of DSCAM and BACE2 to the development of the enteric nervous system (ENS) and HSCR susceptibility. We genotyped 133 tag single-nucleotide polymorphisms (SNPs) in DSCAM and BACE2 gene region in 420 HSCR patients and 1,665 controls of Han Chinese. Expression of DSCAM and BACE2 homologs was investigated in the developing gut of zebrafish. Overexpression and knockdown of the homologs were performed in zebrafish to investigate their roles in the development of ENS. Two DSCAM SNPs, rs430255 (P_Addtive = 0.0052, OR = 1.36, 95% CI: 1.10–1.68) and rs2837756 (P_Addtive = 0.0091, OR = 1.23, 95% CI: 1.05–1.43), showed suggestive association with HSCR risk. Common variants in BACE2 were not associated with HSCR risk. We observed dscama, dscamb, and bace2 expression in the developing gut of zebrafish. Knockdown of dscama, dscamb, and bace2 caused a reduction of enteric neurons in the hindgut of zebrafish. Overexpression of DSCAM and bace2 had no effects on neuron number in the hindgut of zebrafish. Our results suggested that common variation of DSCAM contributed to HSCR risk in Han Chinese. The dysfunction of both dscams and bace2 caused defects in enteric neuron, indicating that DSCAM and BACE2 might play functional roles in the occurrence of HSCR. These novel findings might shed new light on the pathogenesis of HSCR.

Synergistic growth inhibition effect of TiO2 nanoparticles and tris(1,3-dichloro-2-propyl) phosphate on earthworms in soil

The co-existence of organic pollutants and nanoparticles in the environment may lead to combined biological effects. The joint toxicity of pollutants and nanoparticles has been receiving increasing attention from researchers, but few studies have focused on soil biota due to the complexity of soil matrices. This study investigated the effects of tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) at 0, 5, and 25 mg/kg and nanoparticulate TiO₂ (nTiO₂) at 0, 500, and 2500 mg/kg in a 3 × 3 factorial arrangement of treatments for 28 days (d) on Eisenia fetida (earthworm). Compared with the control group (the 0 mg/kg TDCIPP + 0 mg/kg nTiO₂ treatment), all other single (TDCIPP or nTiO₂) and binary (TDCIPP + nTiO₂) treatments except for the single 500 mg/kg nTiO₂ treatment significantly reduced the weight gain rate of E. fetida. The binary treatments had significantly greater such effect than their corresponding single treatments, exhibiting a synergistic toxicity between TDCIPP and nTiO2 on the growth of E. fetida. Since TDCIPP and nTiO₂ had no significant effect on their concentrations in the soil or in E. fetida during binary exposure, the synergistic toxicity could be a result of the superimposition of the toxicity pathways of TDCIPP and nTiO₂. Transcriptomic analysis of E. fetida intestinal region revealed that exposure to 25 mg/kg TDCIPP or 2500 mg/kg nTiO₂ affected nutrient-related or cell apoptosis and DNA damage related genes, respectively; their co-exposure greatly inhibited genes related to nutrient digestion and absorption, while causing abnormal transcription of genes related to the development and maintenance of E. fetida's muscles, leading to synergistic toxicity. These findings provide new insights into the environmental risks of organophosphorus flame retardants, nanoparticles, and their co-exposure.

In vivo hepatotoxicity screening of different extracts, components, and constituents of Polygoni Multiflori Thunb. in zebrafish (Danio rerio) larvae

Polygonum multiflorum Thunb. (PM) is a traditional Chinese medicine, commonly used to treat a variety of diseases. However, the hepatotoxicity associated with PM hampers its clinical application and development. In this study, we refined the zebrafish hepatotoxicity model with regard to the following endpoints: liver size, liver gray value, and the area of yolk sac. The levels of alanine aminotransferase, aspartate transaminase, albumin, and microRNAs-122 were evaluated to verify the model. Subsequently, this model was used to screen different extracts, components, and constituents of PM, including 70 % EtOH extracts of PM, four fractions from macroporous resin (components A, B, C, and D), and 19 compounds from component D. We found that emodin, chrysophanol, emodin-8-O-β-D-glucopyranoside, (cis)-emodin-emodin dianthrones, and (trans)-emodin-emodin dianthrones showed higher hepatotoxicity compared to other components in PM, whereas polyphenols showed lower hepatotoxicity. To the best of our knowledge, this study is the first to identify that dianthrones may account for the hepatotoxicity of PM. We believe that these findings will be helpful in regulating the hepatotoxicity of PM.