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Insulin-like growth factor binding protein 5 (IGFBP5) exerts an essential biological role in many processes, including apoptosis, cellular differentiation, growth, and immune responses. However, compared to mammalians, our knowledge of IGFBP5 in teleosts remains limited. In this study, TroIGFBP5b, an IGFBP5 homologue from golden pompano ( ) was identified. Quantitative real-time PCR (qRT-PCR) was used to check its mRNA expression level in healthy condition and after stimulation. overexpression and RNAi knockdown method were performed to evaluate the antibacterial profile. We constructed a mutant in which HBM was deleted to better understand the mechanism of its role in antibacterial immunity. Subcellular localization and nuclear translocation were verified by immunoblotting. Further, proliferation of head kidney lymphocytes (HKLs) and phagocytic activity of head kidney macrophages (HKMs) were detected through CCK-8 assay and flow cytometry. Immunofluorescence microscopy assay (IFA) and dual luciferase reporter (DLR) assay were used to evaluate the activity in nuclear factor-κB (NF-κβ) pathway. The TroIGFBP5b mRNA expression level was upregulated after bacterial stimulation. , TroIGFBP5b overexpression significantly improved the antibacterial immunity of fish. In contrast, TroIGFBP5b knockdown significantly decreased this ability. Subcellular localization results showed that TroIGFBP5b and TroIGFBP5b-δHBM were both present in the cytoplasm of GPS cells. After stimulation, TroIGFBP5b-δHBM lost the ability to transfer from the cytoplasm to the nucleus. In addition, rTroIGFBP5b promoted the proliferation of HKLs and phagocytosis of HKMs, whereas rTroIGFBP5b-δHBM, suppressed these facilitation effects. Moreover, the antibacterial ability of TroIGFBP5b was suppressed and the effects of promoting expression of proinflammatory cytokines in immune tissues were nearly lost after HBM deletion. Furthermore, TroIGFBP5b induced NF-κβ promoter activity and promoted nuclear translocation of p65, while these effects were inhibited when the HBM was deleted. Taken together, our results suggest that TroIGFBP5b plays an important role in golden pompano antibacterial immunity and activation of the NF-κβ signalling pathway, providing the first evidence that the HBM of TroIGFBP5b plays a critical role in these processes in teleosts.

Background Multi-population genomic prediction can rapidly expand the size of the reference population and improve genomic prediction ability. Machine learning (ML) algorithms have shown advantages in single-population genomic prediction of phenotypes. However, few studies have explored the effectiveness of ML methods for multi-population genomic prediction. Results In this study, 3720 Yorkshire pigs from Austria and four breeding farms in China were used, and single-trait genomic best linear unbiased prediction (ST-GBLUP), multitrait GBLUP (MT-GBLUP), Bayesian Horseshoe (BayesHE), and three ML methods (support vector regression (SVR), kernel ridge regression (KRR) and AdaBoost.R2) were compared to explore the optimal method for joint genomic prediction of phenotypes of Chinese and Austrian pigs through 10 replicates of fivefold cross-validation. In this study, we tested the performance of different methods in two scenarios: (i) including only one Austrian population and one Chinese pig population that were genetically linked based on principal component analysis (PCA) (designated as the “two-population scenario”) and (ii) adding reference populations that are unrelated based on PCA to the above two populations (designated as the “multi-population scenario”). Our results show that, the use of MT-GBLUP in the two-population scenario resulted in an improvement of 7.1% in predictive ability compared to ST-GBLUP, while the use of SVR and KKR yielded improvements in predictive ability of 4.5 and 5.3%, respectively, compared to MT-GBLUP. SVR and KRR also yielded lower mean square errors (MSE) in most population and trait combinations. In the multi-population scenario, improvements in predictive ability of 29.7, 24.4 and 11.1% were obtained compared to ST-GBLUP when using, respectively, SVR, KRR, and AdaBoost.R2. However, compared to MT-GBLUP, the potential of ML methods to improve predictive ability was not demonstrated. Conclusions Our study demonstrates that ML algorithms can achieve better prediction performance than multitrait GBLUP models in multi-population genomic prediction of phenotypes when the populations have similar genetic backgrounds; however, when reference populations that are unrelated based on PCA are added, the ML methods did not show a benefit. When the number of populations increased, only MT-GBLUP improved predictive ability in both validation populations, while the other methods showed improvement in only one population.

MicroRNAs (miRNAs) could regulate various biological processes. Nervous necrosis virus (NNV) is one of the primary germs of the Humpback grouper (Cromileptes altivelis), a commercial fish of great importance for Asian aquaculture. However, there is limited available information on the host-virus interactions of C. altivelis. miRNAs have been shown to play key roles in the host response to infection by a variety of pathogens. To better understand the regulatory mechanism of miRNAs, we constructed miRNA transcriptomes and identified immune-related miRNAs of C. altivelis spleen in response to NNV infection. Reads from the three libraries were mapped onto the Danio rerio reference genome. As a result, a total of 942 mature miRNAs were determined, with 266 known miRNAs and 676 novel miRNAs. Among them, thirty-two differentially expressed miRNAs (DEmiRs) were identified compared to the PBS control. These DEmiRs were targeted on 895 genes, respectively, by using miRanda v3.3a. Then, 14 DEmiRs were validated by qRT-PCR and showed consistency with those obtained from high-throughput sequencing. In order to study the relationship between viral infection and host miRNA, a cell line from C. altivelis brain (CAB) was used to examine the expressions of five known DEmiRs (miR-132-3p, miR-194a, miR-155, miR-203b-5p, and miR-146) during NNV infection. The results showed that one miRNA, cal-miRNA-155, displayed significantly increased expression in response to the virus infection. Subsequently, it was proved that overexpression of cal-miR-155 enhanced cell apoptosis with or without NNV infection and inhibited virus replication in CAB cells. Oppositely, the cal-miRNA-155 inhibitor markedly suppressed apoptosis in CAB cells. The results of the apoptosis-related genes mRNA expression also showed the regulation of cal-miR-155 on the apoptosis process in CAB cells. These findings verify that miR-155 might exert a function as a pro-apoptotic factor in reply to NNV stimulation in CAB cells and help us further study the molecular mechanisms of the pathogenesis of NNV in C. altivelis.

The spread of invasive species (IS) has the potential to upset ecosystem balances. In extreme cases, this can hinder economical utilization of both aquatic (fisheries) and terrestrial (agricultural) systems. As a result, many countries regard risk assessment of IS as an important process for solving the problem of biological invasion. Yet, some IS are purposefully introduced for what is seen as their potential economic benefits. Thus, conducting IS risk assessments and then formulating policies based on scientific information will allow protocols to be developed that can reduce problems associated with IS incursions, whether occurring purposefully or not. However, the risk assessment methods currently adopted by most countries use qualitative or semiquantitative methodologies. Currently, there is a mismatch between qualitative and quantitative assessments. Moreover, most assessment systems are for terrestrial animals. What is needed is an assessment system for aquatic animals; however, those currently available are relatively rudimentary. To fill this gap, we used the analytic hierarchy process (AHP) to build a risk assessment model system for aquatic IS. Our AHP has four primary indexes, twelve secondary indexes, and sixty tertiary indexes. We used this AHP to conduct quantitative risk assessments on five aquatic animals that are typically introduced in China, which have distinct biological characteristics, specific introduction purposes, and can represent different types of aquatic animals. The assessment results show that the risk grade for Pterygoplichthys pardalis is high; the risk grade for Macrobrachium rosenbergii, Crassostrea gigas, and Trachemys scripta elegans is medium; and the grade risk for Ambystoma mexicanum is low. Risk assessment of the introduction of aquatic animals using our AHP is effective, and it provides support for the introduction and healthy breeding of aquatic animals. Thus, the AHP model can provide a basis for decision-making risk management concerning the introduction of species.

MicroRNAs (miRNAs) could regulate various biological processes. Nervous necrosis virus (NNV) is one of the primary germs of the Humpback grouper (Cromileptes altivelis), a commercial fish of great importance for Asian aquaculture. However, there is limited available information on the host-virus interactions of C. altivelis. miRNAs have been shown to play key roles in the host response to infection by a variety of pathogens. To better understand the regulatory mechanism of miRNAs, we constructed miRNA transcriptomes and identified immune-related miRNAs of C. altivelis spleen in response to NNV infection. Reads from the three libraries were mapped onto the Danio rerio reference genome. As a result, a total of 942 mature miRNAs were determined, with 266 known miRNAs and 676 novel miRNAs. Among them, thirty-two differentially expressed miRNAs (DEmiRs) were identified compared to the PBS control. These DEmiRs were targeted on 895 genes, respectively, by using miRanda v3.3a. Then, 14 DEmiRs were validated by qRT-PCR and showed consistency with those obtained from high-throughput sequencing. In order to study the relationship between viral infection and host miRNA, a cell line from C. altivelis brain (CAB) was used to examine the expressions of five known DEmiRs (miR-132-3p, miR-194a, miR-155, miR-203b-5p, and miR-146) during NNV infection. The results showed that one miRNA, cal-miRNA-155, displayed significantly increased expression in response to the virus infection. Subsequently, it was proved that overexpression of cal-miR-155 enhanced cell apoptosis with or without NNV infection and inhibited virus replication in CAB cells. Oppositely, the cal-miRNA-155 inhibitor markedly suppressed apoptosis in CAB cells. The results of the apoptosis-related genes mRNA expression also showed the regulation of cal-miR-155 on the apoptosis process in CAB cells. These findings verify that miR-155 might exert a function as a pro-apoptotic factor in reply to NNV stimulation in CAB cells and help us further study the molecular mechanisms of the pathogenesis of NNV in C. altivelis.

Despite the increasing number of genomes, the annotation of protein-coding genes is still lacking. In some genomes where transcriptome data is not available, various tools have been developed to annotate genes based on homologous proteins, but each tool has its limitations. Here, we propose quickprot, a user-friendly command-line tool that constructs a set of redundancy-free gene models from the target genome based on the homologous protein sequences of a set of closely related species. We tested its applicability in stonefish, and the results showed that it has high accuracy and runs faster than existing tools. This low-cost, high-precision annotation method is expected to become a useful tool for genome annotation, which will contribute to the research of comparative genomics. The software is implemented in Python and licensed under the MIT License. The source code, documentation, and tutorials can be obtained at https://github.com/thecgs/quickprot.

Bone metastasis is associated with cancer‐related death in patients with prostate cancer (PCa). Long noncoding RNAs (lncRNAs) play critical roles in tumor progression of PCa. Nevertheless, the biological function of lncRNAs in PCa bone metastasis remains unclear. PCAT7 was identified as a bone metastasis‐related lncRNA via analyzing TCGA dataset. Meanwhile, PCAT7 was found to be elevated in primary PCa tissues with bone metastasis and associated with bone metastasis status and poor prognosis of patients with PCa. Functionally, our results reveal that PCAT7 overexpression promotes PCa bone metastasis in vivo, as well as migration, invasion, and EMT of PCa cells in vitro; on the contrary, PCAT7 knockdown has an inverse effect. Mechanistically, PCAT7 activates TGF‐β/SMAD signaling by upregulating TGFBR1 expression via sponging miR‐324‐5p. In turn, TGF‐β signaling forms a positive feedback loop with PCAT7 via SMAD3/SP1 complex‐induced PCAT7 upregulation. Finally, the clinical positive correlation between PCAT7 and TGFBR1 and TGF‐β signaling activity, and the negative association with miR‐324‐5p are further demonstrated in PCa tissues and clinical primary PCa cells. This study reveals a novel mechanism that is responsible for the constitutive activation of TGF‐β signaling in PCa bone metastasis, implying that PCAT7 can act as a potential therapeutic target against bone metastasis of PCa via disrupting the constitutive active loop between PCAT7 and TGF‐β signaling. lncRNA PCAT7 is upregulated in primary prostate cancer tissues with bone metastasis. PCAT7 activates TGF‐β/SMAD signaling by upregulating TGFBR1 expression via sponging miR‐324‐5p. In turn, TGF‐β signaling forms a positive feedback loop with PCAT7 via SMAD3/SP1 complex‐induced PCAT7 upregulation. This feedback loop promotes prostate cancer bone metastasis.

We previously showed that the fatty liver formations observed in overfed geese are accompanied by the activation of the PI3K-Akt-mTOR pathway and an increase in plasma insulin concentrations. Recent studies have suggested a crucial role for the PI3K-Akt-mTOR pathway in regulating lipid metabolism; therefore, we hypothesized that insulin affects goose hepatocellular lipid metabolism through the PI3K-Akt-mTOR signaling pathway. Goose primary hepatocytes were isolated and treated with serum-free media supplemented with PI3K-Akt-mTOR pathway inhibitors (LY294002, rapamycin, and NVP-BEZ235, respectively) and 50 or 150 nmol/L insulin. Insulin induced strong effects on lipid accumulation as well as the mRNA and protein levels of genes involved in lipogenesis, fatty acid oxidation, and VLDL-TG assembly and secretion in primary goose hepatocytes. The stimulatory effect of insulin on lipogenesis was significantly decreased by treatment with PI3K-Akt-mTOR inhibitors. These inhibitors also rescued the insulin-induced down-regulation of fatty acid oxidation and VLDL-TG assembly and secretion. These findings suggest that the stimulatory effect of insulin on lipid deposition is mediated by PI3K-Akt-mTOR regulation of lipogenesis, fatty acid oxidation, and VLDL-TG assembly and secretion in goose hepatocytes.