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The grass carp (Ctenopharyngodon idella) is the most productive freshwater fish in the world. However, little is known about the functional genes and genetic regulatory systems that control its growth traits. In this study, we used two superior grass carp parents with fast-growing offspring and two inferior grass carp parents with slow-growing offspring to create three grass carp families, namely, the superior-superior family (SS), the inferior-inferior family (II) and the superior-inferior family (SI). The average body weight of the offspring of these families showed a stable ranking (SS > SI > II) under the satiation and starvation feeding modes. Then, the transcriptomes of the brain and the hepatopancreas of grass carp with different growth rates were obtained for each family, and it was found that the number of differentially expressed genes (DEGs) in the different organs showed family specificity. The DEGs were mainly found in the hepatopancreas of SS and the whole brain of II, while they were more balanced in SI. There were 14 common DEGs among the three families, including 3 negatively correlated genes (ahsg2, lect2 and drd5) and 11 positively correlated genes (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3, fabp7 and endod1). Deleting ahsg2 in zebrafish significantly increased the upper limit of individual body weight during the experiment, but only slightly increased the average growth rate of the population. In addition, we analyzed the SNP in each family and preliminarily analyzed the potential genetic mechanisms of family-specific regulation of growth traits. This study revealed for the first time the family specificity of the growth regulation mechanism of grass carp at the transcriptional level, verified the function of a growth negative regulatory gene ahsg2, and further analyzed the possible molecular mechanism of growth differences among different families. This study provides new insights into the genetic regulation mechanism of grass carp growth.

BackgroundAlthough zebrafish are commonly used to study intestinal mucosal immunity, no dedicated procedure for isolating immune cells from zebrafish intestines is currently available. A speedy and simple operating approach for preparing cell suspension from mucosa has been devised to better understanding of intestinal cellular immunity in zebrafish.Methods and resultsThe mucosal villi were separated away from the muscle layer by repeated blows. The complete deprivation of mucosa was done and evidenced by HE and qPCR results. Higher expression of both innate (mpeg1, mpx, and lck) and adaptive immune genes (zap70, blnk, foxp3a, and foxp3b) was revealed compared to cells obtained by typical mesh rubbing. The cytometric results also revealed that the tested operation group had a higher concentration and viability. Further, fluorescent-labelled immune cells from 3mo Tg(lyz:DsRED2), Tg(mpeg1:EGFP), Tg(Rag2:DsRED), and Tg(lck:EGFP), were isolated and evaluated for the proportion, and immune cells’ type could be inferred from the expression of marker genes. The transcriptomic data demonstrated that the intestinal immune cell suspension made using the new technique was enriched in immune-related genes and pathways, including il17a/f, il22, cd59, and zap70, as well as pattern recognition receptor signaling and cytokine-cytokine receptor interaction. In addition, the low expression of DEG for the adherent and close junctions indicated less muscular contamination. Also, lower expression of gel-forming mucus-associated genes in the mucosal cell suspension was consistent with the current less viscous cell suspension. To apply and validate the developed manipulation, enteritis was induced by soybean meal diet, and immune cell suspensions were analyzed by flow cytometry and qPCR. The finding that in enteritis samples, there was inflammatory increase of neutrophils and macrophages, was in line with upregulated cytokines (il8 and il10) and cell markers (mpeg1 and mpx).ConclusionAs a result, the current work created a realistic technique for studying intestinal immune cells in zebrafish. The immune cells acquired may aid in further research and knowledge of intestinal illness at the cellular level.

Background: Delayed postoperative extubation and admission to intensive care units (ICU) in children undergoing major scoliosis surgery may increase postoperative complications, prolong hospital stay and increase medical costs. However, after scoliosis orthopaedic surgery, whether a child will require delayed extubation or ICU admission is not fully understood. This study reviewed the risk factors for delayed extubation and ICU admission after scoliosis orthopaedic surgery in children.Method: We reviewed and analysed the electronic medical records of paediatric patients (≤ 18 years) undergoing posterior spinal fusion surgery from January 2018 to November 2021. The patients’ characteristics (age, sex, body mass index, American Society of Anesthesiologists grade, preoperative lung function, combined heart disease), preoperative Cobb angle, scoliosis type, orthopaedic rate, vertebral fusion segments, pedicle screws, surgical osteotomy, intraoperative bleeding, intraoperative allotransfusion, intraoperative haemoglobin changes, intraoperative mean arterial pressure changes, intraoperative tidal volume (ml/kg), surgical time, postoperative extubation and admission to the ICU were collected. The main outcomes were delayed postoperative extubation and postoperative admission to the ICU. Multivariate logistic regression models were used to determine the risk factors for delayed extubation and admission to the ICU.Results: We enrolled 246 children who met the inclusion criteria, of which 23 (9.3%) had delayed extubation and 81 (32.9%) were transferred to the ICU after surgery. High American Society of Anesthesiologists grade (odds ratio (OR) = 5.42; 95% confidence interval (CI): 1.49–19.78; P = 0.010), high Cobb angle (OR = 1.04; 95% CI: 1.02–1.07; P Conclusions: The most common risk factor for delayed postoperative extubation and ICU admission in paediatric patients who underwent posterior spinal fusion was a high Cobb angle. Our results demonstrated that determining poor prognostic risk factors may help optimise perioperative management strategies for children undergoing complicated spinal surgery.

More than one million prostate biopsies are performed in the United States every year. A failure to find cancer is not definitive in a significant percentage of patients due to the presence of equivocal structures or continuing clinical suspicion. We have identified gene expression changes in stroma that can detect tumor nearby. We compared gene expression profiles of 13 biopsies containing stroma near tumor and 15 biopsies from volunteers without prostate cancer. About 3,800 significant expression changes were found and thereafter filtered using independent expression profiles to eliminate possible age-related genes and genes expressed at detectable levels in tumor cells. A stroma-specific classifier for nearby tumor was constructed on the basis of 114 candidate genes and tested on 364 independent samples including 243 tumor-bearing samples and 121 nontumor samples (normal biopsies, normal autopsies, remote stroma, as well as stroma within a few millimeters of tumor). The classifier predicted the tumor status of patients using tumor-free samples with an average accuracy of 97% (sensitivity = 98% and specificity = 88%) whereas classifiers trained with sets of 100 randomly generated genes had no diagnostic value. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for categorizing the presence of tumor in patients when a prostate sample is derived from near the tumor but does not contain any recognizable tumor. Cancer Res; 71(7); 2476–87. ©2011 AACR.

Tissue samples from many diseases have been used for gene expression profiling studies, but these samples often vary widely in the cell types they contain. Such variation could confound efforts to correlate expression with clinical parameters. In principle, the proportion of each major tissue component can be estimated from the profiling data and used to triage samples before studying correlations with disease parameters. Four large gene expression microarray data sets from prostate cancer, whose tissue components were estimated by pathologists, were used to test the performance of multivariate linear regression models for in silico prediction of major tissue components. Ten-fold cross-validation within each data set yielded average differences between the pathologists' predictions and the in silico predictions of 8% to 14% for the tumor component and 13% to 17% for the stroma component. Across independent data sets that used similar platforms and fresh frozen samples, the average differences were 11% to 12% for tumor and 12% to 17% for stroma. When the models were applied to 219 arrays of “tumor-enriched” samples in the literature, almost one quarter were predicted to have 30% or less tumor cells. Furthermore, there was a 10.5% difference in the average predicted tumor content between 37 recurrent and 42 nonrecurrent cancer patients. As a result, genes that correlated with tissue percentage generally also correlated with recurrence. If such a correlation is not desired, then some samples might be removed to rebalance the data set or tissue percentages might be incorporated into the prediction algorithm. A web service, “CellPred,” has been designed for the in silico prediction of sample tissue components based on expression data. Cancer Res; 70(16); 6448–55. ©2010 AACR.

Supplementary Tables 1-4, Figures 1-4 from Diagnosis of Prostate Cancer Using Differentially Expressed Genes in Stroma

Supplementary Figure Legends 1-3 from In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data

Supplementary Figures 1-3 from In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data

Supplementary Tables 1-5 from In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data

Although it is widely accepted that in the early stages of virus infection, fish pattern recognition receptors are the first to identify viruses and initiate innate immune responses, this process has never been thoroughly investigated. In this study, we infected larval zebrafish with four different viruses and analyzed whole-fish expression profiles from five groups of fish, including controls, at 10 h after infection. At this early stage of virus infection, 60.28% of the differentially expressed genes displayed the same expression pattern across all viruses, with the majority of immune-related genes downregulated and genes associated with protein synthesis and sterol synthesis upregulated. Furthermore, these protein synthesis- and sterol synthesis-related genes were strongly positively correlated in the expression pattern of the rare key upregulated immune genes, IRF3 and IRF7, which were not positively correlated with any known pattern recognition receptor gene. We hypothesize that viral infection triggered a large amount of protein synthesis that stressed the endoplasmic reticulum and the organism responded to this stress by suppressing the body’s immune system while also mediating an increase in steroids. The increase in sterols then participates the activation of IRF3 and IRF7 and triggers the fish’s innate immunological response to the virus infection.

K63-linked polyubiquitination of the neurodegenerative disease-associated misfolded protein copper-zinc superoxide dismutase 1 (SOD1) is associated with the formation of inclusion bodies. Highly expressed E3 ligase Smad ubiquitylation regulatory factor 1 (Smurf1) promotes cellular homeostasis through the enhanced capability of aggregate degradation. However, it is not well explored the role of Smurf1 in the dynamics of SOD1 aggresomes. In this study, we report that Smurf1 promotes the recruitment of SOD1 to form aggresomes. Mechanistically, Smurf1 interacts with mutant SOD1 to promote aggresome formation by modification of its K63-linked polyubiquitination. Moreover, overexpressed Smurf1 enhances mutant SOD1 aggresome formation and autophagic degradation to prevent cell death. Thus, our data suggest that Smurf1 plays an important role in attenuating protein misfolding-induced cell toxicity by both driving the sequestration of misfolded SOD1 into aggresomes and autophagic degradation.

A BODIPY-based copper cyclic trinuclear complex has been prepared, exhibiting strong visible light absorption and long-lived triplet excited state, which can serve as a photosensitizer for light-induced oxidation reactions.

Additional file 1: Figure S1. The hydrodynamic sizes of different samples. Figure S2. TG curves, XPS spectra, FT-IR spectra, and zeta potential of different samples. STEM image of FMS. Figure S3. Hydrodynamic size variation of PDGFB-FMS in different media. Figure S4. TEM images of FMS after different treatments and corresponding hydrodynamic size distribution. Figure S5. T1WI and T2WI of FMS. Figure S6. r1 and r2 values of FMS. Figure S7. r1 value of free Mn2+ ions at 3.0 T, hydrodynamic size distribution of FMS-1 to FMS-5, r1 linear fit curves and r2 linear fit curves of FMS-1 to FMS-5. Figure S8. N2 adsorption–desorption isotherms and corresponding pore size distribution of FS, and FMS-1 to FMS-5. Figure S9. T1–T2WI of FMS with different Fe3O4 to Mn2+ ratios. Figure S10. Fe content of 4T1 cells. Figure S11. CLSM observation: the internalization of PC-3 cells. Figure S12. Colocalization and particle uptake ratios of 4T1 cells. Figure S13. Representative color-coded T1 and T2 map images of 4T1 tumor-bearing mice and T1 and T2 map values analysis. Figure S14. Cytotoxicity of PDGFB-FMS against PC-3 cells. Figure S15. Blood routine examination of mice. Figure S16. The viabilities of THLE-3, 293 T, PC-12, and SH-SY5Y cells. Table S1. ∆r1 and ∆r2 value of FMS under different pH conditions. Table S2. ∆r1 and ∆r2 value of FMS under different GSH conditions. Table S3. In vitro ∆R1 and ∆R2 of 4T1 cells treated with PDGFB-FMS at the presence of different concentrations of GSH.

Homologous to E6AP C‐terminus (HECT)‐type E3 ubiquitin ligase SMAD‐specific E3 ubiquitin protein ligase 1 (Smurf1) was originally identified to ubiquitinate Smad protein in the TGF‐β/BMP signaling pathway. Recently, Smurf1 has been reported to promote tumorigenesis by regulating multiple biological processes. High expression of Smurf1 plays a vital role in brain tumor progression by mediating aberrant cell signaling pathways. Previous reports have shown that Smurf1 is degraded mainly through the ubiquitin–proteasome system, but it remains unclear whether Smurf1 is degraded by autophagy in tumor cells. In this study, we show that autophagy activators promote Smurf1 degradation in glioblastoma (GB) cells. The autophagy receptor p62 colocalizes with ubiquitinated substrates to promote sequestration of cytoplasm cargo into the autophagosome. We report that autophagic degradation of Smurf1 is dependent on p62. Moreover, the autophagic degradation of Smurf1 is prevented in the absence of the HECT domain or E3 ubiquitin ligase activity. We further proved that activation of autophagy leads to a decrease of Smurf1 and the inhibition of the phosphoinositide 3‐kinase/protein kinase B signaling pathway in GB cells. Our results suggest that enhancement of autophagic degradation of Smurf1 may be a potential approach to treating GB., In this article, we report that oncogenic SMAD‐specific E3 ubiquitin protein ligase 1 is degraded by autophagy in a p62 and E3 ubiquitin ligase activity‐dependent manner in glioblastoma cells, a finding that was not previously described. Our research identifies a novel degradation pathway for tumor‐related proteins, which has certain guiding significance for tumor treatment.

Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-β, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs.