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Layer chickens were artificially challenged with infectious bursal disease virus (IBDV), and the kinetics of IFN-λ and antiviral genes in the bursa were explored using quantitative real-time PCR. Data showed that after the chickens were infected with IBDV, the virus load in the bursa of the Fabricius peaked at 96 h and gradually decreased. The relative mRNA expression levels of IFN-λ and antiviral genes (zinc-finger antiviral protein [ZAP], interferon alpha-inducible protein 6 [IFI6], laboratory of genetics and physiology 2 [LGP2], virus inhibitory protein [Viperin], and Mx) of the infected group dramatically increased at 24-168 h compared with those of the negative-infected group. Furthermore, the ZAP mRNA expression peaked at 24 h (3.97-fold). The Viperin mRNA transcript level was highest at 48 h (384.60-fold). The mRNA expression levels of IFI6 (96.31-fold), LGP2 (18.29-fold), and Mx (88.85-fold) peaked at 72 h, and that of IFN-λ was most remarkable at 96 h (2978.81-fold). Furthermore, the ZAP change rule was significantly positively correlated with the change rule of the IBDV load. The mRNA expression levels of IFN-λ and antiviral genes (ZAP, IFI6, LGP2, Viperin, and Mx) increased as the virus expression increased and then decreased. These results further corroborated that the IBDV infection seriously interfered with the chicken's innate immune response., Competing Interests: Declaration of competing interest We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Tropisetron, an antagonist of serotonin type 3 receptors (5-HT 3 Rs), has been investigated in colonic inflammatory process. Since substance P/neurokinin 1 receptor (SP/NK1R) signaling pathway plays a key role in several sensory neuronal inflammatory. We evaluated the anti-inflammatory activity of tropisetron in mice cerebral cortex, and discovered that it was a potential inhibitor in LPS-mediated neuron inflammation through SP/NK1R signaling pathway. We found that tropisetron significantly reduced the increased number of iba-1 positive microglia, down-regulated the gene transcription and protein expression of IL-1β,IL-6 and TNF-α in LPS stimulated cerebral cortex. To characterize the inhibitory mechanism of tropisetron at the SP response in inflammation, we further examined the effect of tropisetron on NF-κB and SP/NK1R signaling pathway in the process of mice cerebral cortex inflammation. We found that tropisetron inhibited the gene transcription and protein expression of NF-κB, SP, NK1R via inhibiting 5-HT 3 R activity. These findings might provide new insights into the anti-inflammatory activities of 5-HT 3 R inhibitor tropisetron, which would be the interaction of serotonin receptor signaling and SP/NK1R pathway. These might highlight their potential to design novel therapeutic strategies to manage inflammatory diseases., (Copyright © 2018 Elsevier B.V. All rights reserved.)

S100 proteins belong to a family of small, acidic, EF-hand Ca ( 2+) -binding proteins and have been found to exert both intracellular and extracellular functions in regulation of Ca ( 2+) homeostasis, cytoskeletal dynamics, cell cycle, motility and differentiation. As a result, they have been widely investigated for their association with diseases, such as, neurological diseases, cardiomyopathy, neoplasias and inflammatory diseases. To facilitate further studies of S100 proteins, we reported a simple and efficient method for the expression and purification of human S100A4 and S100A11 proteins in Escherichia coli. Since S100 proteins share many common physical and chemical characteristics, we expect that this approach can be extended to the production of most S100 proteins.

Several varieties oflentiviral delivery systems have been used to generate stable cell lines and transgenic animals. Some enhancing elements have been identified to promote stable transgene expression. In this study, we describe that the promoter activity is affected by the lentiviral genomic context. We have examined the promoter activities using green fluorescence protein (GFP) as a reporter in different cell lines to demonstrate that the cytomegalovirus (CMV) promoter may not always be the best choice to overexpress transgenes in all cell types. Our data showed that the polypeptide chain elongation factor 1 alpha (EF1alpha) promoter is relatively active in all three model cell lines (293T, HOS, and Hela) while the CMV promoter is less effective in Hela cells.

We investigated in vivo the effect of recombinant bactericidal/permeability-increasing protein (rBPI21) on high-mobility group box 1 protein (HMGB1) expression in sepsis and its potential mechanism. Using a sepsis model induced by cecal ligation and puncture (CLP), rats were randomly divided into four groups as follows: normal control group, sham-operated group, CLP group, and BPI treatment group. Animals were killed at designated time points, and blood and tissue samples from liver, lungs, kidneys, and small intestine were harvested to determine related variables. In addition, we observed the effect of treatment with rBPI21 on survival rate in septic rats. The results showed that endotoxin content and expression levels of HMGB1 and LPS binding protein/CD14 mRNA in various organs were significantly increased at 12 and 24 h after CLP, which can be attenuated by treatment with rBPI21 (P<0.05-0.01). Meanwhile, treatment with rBPI21 in septic rats can markedly reduce serum alanine aminotransferase, creatinine levels, and pulmonary myeloperoxidase activity at 12 and 24 h after CLP, increase diamine oxidase activity at both time points (P<0.05-0.01), and improve the 1- to 10-day survival rates in animals subjected to CLP (P=0.012). These findings suggest that treatment with rBPI21 can significantly reduce endotoxin contents and expression levels of HMGB1 and LPS binding protein/CD14 mRNA in various organs in sepsis induced by CLP, and can protect against multiple organ damage resulting from sepsis. The effect of rBPI21 inhibiting HMGB1 gene expression in sepsis might be associated with endotoxin-dependent mechanisms.

Objective: To observe the effect of human cytomegalovirus infection on the host cellular DNA synthesis and expression of cyclones., Methods: HCMV infected cell was established in vitro by incubating passage cultured HEL and HCMV AD169 strain with different titres. The cells were synchronized in the G0/G1 stage by contact inhibition and infected with strain AD169 of HCMV at an MOI of 5 PFU per cell. We harvested infected cell at different time 0 h, 3 h, 6 h, 24 h, 72 h and 96 h post infection. Then the cell cycle progress was measured. Meanwhile, the DNA content and expression of proteins of cycline E, cycline A and cycline D1 were determined with FCM and Western Blot respectively., Results: We found that the amount of S stage cell infected by HCMV had increased dramatically, and that of G2/M stage cell reduced during 24 h-96 h PI, and no G2/M stage cell was detected within 96 h PI. The content of 2N DNA maintained unchangeable for 24 h after infection and the content of total DNA in infected cells began to increase within 48 h PI, and the substantial cell with 2N DNA were observed 72 h after infection. However, DNA content was not altered in control group of normal HEL and HCMV PAA group. CyclinE protein was induced 12 h PI and peak induction occurred 24 h PI in contact-inhibited cells. CyclinA protein expression was not induced in HCMV infected density-arrested cells. The abundance of cyclinD1 decreased 24 h PI., Conclusion: The expression of cyclinE and activity of cyclinE/Cdk2 kinase are increased obviously in G0/G1 stage cells infected with HCMV, which may induce the cell cycle to overpass G1/S restriction point and make the cell cycle arrested in later G1 stage. HCMV can not activate cellular DNA synthesis, and increase of total DNA content in infected cells result from the viral DNA replication.

Purpose: The incidence of prostate cancer is frequent, occurring in almost one-third of men older than 45 years. Only a fraction of the cases reach the stages displaying clinical significance. Despite the advances in our understanding of prostate carcinogenesis and disease progression, our knowledge of this disease is still fragmented. Identification of the genes and patterns of gene expression will provide a more cohesive picture of prostate cancer biology., Patients and Methods: In this study, we performed a comprehensive gene expression analysis on 152 human samples including prostate cancer tissues, prostate tissues adjacent to tumor, and organ donor prostate tissues, obtained from men of various ages, using the Affymetrix (Santa Clara, CA) U95a, U95b, and U95c chip sets (37,777 genes and expression sequence tags)., Results: Our results confirm an alteration of gene expression in prostate cancer when comparing with nontumor adjacent prostate tissues. However, our study also indicates that the gene expression pattern in tissues adjacent to cancer is so substantially altered that it resembles a cancer field effect., Conclusion: We also found that gene expression patterns can be used to predict the aggressiveness of prostate cancer using a novel model.

Leiomyosarcoma of the somatic soft tissue is a rare malignant mesenchymal neoplasm that metastasizes to other organs in a subset of cases. Much remains to be learned about the mechanisms underlying the development of aggressive behavior of this tumor. It has been difficult to predict the clinical behavior of leiomyosarcomas using the morphology-based grading system, even though tumor size and histological grade have correlated with biologic behavior in some studies. In this study we analyzed the gene expression patterns of 35 samples of mesenchymal origin, including 11 cases of leiomyosarcomas of different histological grades arising in soft tissue and the retroperitoneum, using the Affymetrix U133a chips, which contain more than 22,000 genes and expression sequence tags (ESTs). We identified a set of genes whose expression was commonly altered in all leiomyosarcoma samples. In addition, we identified specific gene expression patterns in several subsets of the tumor. We used these alterations of gene expression to subclassify the leiomyosarcomas into 3 groups. Interestingly, the grouping of these samples correlated well with tumor differentiation and clinical aggressiveness. The analysis identified 92 genes that distinguish low-grade, well-differentiated leiomyosarcomas from less well-differentiated, high-grade, and metastatic leiomyosarcoma. Thesse alterations of gene expression appear to be correlated with the clinical behavior and histological grade of the tumor. The striking differences in terms of gene expression pattern among leiomyosarcomas of different differentiation status and clinical aggressiveness imply that several genetic abnormalities are responsible for the genesis and progression of this tumor.

Objective: To investigate the potential role of Janus kinase/signal transducers and activators of transcription (JAK/STAT) signal transduction pathway in regulating Toll-like receptor 2 (TLR2) gene expression in postburn Staphylococcus aureus infection., Methods: Thirty-eight male Wistar rats were randomly divided into four groups as follows: normal control group (n=6), postburn sepsis group (n=12), AG490 treatment group (n=10) and Rapamycin (RPM) treatment group (n=10). Tissue samples from the liver, kidneys and lungs were collected to determine TLR2 and TNF-alpha mRNA expressions., Results: It was found that, 0.5 and 2 hours after Staphylococcus aureus challenge, TLR2 mRNA expressions in the liver, kidneys and lungs from postburn septic animals were up-regulated rapidly (P<0.05 or P<0.01). Treatment with RPM could effectively inhibit TLR2 mRNA expressions in the liver and kidneys. However, TLR2 mRNA expressions in the above tissues from AG490 treated animals had no significant differences with those from normal controls. Two hours after Staphylococcus aureus challenge, TNF-alpha mRNA expressions in the liver, kidneys and lungs were also increased markedly (all P<0.01). Both treatment with RPM and AG490 could significantly inhibit the up-regulation of all tissue TNF-alpha mRNA expressions (P<0.05 or P<0.01), and AG490 were more significant in liver and kidneys (both P<0.01)., Conclusion: It is suggested that scald injury combined with Staphylococcus aureus infection can up-regulate TLR2 expression, which appears to be associated with the signal transduction of STAT.

Objective: To investigate the role of Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway in mediating mRNA expression of high mobility group box 1 protein (HMGB1) in the liver in septic rats., Methods: Using a sepsis model of cecal ligation and puncture (CLP), 98 male Wistar rats were randomly divided into normal control group (n=10), CLP group (n=40), AG490 treatment group (n=24), and Rapamycin (RPM) treatment group (n=24). At serial time points animals in each group were sacrificed, and blood as well as hepatic tissue samples were harvested to determine HMGB1 mRNA expression and serum aspartate aminotransferase (AST) as well as alanine aminotransferase (ALT) contents., Results: Compared with normal controls, HMGB1 mRNA levels were significantly increased in the liver during 6-48 hours after CLP (P<0.01), and serum AST and ALT contents were significantly elevated at different time points respectively (P<0.05 or P<0.01). Treatment with AG490 and RPM could markedly inhibit HMGB1 mRNA expression in the liver at 24 hours, 48 hours, 6 hours and 24 hours after CLP, respectively. In addition, compared to CLP group, serum AST and ALT contents in both treatment groups could be markedly reduced at various intervals after CLP (P<0.05 or P<0.01)., Conclusion: These data suggest that the activation of JAK/STAT pathway might be involved in mediating up-regulation of HMGB1 mRNA expression in the liver in CLP-induced sepsis. Treatment with inhibitors of JAK/STAT pathway could markedly down-regulate HMGB1 mRNA expression and attenuate acute liver injury associated with sepsis.

Background: We hypothesized that lipopolysaccharide-binding protein (LBP) and lipopolysaccharide receptor CD14 would present a pair of key molecules in pathophysiologic alterations induced by low concentrations of endotoxin after trauma. The aim of this study was to investigate the relationship between endotoxin translocation and tissue LBP/CD14 messenger ribonucleic acid (mRNA) expression after burn injury, and to define the potential role of LBP/CD14 in mediating inflammatory mediator induction, as well as the pathogenesis of organ damage., Methods: Wistar rats were subjected to a 35% full-thickness scald injury, and tissue samples from liver, kidneys, lungs, and intestine were collected to measure LBP/CD14 and tumor necrosis factor-alpha (TNF-alpha) mRNA expression. Peritoneal macrophages were harvested by peritoneal lavage to determine CD14 mRNA expression., Results: It was found that endotoxin levels in liver, spleen, and lung increased markedly after thermal injury, with the highest level in liver. Both tissue LBP and CD14 mRNA expression increased markedly after burns, peaking at 12 hours, and then decreasing gradually. At 48 hours, LBP gene expression had a tendency to the baseline level, whereas CD14 mRNA expression increased again. Likewise, CD14 mRNA levels were up-regulated markedly in peritoneal macrophages. Conversely, gene expression of TNF-alpha in tissues elevated markedly after acute insults. There were positive correlations between lipopolysaccharide levels and LBP/CD14 mRNA as well as TNF-alpha mRNA expression in tissues. Similar results were also obtained between CD14, TNF-alpha mRNA expression in liver tissue and liver function parameters, and between pulmonary TNF-alpha mRNA and myeloperoxidase activities (p < 0.01)., Conclusion: Thermal injury per se can markedly up-regulate both LBP and CD14 gene expression in various organs. Excessive LBP and CD14 mRNA expression might be associated with enhanced synthesis and release of TNF-alpha stimulated by endotoxin translocation after major burns.

Background: Lung cancer is a common malignant tumor with high morbidity and mortality rate. Glucosamine 6-phosphate N-acetyltransferase (GNPNAT1), which serves as a critical enzyme in hexosamine biosynthetic pathway (HBP), has been identified as a metastasis-associated gene and is upregulated in lung adenocarcinoma (LUAD). However, the exact role and related mechanism of GNPNAT1 in LUAD metastasis remain unknown. Methods: We analyzed the expression of GNPNAT1 in the public databases and confirmed the results by immunohistochemistry (IHC). The biological functions of GNPNAT1 in LUAD were investigated based on The Cancer Genome Atlas (TCGA). Correlations between GNPNAT1 and cancer immune characteristics were analyzed via the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) and Cell-type Identification by Estimating Relative Subsets of RNA Transcript (CIBERSORT) R package. The underlying mechanisms of altered GNPNAT1 expression on LUAD cell tumorigenesis, proliferation, migration, invasion, and metastasis were explored in vitro and in vivo. Results: We demonstrated that GNPNAT1 expression was significantly increased in LUAD and negatively associated with the overall survival (OS) of patients. hsa-miR-1-3p and hsa-miR-26a-5p were identified as upstream miRNA targets of GNPNAT1. GNPNAT1 was associated with the infiltration levels of CD8 T cells, memory-activated CD4 T cells, NK cells resting, macrophages M0, macrophages M1, neutrophils, gamma delta T cells, and eosinophils, while it was negatively correlated with memory-resting CD4 T cells, regulatory T cells (Tregs), resting NK cells, monocytes, resting dendritic cells, and resting mast cells. GNPNAT1 knockdown significantly inhibited proliferation, migration, invasion, epithelial–mesenchymal transition (EMT) process, and metastasis of LUAD cells, while overexpression of GNPNAT1 revealed the opposite effects. Rescue assay showed that Snai2 knockdown reversed GNPNAT1-induced LUAD cells migration, invasion, and EMT. Mechanistically, GNPNAT1 promoted cancer cell metastasis via repressing ubiquitination degradation of Snai2 in LUAD. Conclusions: Taken together, these data indicate that GNPNAT1 serves as a prognostic biomarker for LUAD patient. Additionally, GNPNAT1 is critical for promoting tumorigenesis and metastasis of LUAD cells and may be a potential therapeutic target for preventing LUAD metastasis. [ABSTRACT FROM AUTHOR]

Fusarium wilt in Cymbidium ensifolium, caused by Fusarium oxysporum, is highly contagious and poses a severe hazard. It significantly reduces the ornamental value of C. ensifolium and causes substantial economic losses in agricultural production. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are key regulatory factors in plant disease resistance responses, playing vital roles in defending against pathogen invasions. In our study, we conducted a comprehensive analysis of the NBS-LRR gene family in the genome of Cymbidium ensifolium. Phylogenetic analysis identified a total of 31 NBS-LRR genes encoding NB-ARC proteins, which were categorized into five classes (CNL, CN, NL, N, RNL) based on their protein structural domains. These genes were found to be unevenly distributed across eight chromosomes. Physicochemical analysis revealed significant variances in molecular weight and sequence length among the family members. Subcellular localization results indicated that most genes primarily reside in the cytoplasm and cell membrane, suggesting that the primary sites of disease resistance responses may be the cell membrane and cyto-plasm. Furthermore, noticeable disparities were observed in gene structures and conserved motifs among different categories of family genes. Promoter analysis indicated that cis-regulatory elements are mainly associated with plant stress, jasmonic acid, gibberellin, and other development-related factors, suggesting that CeNBS-LRR genes mainly resist external stress through hormones such as abscisic acid and jasmonic acid. We characterized twenty-seven CeNBS-LRR gene expression patterns of healthy C. ensifolium at different periods after Fusarium wilt infection, and found that those genes exhibit a temporospatial expression pattern, and that their expression is also responsive to Fusarium wilt infection. By analyzing the expression pattern via transcriptome and qRT-PCR, we speculated that JL006442 and JL014305 may play key roles in resisting Fusarium wilt. This study lays the groundwork and holds considerable significance as a reference for identifying disease-resistant genes and facilitating genetic breeding in C. ensifolium. [ABSTRACT FROM AUTHOR]

Sugarcane is a significant primitive source of sugar and energy worldwide. The progress in enhancing the sugar content in sugarcane cultivars remains limited due to an insufficient understanding of specific genes related to sucrose production. The present investigation examined the enzyme activities, levels of reducing and non-reducing sugars, and transcript expression using RT-qPCR to assess the gene expression associated with sucrose metabolism in a high-sucrose sugarcane clone (GXB9) in comparison to a low-sucrose sister clone (B9). Sucrose phosphate synthase (SPS), sucrose phosphate phosphatase (SPP), sucrose synthase (SuSy), cell wall invertase (CWI), soluble acid invertase (SAI), and neutral invertase (NI) are essential enzymes involved in sucrose metabolism in sugarcane. The activities of these enzymes were comparatively quantified and analyzed in immature and maturing internodes of the high- and low-sucrose clones. The results showed that the higher-sucrose-accumulating clone had greater sucrose concentrations than the low-sucrose-accumulating clone; however, maturing internodes had higher sucrose levels than immature internodes in both clones. Hexose concentrations were higher in immature internodes than in maturing internodes for both clones. The SPS and SPP enzymes activities were higher in the high-sucrose-storing clone than in the low-sucrose clone. SuSy activity was higher in the low-sucrose clone than in the high-sucrose clone; further, the degree of SuSy activity was higher in immature internodes than in maturing internodes for both clones. The SPS gene expression was considerably higher in mature internodes of the high-sucrose clones than the low-sucrose clone. Conversely, the SuSy gene exhibited up-regulated expression in the low-sucrose clone. The enhanced expression of SPS in the high-sucrose clone compared to the low-sucrose clone suggests that SPS plays a major role in the increased accumulation of sucrose. These findings provide the opportunity to improve sugarcane cultivars by regulating the activity of genes related to sucrose metabolism using transgenic techniques. [ABSTRACT FROM AUTHOR]

In insects, vitellogenin (Vg) is generally viewed as a female‐specific protein. Its primary function is to supply nutrition to developing embryos. Here, we reported Vg from the male adults of a natural predator, Chrysopa pallens. The male Vg was depleted by RNAi. Mating with Vg‐deficient male downregulated female Vg expression, suppressed ovarian development and decreased reproductive output. Whole‐organism transcriptome analysis after male Vg knockdown showed no differential expression of the known spermatogenesis‐related regulators and seminal fluid protein genes, but a sharp downregulation of an unknown gene, which encodes a testis‐enriched big protein (Vcsoo). Separate knockdown of male Vg and Vcsoo disturbed the assembly of spermatid cytoplasmic organelles in males and suppressed the expansion of ovary germarium in mated females. These results demonstrated that C. pallens male Vg signals through the downstream Vcsoo and regulates male and female reproduction. [ABSTRACT FROM AUTHOR]

Simple Summary: Lactoferrin (LF) is considered to be an important active protein in goat milk, and it plays an important role in immunity. In this study, we tried to find factors affecting the expression of lactoferrin. Furthermore, we further explored the anti-inflammatory effect of LF and related molecular mechanisms in order to further understand how lactoferrin affects the immune system and provide a reference for further study and application of lactoferrin in the future. Lactoferrin (LF) is believed to be an important active protein in goat milk, which plays an anti-inflammatory role. Although LF has been reported to be associated with body health, its exact underlying mechanism remains unclear. Here, we aimed to elucidate the mechanism of this anti-inflammatory effect of LF in vitro. We first identified that miR-214-5p inhibited the expression of LF mRNA and protein in cells through the 3′UTR of LF mRNA. We next identified the alterations in miRNA following LF overexpression in goat mammary epithelial cells (GEMCs). Overexpression of LF significantly increased (p < 0.05) miR-224-5p expression. We further revealed that transcriptional activation of ADAM17, TNF-α, IL-1β, and IL-6 was efficiently decreased (p < 0.05) in GMECs treated by miR-224-5p mimic. Conversely, knockdown of miR-224-5p increased (p < 0.05) ADAM17, TNF-α, IL-1β, and IL-6 expression. Additionally, TNF-α, IL-1β, and IL-6 expression levels were dramatically decreased in GMECs after administration of siADAM17. Herein, we indicate that the miR-214-5p/LF/miR-224-5p/ADAM17 axis is involved in the immune regulation of GEMCs. [ABSTRACT FROM AUTHOR]

Simple Summary: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. HCC is often diagnosed at a late stage when treatment effectiveness is limited and its prognosis remains dire. Exosomes are secreted by all living cells, including cancer cells, and contain biological material with potential to highlight disease conditions or dysregulated pathways involved in tumourigenesis. This study employs artificial intelligence methods to identify a signature of exosomal RNAs from 114,602 exosomal RNAs in 118 HCC patients and 112 healthy individuals that can predict HCC. A signature of nine exosomal RNAs, mainly in the immune, platelet/neutrophil and cytoskeletal pathways, was identified to predict HCC with an accuracy of ~85%. Hence, these nine exosomal RNAs have potential to be developed as clinically useful minimally invasive biomarkers for HCC. Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Although alpha fetoprotein (AFP) remains a commonly used serological marker of HCC, the sensitivity and specificity of AFP in detecting HCC is often limited. Exosomal RNA has emerged as a promising diagnostic tool for various cancers, but its use in HCC detection has yet to be fully explored. Here, we employed Machine Learning on 114,602 exosomal RNAs to identify a signature that can predict HCC. The exosomal expression data of 118 HCC patients and 112 healthy individuals were stratified split into Training, Validation and Unseen Test datasets. Feature selection was then performed on the initial training dataset using permutation importance, and the predictive performance of the selected features were tested on the validation dataset using Support Vector Machine (SVM) Classifier. A minimum of nine features were identified to be predictive of HCC and these nine features were then evaluated across six different models in an unseen test set. These features, mainly in the immune, platelet/neutrophil and cytoskeletal pathways, exhibited good predictive performance with ROC-AUC from 0.79–0.88 in the unseen test set. Hence, these nine exosomal RNAs have potential to be clinically useful minimally invasive biomarkers for HCC. [ABSTRACT FROM AUTHOR]

Breeding rapeseed varieties with more main inflorescence siliques is an idea for developing rapeseed varieties that are suitable for light and simplified cultivation. The Brassica napus exhibited cluster bud of the main inflorescence (Bnclib) gene. At the fruiting stage, the main inflorescence had more siliques, higher density, and more main inflorescences. Moreover, the top of the main inflorescence bifurcated. Genetic analysis showed that the separation ratio between Bnclib and the wild type in the F2 generation was 3:1, which indicated that the trait was a single-gene-dominant inheritance. Among the 24 candidate genes, only one gene, BnaA03g53930D, showed differential expression between the groups (False discovery rate, FDR ≤ 0.05, |log2FC|≤ 1). qPCR verification of the BnaA03g53930D gene between Huyou 17 and its Bnclib near-isogenic line showed that BnaA03g53930D was significantly differentially expressed in the stem tissue of Huyou 17 and its Bnclib near-isogenic line (Bnclib NIL). The determination of gibberellin (GA), brassinolide (BR), cytokinin (CTK), jasmonic acid (JA), growth hormone (IAA), and strigolactone (SL) content in the shoot apex of Huyou 17 by Bnclib NIL and wild type showed that all six hormones significantly differed between the Bnclib NIL and Huyou 17. It is necessary to conduct further research on the interactions between JA and the other five hormones and the main inflorescence bud clustering in B. napus. [ABSTRACT FROM AUTHOR]

Metabolic disorder is highly related to obesity, insulin resistance, hypertension, and hyperlipidemia. The present study found that astragaloside IV (ASI) attenuated metabolic disorder related symptoms and modulated hepatic lipid metabolism associated gene mRNA expression in db/db mice. ASI inhibited rosiglitazone-induced adipocyte differentiation of 3T3-L1 cells, and lipid accumulation in palmitic acid (PA)-induced HepG2 cells with down-regulated mRNA expression of lipogenesis-related genes. In addition, it was predicted to bind to the ligand binding domain (LBD) of PPARγ and inhibit its transactivity. Collectively, our study suggested that ASI improves lipid metabolism in obese mice probably through suppressing PPARγ activity. [ABSTRACT FROM AUTHOR]

Background and objective: Host immunity is crucial during periodontal inflammations. B cells are considered to have a function of immunoregulation, and TLRs are considered to be crucial in this process. The present study illustrates the potential roles and rules of CD25+ B cells during periodontitis, especially its effect on regulating host IL‐35 level and Th1, Th17, and Treg differentiation. Material and methods: The proportion of local and systemic CD25+ B cell subpopulations from periodontitis models were identified by flow cytometry. To illustrate further mechanism, B cells were cultured with a different type of TLR activators. Expression of IL‐10, IL‐35, and TGF‐β was detected by ELISA and real‐time PCR. We also set adoptive transfer models by using CD25+ B cells. Alveolar bone erosion, proportion of Th1, Th17, and Tregs, and levels of IFN‐γ, TNF‐α, IL‐1β, and IL‐17 were identified. Result: Periodontitis induces more CD25+ B cell subpopulations and promotes their IL‐10, IL‐35, and TGF‐βproduction. TLR activators enhanced Breg proliferation and function. LPS+CpG obviously induced more CD25+ B cell differentiation and production of IL‐10, IL‐35, and TGF‐β. Adoptive transfer of CD25+ B cells reduces alveolar bone destruction and local Tregs, proportion, especially the local level of IFN‐γ and IL‐17. In addition, adoptive transfer of CD25+ B cells remedies the pathological change in the proportion of IL‐1β and Th1/Th17 in local lesions. We did not find any significant difference in peripheral blood, regardless of group and detected items. Conclusion: Results of the present study clarify that CD25+ B cells enlarged and produced more IL‐10, IL‐35 and TGF‐β during periodontitis, activation of TLR4 and TLR9 played crucial roles in this process. Also, CD25+ B cells alleviated periodontal inflammation and alveolar bone resorption. Our findings further expanded the potential of B cells during periodontitis. [ABSTRACT FROM AUTHOR]

Aim. The aim of this study is to demonstrate the expression and clinicopathological significance of complement C1q B chain (C1QB) in cervical cancer. Methods. In total, 120 cervical cancer tissues, as well as 20 samples each of high-grade squamous intraepithelial lesions (HSILs), low-grade squamous intraepithelial lesions (LSILs), and benign cervical tissue, were collected to evaluate the expression of C1QB protein via immunohistochemical staining. We conducted an integrated analysis of C1QB mRNA expression in cervical cancer using public microarrays and RNA-seq data sets by calculating standard mean differences (SMDs). Simultaneously, we explored the relations of C1QB with clinicopathological parameters and the expression of P16, Ki-67, and P53. Results. The expression of C1QB protein was higher in cervical cancer samples than that in benign cervical tissue, LSIL, and HSIL samples (p < 0.05). A combined SMD of 0.65 (95% CI: [0.52, 0.79], p < 0.001) revealed upregulation of C1QB mRNA in cervical cancer. C1QB expression may also be related to the depth of infiltration, lymphovascular invasion, and perineural invasion in cervical cancer (p < 0.05). We also found that C1QB protein expression was positively correlated with P16 and Ki-67 expression in cervical cancer (p < 0.05). The gene set enrichment analysis showed that C1QB may participate in apoptosis and autophagy. A relationship was predicted between C1QB expression and drug sensitivity to cisplatin, paclitaxel, and docetaxel. Conclusion. We confirmed the overexpression of C1QB in cervical cancer at both mRNA and protein levels for the first time. C1QB may serve as an oncogene in the tumorigenesis of cervical cancer, but this possibility requires further study. [ABSTRACT FROM AUTHOR]

Background: Hypertension and its associated dysfunction of the blood-brain barrier (BBB) are considered to contribute to cerebral small vessel disease (cSVD). Angiotensin II (Ang II), as an important vasoactive peptide of the renin-angiotensin system (RAS), is not only a pivotal molecular signal in hypertension, but also causes BBB leakage, cSVD and its related cognitive impair. Hyperoside (Hyp), a flavone glycoside, has antioxidant, antiphlogistic and anti-apoptosis effects. In this study, we investigate the protection of Hyp on apoptosis of bEnd.3 cells and BBB disruption in vitro induced by Ang II. Methods: We used bEnd.3 cells to imitate a BBB monolayer model and explored the protection of Hyp on Ang II-induced BBB leakage. The apoptotic activity was assessed by TUNEL staining and flow cytometry. The expression of apoptosis pathway related proteins, tight junction proteins and transcytosis related proteins were detected by western blot assay. The BBB model permeability was detected through measuring the flux of sodium fluorescein (Na-F). Results: We found that Hyp can not only effectively inhibit the apoptosis of bEnd.3 induced by Ang II, but also protect the structural soundness and functional integrity of BBB model by affecting the expression levels of junctional adhesion molecule A (JAM-A), Claudin-5, zonula occludens-1 (ZO-1), Caveolin-1 (Cav-1) and major facilitator superfamily domain-containing protein 2a (Mfsd2a). Conclusion: Hyp might be a potent compound for preventing Ang II-induced BBB disruption. [ABSTRACT FROM AUTHOR]

Hepatic inflammation is always accompanied with abnormal lipid metabolism. Whether N6-methyladenosine (m6A) mRNA methylation affects irregular inflammatory lipid level is unclear. Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7,815 m6A peaks distributed in 5,066 genes were identified in the normal chicken liver and were mostly located in the CDS, 3′UTR region, and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed and showed 1,200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the latter in the 3′UTR and in the region near the stop codon. The hyper- or hypo-methylated genes were enriched in different GO ontology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, computational prediction of protein–protein interaction (PPI) showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication, and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation. [ABSTRACT FROM AUTHOR]

As ultra high‐dimensional longitudinal data are becoming ever more apparent in fields such as public health and bioinformatics, developing flexible methods with a sparse model is of high interest. In this setting, the dimension of the covariates can potentially grow exponentially as exp(n1/2) with respect to the number of clusters n. We consider a flexible semiparametric approach, namely, partially linear single‐index models, for ultra high‐dimensional longitudinal data. Most importantly, we allow not only the partially linear covariates but also the single‐index covariates within the unknown flexible function estimated nonparametrically to be ultra high dimensional. Using penalized generalized estimating equations, this approach can capture correlation within subjects, can perform simultaneous variable selection and estimation with a smoothly clipped absolute deviation penalty, and can capture nonlinearity and potentially some interactions among predictors. We establish asymptotic theory for the estimators including the oracle property in ultra high dimension for both the partially linear and nonparametric components, and we present an efficient algorithm to handle the computational challenges. We show the effectiveness of our method and algorithm via a simulation study and a yeast cell cycle gene expression data. [ABSTRACT FROM AUTHOR]

Tomato seedlings were used as experimental materials and treated with 1.0, 2.0, 3.0, and 4.0 mg/L ozone water irrigation and 0.2, 0.4, 0.6, and 0.8 mg/L ozone water spray treatments. Indexes including the malondialdehyde (MDA) content, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), activities, soil and plant analysis development (SPAD) value, and nitrogen content of leaves were measured. Furthermore, the expression of antioxidant enzyme, chlorophyll synthesis and nitrogen absorption genes was analyzed after optimal ozone water treatment. The results showed that the activities of antioxidant enzymes in tomato leaves were significantly increased, and the MDA content in tomato leaves was significantly reduced by ozone water irrigation and spray treatment, which indicated that ozone water treatment can significantly improve the stress tolerance of tomato seedlings. Ozone water irrigation and spraying could also significantly increase the leaf SPAD value and nitrogen content of tomato seedlings, and the optimal concentrations of ozone water irrigation and spraying were 3.0 mg/L and 0.6 mg/L, respectively. The effect of ozone water irrigation on improving the physiological characteristics of tomato seedlings was better than that of spraying. After treatment with the optimal concentration of ozone water, the relative expression of antioxidant enzyme, chlorophyll synthesis, and nitrogen absorption genes was significantly increased, and the maximum expression level was reached at 12 h. In addition, ozone water irrigation could promote the expression of genes more than ozone water spraying, which was consistent with the improvements in the physiological characteristics of the tomato seedlings. [ABSTRACT FROM AUTHOR]

Gut microbiota has been proven to play an important role in many metabolic diseases and cardiovascular disease, particularly atherosclerosis. Ophiopogonin D (OPD), one of the effective compounds in Ophiopogon japonicus, is considered beneficial to metabolic syndrome and cardiovascular diseases. In this study, we have illuminated the effect of OPD in ApoE knockout (ApoE − / −) mice on the development of atherosclerosis and gut microbiota. To investigate the potential ability of OPD to alleviate atherosclerosis, 24 eight-week-old male ApoE − / − mice (C57BL/6 background) were fed a high-fat diet (HFD) for 12 weeks, and 8 male C57BL/6 mice were fed a normal diet, serving as the control group. ApoE − / − mice were randomly divided into the model group, OPD group, and simvastatin group (n = 8). After treatment for 12 consecutive weeks, the results showed that OPD treatment significantly decreased the plaque formation and levels of serum lipid compared with those in the model group. In addition, OPD improved oral glucose tolerance and insulin resistance as well as reducing hepatocyte steatosis. Further analysis revealed that OPD might attenuate atherosclerosis through inhibiting mTOR phosphorylation and the consequent lipid metabolism signaling pathways mediated by SREBP1 and SCD1 in vivo and in vitro. Furthermore, OPD treatment led to significant structural changes in gut microbiota and fecal metabolites in HFD-fed mice and reduced the relative abundance of Erysipelotrichaceae genera associated with cholesterol metabolism. Collectively, these findings illustrate that OPD could significantly protect against atherosclerosis, which might be associated with the moderation of lipid metabolism and alterations in gut microbiota composition and fecal metabolites. [ABSTRACT FROM AUTHOR]

BASP1 is involved in signal transduction and cytoskeleton formation and plays a tumor-promoting or tumor-suppressing role in cancers. We found BASP1 was overexpressed in lung adenocarcinoma tissues and promoted the proliferation and migration of lung adenocarcinoma cells. The mechanism may be related to inhibition of cell apoptosis and abnormal activation of the Wnt/β-catenin pathway and epithelial-mesenchymal transformation. BASP1 is associated with poor prognosis in lung adenocarcinoma. [ABSTRACT FROM AUTHOR]

RNA-sequencing enables accurate and low-cost transcriptome-wide detection. However, expression estimates vary as reference genomes and gene annotations are updated, confounding existing expression-based prognostic signatures. Herein, prognostic 9-gene pair signature (GPS) was applied to 197 patients with stage I lung adenocarcinoma derived from previous and latest data from The Cancer Genome Atlas (TCGA) processed with different reference genomes and annotations. For 9-GPS, 6.6% of patients exhibited discordant risk classifications between the two TCGA versions. Similar results were observed for other prognostic signatures, including IRGPI, 15-gene and ORACLE. We found that conflicting annotations for gene length and overlap were the major cause of their discordant risk classification. Therefore, we constructed a prognostic 40-GPS based on stable genes across GENCODE v20-v30 and validated it using public data of 471 stage I samples (log-rank P  < 0.0010). Risk classification was still stable in RNA-sequencing data processed with the newest GENCODE v32 versus GENCODE v20–v30. Specifically, 40-GPS could predict survival for 30 stage I samples with formalin-fixed paraffin-embedded tissues (log-rank P  = 0.0177). In conclusion, this method overcomes the vulnerability of existing prognostic signatures due to reference genome and annotation updates. 40-GPS may offer individualized clinical applications due to its prognostic accuracy and classification stability. [ABSTRACT FROM AUTHOR]

The characterization of human gene expression is limited by short read lengths, high error rates and large input requirements. Here, we used a synthetic long read (SLR) sequencing approach, LoopSeq, to generate accurate sequencing reads that span full length transcripts using standard short read data. LoopSeq identified isoforms from control samples with 99.4% accuracy and a 0.01% per-base error rate, exceeding the accuracy reported for other long-read technologies. Applied to targeted transcriptome sequencing from colon cancers and their metastatic counterparts, LoopSeq revealed large scale isoform redistributions from benign colon mucosa to primary colon cancer and metastatic cancer and identified several previously unknown fusion isoforms. Strikingly, single nucleotide variants (SNVs) occurred dominantly in specific isoforms and some SNVs underwent isoform switching in cancer progression. The ability to use short reads to generate accurate long-read data as the raw unit of information holds promise as a widely accessible approach in transcriptome sequencing. Silvia Liu et al. present LoopSeq, a synthetic long-read sequencing method that generates accurate long-read transcriptome data from short Illumina reads. As an example of possible applications, they use LoopSeq to investigate differential isoform expression, isoform-specific single nucleotide variants, and potential fusion genes in multiple stages of colon cancer. Altogether, LoopSeq is a valuable method for analyzing complex transcriptomes and investigating gene expression at the isoform level. [ABSTRACT FROM AUTHOR]

Background. Atractylodes lancea (AL) has been used in traditional Chinese medicine for the treatment of various diseases including digestive disorders. Ulcerative colitis (UC) is a common digestive system disease with a low cure rate and easy recurrence. However, it is still not clear whether AL is suitable for UC treatment. Currently, stir-baking with wheat bran is most commonly used to process AL. Here, we aimed to address the effects of the crude and bran-processed AL on UC in vitro and uncover the underlying mechanism based on regulating the IKK/NF-kappa B signaling pathway. Methods. Human colonic epithelial cells (HCoEpiC) were treated with lipopolysaccharide (LPS) to mimic the inflammatory injury of UC in vitro. The essential oil from crude and bran-processed AL was used to treat LPS-induced HcoEpiC cells. The cell viability was detected by an MTT assay. The levels of IL-4, IL-6, IL-8, IL-12, IL-1-β, TNF-α, and NO were determined by ELISA, and the mRNA expressions of IKK-α, NF-κB, IL-4, IL-6, IL-8, and TNF-α were determined by RT-PCR. Meanwhile, the expressions of IKK-α, p-IKK-α, p-IKK-β, NF-κB, IL-6, and IL-8 proteins were determined by Western blot. Results. The essential oil of AL, whether it was from crude or bran-processed AL, could significantly increase the viability of LPS-induced HCoEpiC cells. The treatment of AL essential oil also notably inhibited the productions of IL-6, IL-8, IL-12, IL-1-β, TNF-α, NO, p-IKK-α, p-IKK-β, and NF-κB and downregulated the mRNA expressions of NF-κB, IL-6, IL-8, and TNF-α. Meanwhile, IL-4 protein and mRNA expression were significantly stimulated by AL essential oil. Moreover, the essential oil from bran-processed AL was more effective than that from crude AL. Conclusion. Both kinds of AL essential oil had the anti-inflammatory effect on LPS-induced HCoEpiC, and the essential oil from bran-processed AL was more effective. The mechanism could be through the IKK/NF-κB signaling pathway in vitro. [ABSTRACT FROM AUTHOR]