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Simple Summary: The β-defensin-1 (BD-1) is rich in disulfide bonds and antibacterial peptides with direct bactericidal function activity. Equine BD-1 was initially reported in 2004, however, there are no reports on the specific mechanisms that characterize the impact of Equine BD-1 on innate immune function. In this study, we map the tissue distribution of Equus BD-1 (i.e., Equine BD-1, ass BD-1, and mule BD-1) and compare their expression levels in various tissues, and we showed that Equine BD-1, ass BD-1, and mule BD-1 have an identical (100%) open reading frame (ORF). Next, we expressed the ORF of Equus BD-1 sequence fragment (OEBD-1) in the E. coli expression system and used this to treat an S. aureus-infected murine macrophage cell line in vitro. Results indicated that the OEBD-1 increased cytokines expression and associated signaling pathway, furthermore, OEBD-1 promoted macrophage phagocytose S. aureus in vitro. The report provides a theoretical basis for the development of defensins as potential alternatives to antibiotics. Beta-defensin-1 (BD-1) is among the class of antibacterial peptides that are rich in disulfide bonds, have direct antibacterial activity and showed enhanced expression following external stimulation. However, existing research studies only treated BD-1 to cell models without stimulation from pathogen-associated molecular patterns (PAMPs), which will further influence our understanding of the role of BD-1. In this study, we map the tissue distribution of Equus BD-1 (i.e., eBD-1, ass BD-1, and mule BD-1) and compare their expression levels in various tissues. We further characterize the three kinds of Equus BD-1 by analyzing their full-length cDNA. We showed that eBD-1, ass BD-1, and mule BD-1 have an identical (100%) open reading frame (ORF). The ORF encoding OEBD-1 expressed the ORF in the E. coli Top10 expression system. This expression system was combined with an S. aureus-infected J774A.1 macrophage cell line to determine the influence on innate immune mediator expression. Using this expression model system, it was determined that the OEBD-1 protein enhanced IL-6 and TNF-α secretion. It can also promote TLR2, IL-1β, CCL2, CCL7, CXCL10 and NF-κB p65 mRNA expression. Moreover, OEBD-1 upregulates phosphorylation of ATK, Syk and IκB-α. In addition, OEBD-1 enhances the macrophage's ability to phagocytose S. aureus. In conclusion, Equus BD-1 was shown to play an essential role in macrophage-involved innate immune responses in an in vitro system. [ABSTRACT FROM AUTHOR]

Background: ccRCC is considered as the main subtype of RCC, which accounted for sixth deadliest cancer worldwide. Recently, ubiquitination has been reported to be closely involved in the progression of tumore. The purpose of this study was to identify the ubiquitination-associated genes and co-expressed lncRNAs on the prognosis of clear cell renal cell carcinoma (ccRCC) patients. Methods and patients: We downloaded 530 cases and the corresponding transcriptome profiling from The Cancer Genome Atlas (TCGA) database. We distinguished mRNA and lncRNA expression data from the transcriptome profiling and then extracted the expression of mRNAs that regulate protein ubiquitination. We obtained lncRNAs associated with protein ubiquitination regulation from the lncRNA data by gene co-expression analysis. Cox regression analysis of survival time, survival status, and lncRNA expression level was carried out, and a prognostic index (PI) was constructed. Results: The PI was established based on 8 prognostic lncRNAs that regulate protein ubiquitination and distinguish the high-risk group patients from all patients. Multivariate analysis indicated that this PI was an individualized clinical prognostic factor for patients with ccRCC. Regarding clinical characteristics, a ubiquitination-associated clinical-prognostic index (UCPI), containing 8 ubiquitination-related lncRNAs and age, was established and tested with AUC of 0.80. Conclusion: We established a UCPI containing 8 lncRNAs related to protein ubiquitination. This UCPI may become an appropriate model to predict the prognosis in ccRCC patients and guide clinicians to adjust the follow-up regimen. [ABSTRACT FROM AUTHOR]

Post‐operative progression and chemotherapy resistance are the main causes of treatment failure in glioma patients. There is a lack of ideal prediction models for post‐operative glioma patient progression and drug sensitivity. We aimed to develop a prognostic model of parthanatos mRNA biomarkers for glioma outcomes. A total of 11 parthanatos genes were obtained from ParthanatosCluster database. ConsensusClusterPlus and R "Limma" package were used to cluster The Cancer Genome Atlas (TCGA)‐glioma cohort and analyze the differential mRNAs. Univariate Cox regression analysis, random survival forest model, and least absolute shrinkage and selection operator (LASSO) regression analysis were used to determine the nine ParthanatosScore prognostic genes combination. ParthanatosScore was verified by 656 patients and 979 patients in TCGA and CGCA‐LGG/GBM datasets. Differences in genomic mutations, tumor microenvironments, and functional pathways were assessed. Drug response prediction was performed using pRRophetic. Kaplan–Meier survival analysis was analyzed. Finally, COL8A1 was selected to evaluate its potential biological function and drug sensitivity of temozolomide and AZD3759 in glioma cells. ParthanatosScore obtained a combination of nine glioma prognostic genes, including CD58, H19, TNFAIP6, FTLP3, TNFRSF11B, SFRP2, LOXL1, COL8A1, and FABP5P7. In the TCGA‐LGG/GBM dataset, glioma prognosis was poor in high ParthanatosScore. Low‐score glioma patients were sensitive to AZD3759_1915, AZD5582_1617, AZD8186_1918, Dasatinib_1079, and Temozolomide_1375, while high‐score patients were less sensitive to these drugs. Compared with HA cells, COL8A1 was significantly over‐expressed in LN229 and U251 cells. Silencing COL8A1 inhibited the malignant characterization of LN229 and U251 cells. Temozolomide and AZD3759 also promoted parthanatos gene expression in glioma cells. Temozolomide and AZD3759 inhibited COL8A1 expression and cell viability and promoted apoptosis in glioma cells and PGM cells. ParthanatosScore can accurately predict clinical prognosis and drug sensitivity after glioma surgery. Silencing COL8A1 inhibited the malignant characterization. Temozolomide and AZD3759 inhibited COL8A1 expression and cell viability and promoted apoptosis and parthanatos gene expression, which is a target to improve glioma. [ABSTRACT FROM AUTHOR]

Objectives. Enhanced migration and osteogenic differentiation of mesenchymal stem cells (MSCs) are beneficial for MSC-mediated periodontal tissue regeneration, a promising method for periodontitis treatment. FBXO5, a member of the F-box protein family, is involved in the osteogenic differentiation of MSCs. Here, we investigated the effect of FBXO5 on human periodontal ligament stem cells (hPDLSCs). Materials and Methods. hPDLSCs were isolated from periodontal ligament tissue. Lentivirus FBXO5 shRNA was used to silence FBXO5 expression. Two transcripts of FBXO5 were overexpressed and transduced into hPDLSCs via retroviral infection. Migration and osteogenic differentiation of hPDLSCs were evaluated using the scratch migration assay, alkaline phosphatase (ALP) activity, ALP staining, alizarin red staining, western blotting, and real-time polymerase chain reaction. Results. The expression of FBXO5 was upregulated after osteogenic induction in hPDLSCs. FBXO5 knockdown attenuated migration, inhibited ALP activity and mineralization, and decreased RUNX2, OSX, and OCN expression, while the overexpression of two transcript isoforms significantly accelerated migration, enhanced ALP activity and mineralization, and increased RUNX2, OSX, and OCN expression in hPDLSCs. Conclusions. Both isoforms of FBXO5 promoted the migration and osteogenic differentiation potential of hPDLSCs, which identified a potential target for improving periodontal tissue regeneration. [ABSTRACT FROM AUTHOR]

Osteoporosis is characterized by increased bone loss and deterioration of bone microarchitecture, which will lead to reduced bone strength and increased risk of fragility fractures. Previous studies have identified many genetic loci associated with osteoporosis, but functional mechanisms underlying the associations have rarely been explored. In order to explore the potential molecular functional mechanisms underlying the associations for osteoporosis, we performed integrative analyses by using the publically available datasets and resources. We searched 128 identified osteoporosis associated SNPs (P<10−6), and 8 SNPs exert cis-regulation effects on 11 eQTL target genes. Among the 8 SNPs, 2 SNPs (RPL31 rs2278729 and LRP5 rs3736228) were confirmed to impact the expression of 3 genes (RPL31, CPT1A and MTL5) that were differentially expressed between human subjects of high BMD group and low BMD group. All of the functional evidence suggested the important functional mechanisms underlying the associations of the 2 SNPs (rs2278729 and rs3736228) and 3 genes (RPL31, CPT1A and MTL5) with osteoporosis. This study may provide novel insights into the functional mechanisms underlying the osteoporosis associated genetic variants, which will help us to comprehend the potential mechanisms underlying the genetic association for osteoporosis. [ABSTRACT FROM AUTHOR]

Purpose: In primary open angle glaucoma (POAG) patients, elevated intraocular pressure usually leads to extracellular matrix remodeling and astrocytes activation. Thus, lamina cribrosa (LC) cells may play an important role in POAG progression. The objective of this study was to comprehensively explore gene expression profiles in LC cells of POAG patients. Materials and methods: Using the GSE13534 microarray datasets downloaded from Gene Expression Omnibus database, the differentially expressed genes (DEGs) between LC cells from POAG patients and controls were firstly screened based on the classical t-test and false discovery rate <0.05 as a significant threshold. Subsequently, these DEGs were grouped into gene sets using a graph-clustering approach. The underlying molecular mechanisms were investigated by the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Results: A total of 57 DEGs were identified and 478 co-expression relationships were constructed among these DEGs. Among them, cytochrome p450 family 1 subfamily B (CYP1B1), brain-derived neurotrophic factor (BDNF) and myelin basic protein (MBP) showed high-degree relationships and they could interact with several genes. CYP1B1 is an important genetic gene involved in POAG and BDNF is an effective growth neurotrophic factor to weak POAG damage. MBP, versican (VCAN), integrin, alpha 4 (ITGA4) and N-cadherin (CDH2) may be involved in extracellular matrix remodeling in LC cells. FZD2 and FZD7 were enriched in basal cell carcinoma pathway. Conclusions: The results demonstrate that the genes above may be associated with the pathogenesis of POAG. [ABSTRACT FROM AUTHOR]

In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. [ABSTRACT FROM AUTHOR]

Precise three-dimensional (3D) mapping of a large number of gene expression patterns, neuronal types and connections to an anatomical reference helps us to understand the vertebrate brain and its development. We developed the Virtual Brain Explorer (ViBE-Z), a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern; here we demonstrate its utility for mapping neurons of the dopaminergic system. The ViBE-Z database, atlas and software are provided via a web interface. [ABSTRACT FROM AUTHOR]

Abstract: The α-tocopherol transfer protein (α-TTP) is a ~32kDa protein that exhibits a marked ligand specificity and selectively recognizes of α-tocopherol, which is the most active form of vitamin E. The α-TTP gene has been cloned and its physiological functions have been studied in numbers of species, however, the understanding of sheep α-TTP is still in his infancy. In this study, the full-length cDNA of sheep α-TTP gene was cloned from sheep liver by using of rapid amplification of complementary DNA ends (RACE). As a result, the sheep α-TTP gene was 1098bp in nucleotide which contained 23bp 5''-untranslated region (UTR), 226bp 3''-UTR and 849bp open reading frame (ORF) that encoded a basic protein of 282 amino acids. Further bioinformatic analysis indicated that the sheep α-TTP gene had a high homologous of both nucleotide and amino acid sequences compared with that of other species and had a Sec14p-like lipid-binding domain which called the CRAL-TRIO domain. Moreover, the expression of sheep α-TTP mRNA and protein in response to different vitamin E supplemented levels were observed according to quantitative real-time PCR (qRT-PCR) and Western blotting analysis. The results showed that dietary vitamin E levels did not affect α-TTP mRNA expression significantly while the low vitamin E supplemented level groups of sheep had significantly higher α-TTP protein compared to high-vitamin E groups. [Copyright &y& Elsevier]

Abstract: Fibrinogen-like protein 2 (fgl2), a novel prothrombinase, is involved in microthrombosis. We examined fgl2 expression in the glomerular and tubulointerstitial capillaries and its correlation with microthromsis in rats with streptozocin-induced type 2 diabetic nephropathy. Our RT-PCR and immunoblotting analysis showed that fgl2 mRNA and protein levels were increased in microvascular endothelial cells of the glomeruli and renal interstitia at week 19 and became significantly elevated with the development of diabetic nephropathy (P < 0.01). Fgl2 was not or only weakly expressed in the renal tissues of normal rats. Furthermore, a direct significant correlation (r = 0.543, P < 0.01) was found between fgl2 expression and microthrombotic capillaries in the renal tissues. Enzyme linked immunosorbent assays (ELISA) additionally showed that circulating TNF-α levels in rats with type 2 diabetes were significantly elevated and closely correlated with fgl2 expression (r = 0.871, P < 0.01). Our results suggest that fgl2 may activate renal microthrombosis, thus contributing to glomerular hypertension and renal ischemia. [Copyright &y& Elsevier]

Summary: Accompanying the continuously deepening understanding of the mechanism of pulmonary hypertension that many genes are found to be aetiologically involved in its development, burgeoning literature manifest that gene therapies aimed at correcting these genetic defects have the ability to restore deficient pulmonary gene expression, over-express biologically active gene products, reverse established disease and regenerate pulmonary vasculature, and may constitute a promising therapeutic strategy for pulmonary hypertension. Therefore, to provide new information to basic scientists and clinical investigators, we present a review that attempts a clear description of the therapeutic potential of gene therapy in the treatment of pulmonary hypertension. [Copyright &y& Elsevier]

Background: The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge. Methods: To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods. Results: By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT (http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified. Conclusions: We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification. [ABSTRACT FROM AUTHOR]

Background: In recent years, the differences between left-sided colon cancer (LCC) and right-sided colon cancer (RCC) have received increasing attention due to the clinicopathological variation between them. However, some of these differences have remained unclear and conflicting results have been reported.Methods: From The Cancer Genome Atlas (TCGA), we obtained RNA sequencing data and gene mutation data on 323 and 283 colon cancer patients, respectively. Differential analysis was firstly done on gene expression data and mutation data between LCC and RCC, separately. Machine learning (ML) methods were then used to select key genes or mutations as features to construct models to classify LCC and RCC patients. Finally, we conducted correlation analysis to identify the correlations between differentially expressed genes (DEGs) and mutations using logistic regression (LR) models.Results: We found distinct gene mutation and expression patterns between LCC and RCC patients and further selected the 30 most important mutations and 17 most important gene expression features using ML methods. The classification models created using these features classified LCC and RCC patients with high accuracy (areas under the curve (AUC) of 0.8 and 0.96 for mutation and gene expression data, respectively). The expression of PRAC1 and BRAF V600E mutation (rs113488022) were the most important feature for each model. Correlations of mutations and gene expression data were also identified using LR models. Among them, rs113488022 was found to have significance relevance to the expression of four genes, and thus should be focused on in further study.Conclusions: On the basis of ML methods, we found some key molecular differences between LCC and RCC, which could differentiate these two groups of patients with high accuracy. These differences might be key factors behind the variation in clinical features between LCC and RCC and thus help to improve treatment, such as determining the appropriate therapy for patients. [ABSTRACT FROM AUTHOR]

Auxin response factors (ARF) are important transcription factors which mediate the transcription of auxin responsive genes by binding directly to auxin response elements (AuxREs) found in the promoter regions of these genes. To date, no information has been available about the genome-wide organization of the ARF transcription factor family in physic nut. In this study, 17 ARF genes (JcARFs) are identified in the physic nut genome. A detailed investigation into the physic nut ARF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under various conditions. Phylogenetic analysis suggests that the 17 JcARF proteins are clustered into 6 groups, and most JcARF proteins from the physic nut reveal closer relationships with those from Arabidopsis than those from rice. Of the 17 JcARF genes, eight are predicted to be the potential targets of small RNAs; most of the genes show differential patterns of expression among four tissues (root, stem cortex, leaf, and seed); and qRT-PCR indicates that the expression of all JcARF genes is inhibited or induced in response to exogenous auxin. Expression profile analysis based on RNA-seq data shows that in leaves, 11 of the JcARF genes respond to at least one abiotic stressor (drought and/or salinity) at, as a minimum, at least one time point. Our results provide valuable information for further studies on the roles of JcARF genes in regulating physic nut's growth, development and responses to abiotic stress. [ABSTRACT FROM AUTHOR]

Background:Aquaporin (AQP) water channels are important for water homeostasis in all organisms. Malaria transmission is dependent on Anopheles mosquitoes. Water balance is a major factor influencing mosquito survival, which may indirectly affect pathogen transmission. Methodology/Principal Findings:We obtained full-length mRNA sequences for Anopheles gambiae aquaporin 1 (AgAQP1) and identified two splice variants for the gene. Invitro expression analysis showed that both variants transported water and were inhibited by Hg2+. One splice variant (AgAQP1A) was exclusively expressed in adult female ovaries indicating a function in mosquito reproduction. The other splice variant (AgAQP1B) was expressed in the midgut, malpighian tubules and the head in adult mosquitoes. Immunolabeling showed that in malpighian tubules, AgAQP1 is expressed in principal cells in the proximal portion and in stellate cells in the distal portion. Moreover, AgAQP1 is expressed in Johnston’s organ (the “ear”), which is important for courtship behavior. Conclusions And Significance:These results suggest that AgAQP1 may play roles associated with mating (courtship) and reproduction in addition to water homeostasis in this important African malaria vector. [ABSTRACT FROM AUTHOR]

Plants are affected by changes in light and adaptation mechanisms can affect secondary metabolite synthesis. In this study, the physiological response and regulation of the coumarin biosynthetic pathway of Angelica dahurica to different light intensities (natural light (CK), shade rate 50% (L1), shade rate 70% (L2), and shade rate 90% (L3)) were examined. The chlorophyll content, level of the enzymes of the antioxidant system, extent of lipid peroxidation, and concentrations of the osmoregulatory solute levels were determined in potted plants. Root transcriptome under different light intensities was sequenced using high-throughput technology, and differentially expressed genes (DEGs) related to coumarin biosynthesis were analyzed by quantitative real-time PCR (qRT-PCR). With increasing shade, Chl a, Chl b, Chl a + b, and Chl a/b content increased, while the Chl a/b ratio decreased. The antioxidant enzyme system activity and extent of membrane lipid peroxidation increased. The soluble protein (SP) and proline (Pro) content decreased with the reduction in the light intensity, and soluble sugar (SS) content was found to be highest at 50% shade. The RNA-seq analysis showed that 9388 genes were differentially expressed in the L3 group (7561 were upregulated and 1827 were downregulated). In both the L1 and L2 groups, DEGs were significantly enriched in "Ribosome biosynthesis"; meanwhile, in the L3 group, the DEGs were significantly enriched in "Amino and ribonucleotide sugar metabolism" in KEGG metabolic pathway analysis. Additionally, 4CL (TRINITY_DN40230_c0_g2) and COMT (TRINITY_DN21272_c0_g1) of the phenylpropanoid metabolic pathway were significantly downregulated in the L3 group. In conclusion, A. dahurica grew best under 50% shade and the secondary-metabolite coumarin biosynthetic pathway was inhibited by 90% shade, affecting the yield and quality of medicinal compounds. [ABSTRACT FROM AUTHOR]

Background: Vascular smooth muscle cell (VSMC) proliferation plays an important role in the failure of autologous vein grafts. The c-myc gene activation is highly involved in the VSMC proliferation. In this study, we made an attempt to determine whether VSMC proliferation and vein graft restenosis could be attenuated by silencing the c-myc gene with small interference RNA (siRNA). Methods: The effects of c-myc siRNA on VSMCs in vitro were examined both in cell proliferation and c-myc expression. Thirty-two Sprague-Dawley rats underwent autologous jugular vein to carotid artery reverse interposition grafting and were randomly divided in to four groups. Vein grafts were treated with pluronic gel or gel containing a scrambled siRNA or c-myc siRNA and the control group received no treatment. Intimal thickness of the vein grafts was evaluated at 3 wk after the surgery. Results: In vitro, c-myc siRNA inhibited cell proliferation by 40%, reduced c-myc mRNA level by 70%, and c-myc protein level by 50% compared with the controls. In vivo, the c-myc siRNA treatment reduced intimal hyperplasia by 75%. Conclusions: Our data suggested that c-myc siRNA, when given immediately after the surgery, is an effective approach for the prevention of vein graft restenosis. [Copyright &y& Elsevier]

Gene-chip technology was employed to study the effect of dietary vitamin E on gene expression in sheep testes based on our previous research. Thirty-five male Tan sheep (20–30 days after weaning) with similar body weight were randomly allocated into five groups and supplemented 0, 20, 100, 200 and 2000 IU sheep − 1 day − 1 vitamin E (treatments denoted as E0, E20, E100, E200, and E2000, respectively) for 120 days. At the end of the study the sheep were slaughtered and the testis samples were immediately collected and stored in liquid nitrogen. Differences in gene expression between different treated groups were identified. Based on GO enrichment analysis and the KEGG database to evaluate the gene expression data we found that vitamin E might affect genes in the testes by modulating the oxidation level, by affecting the expression of various receptors and transcription factors in biological pathways, and by regulating the expression of metabolism-associated genes. The effect of vitamin E supplementation on the expression of oxidative enzyme-related genes was detected by quantitative real-time PCR (qRT-PCR) and Western blot. The results show that dietary vitamin E, at various doses, can significantly increase ( P < 0.05) the mRNA and protein expression of Glutathione peroxidase 3 and Glutathione S-transferase alpha 1. In addition, the results of qRT-PCR of the antioxidant enzyme genes were consistent with those obtained using the gene chip microarray analysis. In summary, the dietary vitamin E treatment altered the expression of a number of genes in sheep testes. The increase in the mRNA and protein levels of antioxidant enzyme genes, coupled with the elevation in the activity of the antioxidant enzymes were primarily responsible for the improved reproductive performance promoted by dietary vitamin E. [ABSTRACT FROM AUTHOR]

Aim and Objective. Hyperlipidemia is a public health matter of global scale, contributing to a wide range of diseases that can result in severe complications and significant annual mortality. Dendrobium officinale (DO) is an edible plant with a long medicinal history in China. Our previous studies revealed that DO may have therapeutic benefits in lipid disorders. However, the mechanism of its active compounds is still unclear. This research aimed at uncovering the hidden anti-hyperlipidemia mechanisms of DO through network pharmacology and experimental validation. Materials and Methods. The active compounds in DO, their targets, and targets associated with hyperlipidemia were screened across various databases, and the hidden targets of DO in treating hyperlipidemia were forecast. The compound-target (C-T), protein-protein interaction (PPI), and compound-target-pathway (C-T-P) networks of DO were set up with Cytoscape software. The hub genes and core clusters of DO predicted to be active against hyperlipidemia were calculated by Cytoscape. The DAVID database was adopted for Gene Ontology (GO) analysis and KEGG pathway enrichment analysis. Next, we used the high-sucrose-fat diet and alcohol (HFDA)-induced hyperlipidemia rats to evaluate the hypolipidemic effect of DO. Results. In this study, we obtained 264 compounds from DO, revealed 11 bioactive compounds, and predicted 89 potential targets of DO. The network analysis uncovered that naringenin, isorhamnetin, and taxifolin might be the compounds in DO that are mainly in charge of its roles in hyperlipidemia and might play a role by modulating the targets (including PPARG, ADIPOQ, AKT1, TNF, and APOB). The pathway analysis showed that DO might affect diverse signaling pathways related to the pathogenesis of hyperlipidemia, including PPAR signaling pathway, insulin resistance, AMPK signaling pathway, and non-alcoholic fatty liver disease simultaneously. Meanwhile, in the HFDA-induced hyperlipidemia rat model, DO could significantly decrease the level of TC, TG, LDL-c, and ALT in serum, and increase HDL-c as well. The liver pathological section indicated that DO could ease liver damage and lipid cumulation. Conclusion. In summary, the biological targets of the main bioactive compounds in DO were found to distribute across multiple metabolic pathways. These findings suggest that a mutual regulatory system consisting of multiple components, targets, and pathways is a likely mechanism through which DO may improve hyperlipidemia. Validation experiments indicated that DO may treat hyperlipidemia by affecting NAFLD-related signaling pathways. [ABSTRACT FROM AUTHOR]

Background: Liver hepatocellular carcinoma (LIHC) is one of the most common malignant tumors. However, the etiology and exact molecular mechanism of LIHC are still not fully understood, which makes it urgent for us to further study the molecular events behind. Methods: In this study, differences in mRNA expression between LIHC samples and normal adjacent samples were found through analyzing the TCGA database, and key targets were sought. We analyzed 371 LIHC samples and 50 normal adjacent samples according to P <0.01 and logFC>2.5, a total of 1092 genes were identified differentially expressed, including 995 up-regulated genes and 97 down-regulated genes. We predicted the interactions of these differentially expressed mRNAs, and used Cyto-Hubba to locate the hub gene-dynein cytoplasmic 1 intermediate chain 1 (DYNC1I1). Results: Survival analysis showed that DYNC1I1 was a prognostic factor for LIHC male patients. Functional enrichment indicated that DYNC1I1 and differentially expressed interacting proteins were involved in the cell cycle. Conclusion: In conclusion, this study discovers that DYNC1I1 can be used as a prognostic marker for LIHC male patients. [ABSTRACT FROM AUTHOR]

• The Equine β-defensin-1 (eBD-1) promotes cytokines mRNA expression in S. aureus -infected macrophages regulated by PI-3K-NF-κB pathway. • The eBD-1 increases macrophages phagocytose S. aureus associated with FAK-paxillin signalling pathway. • The eBD-1 has a potential application ability in alternatives to antibiotics. β-defensin-1 (BD-1) is a rich source of disulfide bonds and antibacterial peptides that exhibit direct bactericidal function. The expression of BD-1 is primarily induced by external stimulation and is known to correlate with TLR-mediated inflammation, suggesting its association with innate immune responses. Equine β-defensin-1 (eBD-1) belongs to the BD-1 family. Our previous study demonstrated that eBD-1 enhances cytokine expression and promotes macrophage phagocytosis of S. aureus , although the underlying mechanism remains unknown. In this study, we utilized a PI-3K inhibitor (PKI-402) to treat eBD-1 -treated S. aureus -infected macrophages in vitro. Our results revealed that PKI-402 decreased the expression of eBD-1-promoted TNF-α , IL-6 , CXCL10 , CD40 , RANTES, and p65 mRNA. To further investigate the relationship between eBD-1 and phagocytosis, we examined the expression of paxillin and FcγRIII (CD16 receptor) using western blot and immunofluorescence techniques. Our findings demonstrated that eBD-1 enhanced CD16 and paxillin expression in S. aureus -infected macrophages. Considering the correlation between paxillin expression and focal adhesion kinase (FAK), we transfected FAK siRNA into macrophages and evaluated paxillin expression using western blot analysis. Additionally, we quantified the number of S. aureus phagocytosed by macrophages. The results indicated a reduction in both paxillin expression and the number of S. aureus phagocytosed by macrophages upon FAK siRNA treatment. Our study showed the eBD-1 promotes cytokine mRNA expression in S. aureus -infected macrophages regulated by PI-3K-NF-κB pathway, and it increases macrophage phagocytosis of S. aureus associated with the FAK-paxillin signaling pathway. [ABSTRACT FROM AUTHOR]

Abstract Objective To screen the methylated genes for early diagnosis and biochemical recurrence (BCR) prediction in prostate cancer (PCa) patients. Methods Differentially methylated CpG sites (DMCs) of PCa were screened out from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Combined with TCGA RNA sequencing data and clinical information, the DMCs associated genes with different expression and related to BCR were selected as candidate genes. Then, the expression level of the best candidate gene ZNF154 was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Finally, the prognosis potential of the hypermethylation gene ZNF154 was assessed by Kaplan-Meier, univariate and multivariate cox regression analysis. Results A total of 87 candidate genes were screened out. Compared to benign prostate (BP) tissues, ZNF154 has three hypermethylation sites (cg03234186, cg12506930, cg26465391) in the promoter region in PCa tissues. qRT-PCR results showed that ZNF154 expression level was reduced in PCa tissues than in BP tissues (P = 0.004). Besides, the ZNF154 methylation level was negatively correlated with mRNA expression (r = −0.766, P < 0.001), and was highly cancer-specific in PCa (area under the curves (AUCs) = 90.030%). In addition, Kaplan-Meier analysis showed ZNF154 methylation level was associated with BCR (P = 0.005), and ZNF154 could be an independent factor for BCR prediction in PCa by using univariate and multivariate cox regression analysis (P = 0.035, HR = 8.218). Conclusions 87 PCa specific genes were obtained. Further analysis gave the evidence that ZNF154 can be used as a specific maker for PCa diagnosis. Hypermethylation level of ZNF154 lead to gene expression inhibition and function loss, which contribute to the development and poor outcomes in PCa. In addition, the mean methylation level of ZNF154 can be used as an independent risk factor to predict BCR. Highlights • PSA showed limitations in PCa diagnosis and prognosis. • Epigenetic modifications are important for diagnosis and prognosis in tumor. • Hypermethylated gene ZNF154 is high cancer-specific in PCa diagnosis. • ZNF154 could be an independent factor for biochemical recurrence prediction in PCa. [ABSTRACT FROM AUTHOR]

Background/Aims: Preventing undesirable endothelial-mesenchymal transformation (EnMT) with repetitious in vitro expansion of human corneal endothelial cells (CECs) is a pivotal issue in cornea regeneration. Previous studies have shown that inhibition of the TGF-β pathway reduces epithelial-mesenchymal transformation. However, its potential role in EnMT remains poorly understood. As such, the effect of LY2109761, a novel TGF-β receptor type I and type II dual inhibitor, was investigated on EnMT. Methods: CECs cultured with various concentrations of LY2109761 were evaluated for their growth rate and phenotype. Additionally, the expression of functional markers (sodium-potassium pump Na+/K+-ATPase and the tight junction protein ZO-1) and mesenchymal markers (CD73, fibronectin, and vimentin) was detected using immunostaining and western blot. The mRNA expressions were also assayed by real-time polymerase chain reaction analysis. Results: At a 1 μM concentration, LY2109761 did not influence the proliferation of CECs and subsequent experiments were therefore performed using this concentration. Furthermore, CECs cultured in the presence of 1 μM LY2109761 maintained their ability to grow as a monolayer of hexagonal-shaped cells. The expression of functional markers increased in LY2109761-treated CECs, while the expression of mesenchymal markers decreased (both in protein and mRNA levels). Conclusion: Inhibition of TGF-β receptor type I and type II by LY2109761 maintained the phenotype of CECs and inhibited the EnMT process. These results indicate the possible continuous in vitro expansion of CECs with normal function. [ABSTRACT FROM AUTHOR]

DNA methylation is essential for the regulation of gene expression and important roles in muscle development. To assess the extent of epigenetic modifications and gene expression on the differentially methylated region (DMR) inZBED6, we simultaneously examined DNA methylation and expression in six tissues from two different developmental stages (fetal bovine and adult bovine). The DNA methylation pattern was compared using bisulfite sequencing polymerase chain reaction (BSP) and combined bisulfite restriction analysis (COBRA). The result of quantitative real-time PCR (qPCR) analysis showed thatZBED6has a broad tissue distribution and is highly expressed in adult bovine (P < 0.05 orP < 0.01). The DNA methylation level was significantly different in liver, lung and spleen between the two cattle groups (P < 0.05 orP < 0.01). The adult bovine group exhibited a significantly higher mRNA level and lower DNA methylation level than the fetal bovine group in liver, lung, and spleen. No significant association was detected between DNA methylation level and muscle, heart, and kidney at two different stages. In this study, the statistical analyses indicated that DNA methylation patterns are associated with mRNA level in some tissues, these results may be a useful parameter to investigate muscle developmental in cattle and as a model for studies in other species, potentially contributing to an improvement of growth performance selection in beef cattle breeding program. [ABSTRACT FROM PUBLISHER]

For locally advanced colorectal cancer (CRC), neoadjuvant chemoradiotherapy (nCRT) followed by total mesorectal excision or complete mesocolic excision is the standard therapeutic strategy, which is key to patient survival. Involvement of the tumor immune microenvironment is a factor that regulates tumor progression and sensitivity to nCRT in CRC. In this study, we aimed to identify the effect of heat-shock protein 70 (HSP70)/toll-like receptor-2 (TLR-2) on mFOLFOX sensitization for CRC. A total of 22 patients with advanced CRC who had received neoadjuvant mFOLFOX were enrolled and classified into the mFOLFOX-insensitive or -sensitive group, according to the tumor regression grade. The abundance of immune infiltrates was significantly higher in the post-operative pathological specimens of the mFOLFOX-insensitive group, as compared to those of the mFOLFOX-sensitive group. After transcriptome sequencing, differentially expressed genes between the two groups were annotated to inflammatory and immune responses using Gene Ontology (GO) analysis, and the TLR signaling pathway was analyzed using Kyoto Encyclopedia of Genes and Genomes pathway analysis. Significantly higher expression levels of HSP60, HSP70, HSP90, and TLR-2 in the mFOLFOX-insensitive group were detected using immunofluorescence assays. TIMER2.0 platform was introduced to further narrow the scope of HSP70 (HSPA6 or HSPA7) and TLR-2, which exhibited positive correlations with dendritic cells, Tregs, or CD4+ T cells and negative correlations with CD3+ or CD8+ T cells, implying that HSP70/TLR-2 activation mediates immunosuppressive cells to counteract CD8+ T cells, which may be a novel target of CRC treatment. A promising synergistic effect of mFOLFOX combined with a TLR-2 inhibitor was observed in vivo in mouse allograft models, which could be partly rescued by recombinant HSP70 protein. Immunohistochemical staining of allografts and immunofluorescence assays of clinical specimens corroborated the regulatory effects of the immune microenvironment. In summary, HSP70/TLR-2 activation can regulate the tumor immune microenvironment of CRC and further remodel its sensitivity to mFOLFOX. However, the specific mechanisms remain unclear and require further investigation. This study is expected to provide a new direction for the clinical treatment of CRC. [ABSTRACT FROM AUTHOR]

Purpose: To study the correlation between expression levels of ERCC1/TS mRNA and the susceptibility of preoperative chemotherapy for patients with gastric cancer. Methods: A total of forty cases with advanced gastric cancer of T3-4N1-2M0 were treated with preoperative chemotherapy according to FLEEOX regimen based on endarterial-intravenous coadministration. Sufficient, fresh gastric tissue specimens were obtained with the help of gastroscope, and the expression levels of ERCC1/TS mRNA were detected by qRT-PCR before chemotherapy. The chemotherapeutic response was evaluated with Choi Criteria after chemotherapy, and pathologic remission extent was observed after surgery. The correlation between the expression levels of ERCC1/TS mRNA before chemotherapy and the chemotherapeutic effect based on imageology and pathology was analyzed. Results: The response rate of Chemotherapy in this cohort was 80.0 % based on imageology and 51.43 % based on pathology. The expression levels of ERCC1/TS mRNA were significantly associated with imageology remission extent ( P = 0.033, P = 0.025) and pathologic remission extent ( P = 0.044, P = 0.016), respectively. The chemotherapeutic effect on patients with low-expression levels of ERCC1/TS mRNA was better. Conclusions: From the perspective of pathology and imageology evaluating the preoperative chemotherapeutic response for patients with gastric cancer, ERCC1 and TS were used as the molecular predictors and provided prognostic information in this study. [ABSTRACT FROM AUTHOR]

Abstract: Vascular calcification is a pathobiological process which leads to high morbidity and mortality in cardiovascular disease. The association between vascular calcification and osteoporosis has been reported widely, and there are close relationships among vascular calcification, related cardiovascular disease and osteoporosis, but the biochemical mechanism of vascular calcification is presently unclear. For exploring the possible mechanism of artery calcification we established aorta calcification in an animal model with vitamin D3 and warfarin and tested the effect of alendronate on the expression of osteopontin and osteoprotegerin in calcified aorta tissue of the rat through measuring gene and protein expression of osteopontin and osteoprotegerin respectively. The results indicated compared with control group, the aortic calcium content of calcification group was obviously increased, osteopontin mRNA and osteoprotegerin mRNA were significantly reduced, and osteoprotegerin and osteopontin protein expressions were reduced. Compared with calcification group, the aortic calcium content of alendronate group was obviously reduced, osteopontin mRNA and osteoprotegerin mRNA were significantly increased, and osteopontin and osteoprotegerin protein expression were increased. We conclude that artery calcification may reduce the expression of osteopontin and osteoprotegerin. Alendronate may inhibit rat aorta calcification by up-regulating osteopontin and osteoprotegerin expression. [Copyright &y& Elsevier]

Objective: A sensitive mutation detection method called co-amplification at lower denaturation temperature-polymerase chain reaction (COLD-PCR) was applied to improve the detection frequencies of expressive mutations in the H-ras gene, including exons 1 and 2, in a group of Chinese patients diagnosed with bladder cancer. Materials and Methods: The expressive mutations in the H-ras gene in 86 fresh tissues of human bladder cancer were identified by COLD-PCR or conventional PCR, followed by direct sequencing. Results: A high frequency of silent mutations of 29.1% (25 of 86) in exon 1 (c.81T>C, H27H) and activating mutations of 8.1% (7 of 86) were detected by COLD-PCR, yielding a 36% improvement in mutation detection compared with conventional PCR. No significant association was shown between activating mutations and clinicopathologic parameters, but the frequencies of silent mutations in recurrent tumors were higher than those in primary tumors (p = 0.034). Conclusions: COLD-PCR is a highly sensitive, reliable, and convenient clinical assay for mutation detection. The adoption of the method is straightforward and requires no additional reagents or instruments. Silent mutations might be important genomic alterations in bladder cancer, and play a role in bladder cancer recurrence. Copyright © 2012 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

MicroRNAs have been implicated in the regulation of gene expression of various biological processes in a post-transcriptional manner under physiological and pathological conditions including host responses to viral infections. The 2009 pandemic H1N1 influenza virus is an emerging reassortant strain of swine, human and bird influenza virus that can cause mild to severe illness and even death. To further understand the molecular pathogenesis of the 2009 pandemic H1N1 influenza virus, we profiled cellular microRNAs of lungs from BALB/c mice infected with wild-type 2009 pandemic influenza virus A/Beijing/501/2009 (H1N1) (hereafter referred to as BJ501) and mouse-adapted influenza virus A/Puerto Rico/8/1934 (H1N1) (hereafter referred to as PR8) for comparison. Microarray analysis showed both the influenza virus BJ501 and PR8 infection induced strain- and temporal-specific microRNA expression patterns and that their infection caused a group of common and distinct differentially expressed microRNAs. Characteristically, more differentially expressed microRNAs were aroused on day 5 post infection than on day 2 and more up-regulated differentially expressed microRNAs were provoked than the down-regulated for both strains of influenza virus. Finally, 47 differentially expressed microRNAs were obtained for the infection of both strains of H1N1 influenza virus with 29 for influenza virus BJ501 and 43 for PR8. Among them, 15 microRNAs had no reported function, while 32 including miR-155 and miR-233 are known to play important roles in cancer, immunity and antiviral activity. Pathway enrichment analyses of the predicted targets revealed that the transforming growth factor-β (TGF-β) signaling pathway was the key cellular pathway associated with the differentially expressed miRNAs during influenza virus PR8 or BJ501 infection. To our knowledge, this is the first report of microRNA expression profiles of the 2009 pandemic H1N1 influenza virus in a mouse model, and our findings might offer novel therapy targets for influenza virus infection. [ABSTRACT FROM AUTHOR]