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Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http://www.picb.ac.cn/rnomics/circpedia.
Subject(s)
Animals , Humans , Mice , Databases, Genetic , Gene Expression Regulation , Internet , Molecular Sequence Annotation , RNA , Genetics , User-Computer InterfaceABSTRACT
Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that can cause severe diseases in pigs and result in enormous economic losses in the worldwide swine industry. Previous studies revealed that PEDV exhibits an obvious capacity for modulating interferon (IFN) signaling or expression. The newly discovered type III IFN, which plays a crucial role in antiviral immunity, has strong antiviral activity against PEDV proliferation in IPEC-J2 cells. In this study, we aimed to investigate the effect of PEDV nucleocapsid (N) protein on type III IFN-λ. We found that the N proteins of ten PEDV strains isolated between 2013 and 2017 from different local farms shared high nucleotide identities, while the N protein of the CV777 vaccine strain formed a monophyletic branch in the phylogenetic tree. The N protein of the epidemic strain could antagonize type III IFN, but not type I or type II IFN expression induced by polyinosinic-polycytidylic acid (poly(I:C)) in IPEC-J2 cells. Subsequently, we demonstrated that the inhibition of poly(I:C)-induced IFN-λ3 production by PEDV N protein was dependent on the blocking of nuclear factor-κB (NF-κB) nuclear translocation. These findings might help increase understanding of the pathogenesis of PEDV and its mechanisms for evading the host immune response.
Subject(s)
Animals , Active Transport, Cell Nucleus , Coronavirus Infections , Allergy and Immunology , Virology , Genes, Viral , Host-Pathogen Interactions , Allergy and Immunology , Interferons , Genetics , Interleukins , Genetics , NF-kappa B , Metabolism , Nucleocapsid Proteins , Genetics , Allergy and Immunology , Physiology , Porcine epidemic diarrhea virus , Genetics , Virulence , Physiology , Promoter Regions, Genetic , Swine , Swine Diseases , Allergy and Immunology , VirologyABSTRACT
<p><b>OBJECTIVE</b>To identify the master transcription factors (TF) that might be responsible for the gene expression alteration of OA.</p><p><b>METHODS</b>Raw expression data for rat OA model(GSE30322) was downloaded from NCBI GEO database. Microarray data analysis for rat and human was carried out separately using functions from limma packagein R, gene expression was considered as significantly changed between conditions if adjusted-value<0.05 and the absolute value of fold change>=2. iRegulon was applied to differentially up-regulated and down-regulated genes in OA separately.</p><p><b>RESULTS</b>(1)15 TFs, including FOXN4, NANOS1, E2F6, RAD21, MECOM, ETS1, MEF2A, POU2F3, BRCA1, GATA3, ZNF706, ZBTB33, SUZ12, DBP and SETDB1, were identified as the potential master TFs of up-regulated DEGs with statistical significance. (2)12 TFs, including ARID3A, YY1, RDBP, ATF1, CRX, TAF1, XBP1, SOX3, E2F4, PGR, TIMM8A and HOXA2, were identified as the potential master TFs of down-regulated DEGs with statistical significance.</p><p><b>CONCLUSIONS</b>The newly identified TFs maybe play important roles in pathogenesis of early experimental osteoarthritis, and our study provides new diagnostic markers or therapeutic targets for OA.</p>
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Objective:To investigate the effect of epigallocatechin-3-gallate ( EGCG) on the expression of pro-inflammatory cytokines in murine bone marrow-derived macrophages ( BMDM) induced by IFN-γ/LPS.Methods:The bone marrow cells were isolated from 6-8 weeks C57BL/6 mice,which cultured in RPMI1640 medium with 10%FBS and stimulated with 100 ng/ml M-CSF in vitro,and then exposed to 50 ng/ml IFN-γand 1 μg/ml LPS with various concentrations of EGCG (12.5-50 μmol/L) .The expression of pro-inflammatory factors,IL-1β,TNF-αand iNOS were detected,in murine myeloid macrophages stimulated by IFN-γ/LPS with qRT-PCR and ELISA.Results:IFN-γ/LPS remarkably up-regulated the expression levels of inflammatory cytokines ,IL-1β,TNF-αand iNOS,but EGCG effectively repressed these cytokines expression in IFN-γ/LPS-stimulated murine myeloid macrophages , in dose-dependent manner.Conclusion:EGCG attenuates the pro-inflammatory phenotype of murine myeloid macrophages stimulated with IFN-γ/LPS.
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Objective To investigate the relationship of carotid intimal-medial wall thickness(IMT) and the expression of IL-6 and Fetuin-A in two type diabetes.Methods 80 patients with two type diabetes were chosen,and 60 cases healthypeople of examination for the control group.The levels of IL-6 and Fetuin-A were measured,and measured the intimal-medial thickness (IMT) of internal carotid artery by carotid duplex ultrasonography scanning simultaneously.Results The level of IL-6 was significantly higher in two type diabetes than those in control group,and the level of Fetuin-A was declind (t=8.34 ～15.65,all P＜0.05).IL-6 level in normal IMT (A group,20 cases) was 2.24±0.21 pg/L,Fetuin level was 5.41±0.32 ng/ ml.IL-6 level in abnormal IMT (B group,18 cases) was 3.44±0.18 mm,and Fetuin level was 3.86±0.42 ng/ml.Relatively,IL-6 level in IMT with plaque (C group,22 cases) was 4.95-±-0.31 ng/ml,Fetuin-A level was 2.41±0.32 ng/ml.IL-6 level in lumen narrow (D group,20 cases) was 5.35±0.31 ng/ml,and Fetuin-A level was 2.02 ± 0.08 ng/ml.There were obvious differences for four groups to detect IL-6 was Fetuin-A levels (F=8.69 ～ 11.02,all P＜ 0.05).The level of IL-6 were rised little by little from A group to D group.There were obvious differences for comparison among groups (t=5.32～9.01,all P＜0.05).The level of Fetuin-A were declined little by little from A group to D group,there were obvious differnce for comparison among groups (t=6.14～11.53,all P＜0.05).Conclusion There was a close correlation between IL-6,Fetuin-A level and carotid intimal-medial wall thickness(IMT) in two type diabetes.To detection IL-6 and Fetuin-A levels is a target to distinguish two type diabetes whether or not with atherosclerosis.
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Rabies is very common in Peoples Republic of China. Each year thousands of people die because of this disease, but rabies diagnosed in pregnancy is very rare. Case Presentation In this study, we report the case of a pregnant woman who was infected with the rabies virus after a dog bite. The symptoms of rabies appeared in labor and she died after pregnancy. Her baby and husband did not develop the disease. Conclusion The phenomenon that the newborn infant was healthy may be related to the protective role of placenta in resisting the invasion of the rabies virus or the absence of systemic viremia. The prompt administration of vaccines and anti-rabies immunoglobulin to the infant may have also contributed to his survival.
Subject(s)
Female , Humans , Pregnancy , Infant, Newborn , Survival Analysis , Vaccines/administration & dosage , Vaccines/analysis , Rabies virus/classification , Rabies virus/immunologyABSTRACT
Background Rabies is very common in People's Republic of China. Each year thousands of people die because of this disease, but rabies diagnosed in pregnancy is very rare. Case Presentation In this study, we report the case of a pregnant woman who was infected with the rabies virus after a dog bite. The symptoms of rabies appeared in labor and she died after pregnancy. Her baby and husband did not develop the disease. Conclusion The phenomenon that the newborn infant was healthy may be related to the protective role of placenta in resisting the invasion of the rabies virus or the absence of systemic viremia. The prompt administration of vaccines and anti-rabies immunoglobulin to the infant may have also contributed to his survival.(AU)
Subject(s)
Humans , Female , Pregnancy , Infant, Newborn , Rabies , Rabies virus , Bites and Stings , Immunoglobulins , Pregnant Women , Research ReportABSTRACT
Objective To investigate Bartonella infection in rodent hosts from different environments and types of climate in Fujian coastal regions. Genetypes of the Bartonella strains was also studied to provide scientific basis for prevention and control of the correlated diseases. Methods By random sampling method, we selected six study sites in Fujian southeastern coastal regions. Rodents were captured by cages to Isolate Bartonella strains. Bartonella-like isolates were confirmed by polymerase chain reaction (PCR). The 379 bp fragment of gltA gene was sequenced and the growth and development tree was constructed to determine Bartonella species. Distribution of Bartonella species in the different area and related hosts was also analysed. Results Bartonella species were isolated from 188 of 1161 small animals including five rodent species. The infected animals were grouped into 2 genera and 2 orders. They were Suncus murinus, Rattas norvegicus, Rnttus flavipectus, Mus masculus and Rattus rattus. The overall prevalence of Bartonella bacteremia was 16.19% in the most prevalent species of rodents in Fujian southeastern coastal regions including 21.43% in Suncus murinus, 13.54% in Rattas norvegicus and 18.27% in Rattus flavipectus. Rodents in every investigated areas were infected by Bartonella species (9.25% in Ningde, 9.52% in Fuzhou, 9.38% in Putian, 28.18% in Quanzhou, 17.42% in Xiamen and 13.33% in Zhangzhou). There were significant differences among infected rates in different annual accumulated temperature districts (χ~2=12.93, P<0.001). Isolates from rodents were clustered in three genotypes (B.elizabethae, B.qeenslandensis and B.tribocorum A, B). Conclusion The local rodents in Fujian southeastern coastal regions were widely infected by Bartonella spp. Differences among the prevalent species of Bartonella in Fujian southeastern coastal region, Yunan and Beijing were noticed. Our findings suggested there was a need to study the prevalence, related vectors and the molecular organism of Bartonella spp.
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<p><b>BACKGROUND</b>Although severe acute respiratory syndrome (SARS) has been controlled, the subsequently emerging sporadic cases in 2004 emphasize the necessity of developing a rapid diagnostic method, which would be of great help in clinical diagnosis and also wild host screening. This study aims to establish an effective and rapid serological tool for the diagnosis of SARS-CoV by comparison among whole viral, N and N199 proteins by ELISA.</p><p><b>METHODS</b>SARS-CoV N and N199 (a truncated nucleocapsid gene) genes were cloned, expressed, identified by Western blotting, and applied in screening of human and swine samples. Sera of SARS convalescent-phase patients, normal human sera, sera of patients with other respiratory diseases, and swine sera were screened by ELISA, with whole SARS-CoV F69, N and N199 proteins as antigens.</p><p><b>RESULTS</b>The sensitivity and specificity of N and N199 proteins in human sera diagnosis were approximate (P = 0.743), which was higher than whole viral protein but the difference was not significant (P = 0.234). The N199 protein proved to be more specific in swine sera screening than whole viral and N protein (P < 0.001).</p><p><b>CONCLUSION</b>N199 protein is feasible in both clinical diagnosis and SARS-CoV reservoir screening.</p>