Molecular detection of bornavirus in parrots imported to China in 2022.

BACKGROUND: Avian bornavirus (ABV) is a neurotropic virus, it has been established as the primary causative agent of proventricular dilatation disease (PDD). However, substantial international trade and transnational trafficking of wild birds occur, potentially enabling these birds to harbor and transmit pathogens to domestic poultry, adversely affecting their well-being. Real-time RT-PCR was employed to detect the presence of PaBV-4 in parrots imported to China in 2022. RESULTS: In 2022, a total of 47 cloacal swabs from 9 distinct species of parrots were collected at the Wildlife Rescue Monitoring Center in Guangdong, China. The purpose of this collection was to detect the presence of PaBV-4. Using real-time PCR techniques, it was determined that the positive rate of PaBV-4 was 2.12% (1 out of 47) in parrots. The PaBV-4 virus was detected in a Amazona aestiva that had been adopted for one month. Conversely, all other species tested negative for the virus. Subsequently, the whole genome of the PaBV-4 GD2207 strains was sequenced, and the homology and genetic evolution between these strains and previously published PaBV-4 strains on GenBank were analyzed using DNAStar and MEGA7.0 software. The findings revealed that the full-length genome of PaBV-4 consisted of 8915 nucleotides and encoded six proteins. Additionally, it exhibited the highest nucleotide similarity (99.9%) to the GZ2019 strain, which causes death and severe clinical symptoms in Aratinga solstitialis. Furthermore, when compared to other strains of PaBV-4, the GD2207 strain demonstrated the highest amino acid homology with GZ2019. The phylogenetic analysis demonstrated that the GD2207 strain clustered with various strains found in Japanese, American, and German parrots, indicating a close genetic relationship with PaBV-4, but it revealed a distant relationship with PaBV-5 Cockg5 from America. Notably, the GD2207 was closely associated with the GZ2019 strain from Aratinga solstitialis in China. CONCLUSION: This study presents the preliminary identification of PaBV-4 in Amazona aestiva parrots, emphasizing its importance as the predominant viral genotype linked to parrot infections resulting from trade into China. Through genetic evolution analysis, it was determined that the GD2207 strain of PaBV-4 exhibits the closest genetic relationship with GZ 2019 (Aratinga solstitialis, China), M14 (Ara macao, USA), AG5 (Psittacus erithacus, USA) and 6758 (Ara ararauna, Germany) suggesting a shared ancestry.

Spirometra (Pseudophyllidea, Diphyllobothriidae) severely infecting wild-caught snakes from food markets in Guangzhou and Shenzhen, Guangdong, China: implications for public health.

Sparganosis is a zoonotic disease caused by the spargana of Spirometra, and snake is one of the important intermediate hosts of spargana. In some areas of China, snake is regarded as popular delicious food, and such a food habit potentially increases the prevalence of human sparganosis. To understand the prevalence of Spirometra in snakes in food markets, we conducted a study in two representative cities (Guangzhou and Shenzhen), during January-August 2013. A total of 456 snakes of 13 species were examined and 251 individuals of 10 species were infected by Spirometra, accounting for 55.0% of the total samples. The worm burden per infected snake ranged from 1 to 213, and the prevalence in the 13 species was 0∼96.2%. More than half (58.1%) of the spargana were located in muscular tissue, 25.6% in subcutaneous tissue, and 16.3% in coelomic cavity. The results indicated that Spirometra severely infected snakes in food markets in Guangzhou and Shenzhen, implying that eating snakes has great health risk and improper cooking methods may increase the risk of Spirometra infection in humans in China. Additional steps should be considered by the governments and public health agencies to prevent the risk of snake-associated Spirometra infections in humans.

The complete mitochondrial genome of the red-footed tortoise (Chelonoidis carbonarius Spix 1824).

In this study, we report the complete mitochondrial genome of the red-footed tortoise (Chelonoidis carbonarius). The compete mitochondrial genome of C. carbonarius is 16,639 bp in length, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The mitogenome was deposited in NCBI GenBank under the accession number OQ789392. Furthermore, we also constructed a phylogenetic tree of Chelonoidis using eight species. These results will aid the conservation of Chelonoidis from the perspective of genetic evolution.

Directly investigating the interaction between aptamers and thrombin by atomic force microscopy.

Aptamers are single-stranded nucleic acid molecules that can be used for protein recognition, detection, and inhibition. Over the past decades, two thrombin-binding aptamers (15apt and 27apt) were reported by systemic evolution of ligands by exponential enrichment technique. Though many studies have been reported about the interactions between the aptamers and thrombin by atomic force microscopy, the thrombins in those studies were all immobilized by chemical agents. Recently, we developed a new method using atomic force microscopy to directly investigate the specific interactions between thrombin and its two aptamers without immobilizing the thrombin. Furthermore, the unbinding dynamics and dissociation energy landscapes of aptamer/thrombin were discussed. The results indicate that the underlying interaction mechanisms of thrombin with its two aptamers will be similar despite that the structures of 15apt and 27apt are different in buffer solution.

Comprehensive profiling of Epstein-Barr virus-encoded miRNA species associated with specific latency types in tumor cells.

BACKGROUND: Epstein-Barr virus (EBV) is an etiological cause of many human lymphocytic and epithelial malignancies. EBV expresses different genes that are associated with three latency types. To date, as many as 44 EBV-encoded miRNA species have been found, but their comprehensive profiles in the three types of latent infection that are associated with various types of tumors are not well documented. METHODS: In the present study, we utilized poly (A)-tailed quantitative real-time RT-PCR in combination with microarray analysis to measure the relative abundances of viral miRNA species in a subset of representative lymphoid and epithelial tumor cells with various EBV latency types. RESULTS: Our findings showed that the miR-BHRF1 and miR-BART families were expressed differentially in a tissue- and latency type-dependent manner. Specifically, in nasopharyngeal carcinoma (NPC) tissues and the EBV-positive cell line C666-1, the miR-BART family accounted for more than 10% of all detected miRNAs, suggesting that these miRNAs have important roles in maintaining latent EBV infections and in driving NPC tumorigenesis. In addition, EBV miRNA-based clustering analysis clearly distinguished between the three distinct EBV latency types, and our results suggested that a switch from type I to type III latency might occur in the Daudi BL cell line. CONCLUSIONS: Our data provide a comprehensive profiling of the EBV miRNA transcriptome that is associated with specific tumor cells in the three types of latent EBV infection states. EBV miRNA species represent a cluster of non-encoding latency biomarkers that are differentially expressed in tumor cells and may help to distinguish between the different latency types.

Comprehensive analysis of expression and prognostic value of the claudin family in human breast cancer.

Claudins (CLDN) are structural components of tight junctions that function in paracellular transport and maintain the epithelial barrier function. Altered expression and distribution of members of the claudin family have been implicated in several cancers including breast cancer (BC). We performed a comprehensive analysis of the expression and prognostic value of claudins in BC using various online databases. Compared with normal tissues, CLDN3, 4, 6, 7, 9, and 14 were upregulated in BC tissues, whereas CLDN2, 5, 8, 10, 11, 15, 19, and 20 were downregulated. A high expression of CLDN2, 5, 6, 9, 10, 11, and 14-20 was associated with better relapse-free survival (RFS), whereas a high CLDN3 expression correlated with poor RFS. In addition, a high expression of CLDN3, 4, 14, and 20 was associated with poor overall survival (OS), whereas that of CLDN5 and CLDN11 was linked to a better OS. Although METABRIC and TCGA datasets revealed 22% and 27% gene alterations, respectively, in the members of the claudin family, these were not associated with survival. These findings suggest CLDN3, 5, and 11 could be promising therapeutic targets for patients with BC.

Identification of Key Genes Involved in Diabetic Peripheral Neuropathy Progression and Associated with Pancreatic Cancer.

INTRODUCTION: Diabetes mellitus (DM) patients suffer from high morbidity and premature mortality due to various diabetic complications and even cancers. Therefore, this study aimed to identify key genes involved in the pathogenesis of diabetic peripheral neuropathy (DPN) and pancreatic cancer (PC). METHODS: We analyzed three gene expression profiles (GSE95849, GSE28735 and GSE59953) to obtain differentially expressed genes (DEGs). Then, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was then used to establish a protein-protein interaction (PPI) network. The MCODE and cytoHubba plug-ins of Cytoscape were used to select hub genes. Finally, survival analysis of the hub genes was performed using the Kaplan-Meier plotter and GEPIA online tool. RESULTS: We first analyzed GSE95849 to obtain DPN-related genes. DEGs were obtained from three groups in GSE95849. The DEGs were enriched in the Toll-like receptor signaling pathway, hematopoietic cell lineage and chemokine signaling pathway. Importantly, we identified three shared genes as hub genes, including TLR4, CCR2 and MMP9. We then analyzed and integrated GSE95849 and GSE28735 to obtain genes common in DM and PC. A total of 58 mutual DEGs were identified, and these DEGs were enriched in the ECM-receptor interaction, focal adhesion and pathways in cancer. Five hub genes (including PLAU, MET, CLU, APOL1 and MMP9) were associated with the overall survival of PC patients. However, the results from the analysis of GSE59953 showed that hyperglycemia or TGF-ß1 treatment did not affect the expression level of these hub genes, but the DEGs based on hyperglycemia or TGF-ß1 treatment were mostly enriched in the ECM-receptor interaction, focal adhesion and pathways in cancer. Finally, functional enrichment analysis of MMP9 showed that significant genes correlated with MMP9 were associated with the tumorigenicity of cancers, insulin resistance, development of DM and inflammation. CONCLUSION: In summary, inflammation and immunity-related pathways may play an important role in DM and DPN, while the ECM-receptor interaction, focal adhesion and pathways in cancer pathways may play significant roles in DM and PC. MMP9 may be used as a prognostic marker for PC and may be helpful for the treatment of DM, DPN and PC.

YTHDF2 correlates with tumor immune infiltrates in lower-grade glioma.

Immunotherapy is an effective treatment for many cancer types. However, YTHDF2 effects on the prognosis of different tumors and correlation with tumor immune infiltration are unclear. Here, we analyzed The Cancer Genome Atlas and Gene Expression Omnibus data obtained through various web-based platforms. The analyses showed that YTHDF2 expression and associated prognoses may depend on cancer type. High YTHDF2 expression was associated with poor overall survival in lower-grade glioma (LGG). In addition, YTHDF2 expression positively correlated with expression of several immune cell markers, including PD-1, TIM-3, and CTLA-4, as well as tumor-associated macrophage gene markers, and isocitrate dehydrogenase 1 in LGG. These findings suggest that YTHDF2 is a potential prognostic biomarker that correlates with LGG tumor-infiltrating immune cells.

Corrigendum to "Bioinformatics Analysis of Potential Key Genes in Trastuzumab-Resistant Gastric Cancer".

[This corrects the article DOI: 10.1155/2019/1372571.].

Bioinformatics Analysis of Potential Key Genes in Trastuzumab-Resistant Gastric Cancer.

BACKGROUND: This study was performed to identify genes related to acquired trastuzumab resistance in gastric cancer (GC) and to analyze their prognostic value. METHODS: The gene expression profile GSE77346 was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were obtained by using GEO2R. Functional and pathway enrichment was analyzed by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Search Tool for the Retrieval of Interacting Genes (STRING), Cytoscape, and MCODE were then used to construct the protein-protein interaction (PPI) network and identify hub genes. Finally, the relationship between hub genes and overall survival (OS) was analyzed by using the online Kaplan-Meier plotter tool. RESULTS: A total of 327 DEGs were screened and were mainly enriched in terms related to pathways in cancer, signaling pathways regulating stem cell pluripotency, HTLV-I infection, and ECM-receptor interactions. A PPI network was constructed, and 18 hub genes (including one upregulated gene and seventeen downregulated genes) were identified based on the degrees and MCODE scores of the PPI network. Finally, the expression of four hub genes (ERBB2, VIM, EGR1, and PSMB8) was found to be related to the prognosis of HER2-positive (HER2+) gastric cancer. However, the prognostic value of the other hub genes was controversial; interestingly, most of these genes were interferon- (IFN-) stimulated genes (ISGs). CONCLUSIONS: Overall, we propose that the four hub genes may be potential targets in trastuzumab-resistant gastric cancer and that ISGs may play a key role in promoting trastuzumab resistance in GC.

Integrated metabolomic and proteomics profiling reveals the promotion of Lactobacillus reuteri LR1 on amino acid metabolism in the gut-liver axis of weaned pigs.

Lactobacillus reuteri LR1 improved growth performance of weaned pigs in our previous study. The objective of this study was to reveal effects of L. reuteri LR1 on amino acid (AA) metabolism in weaned pigs and its underlying mechanism using metabolomic and proteomics methods. Weaned pigs were fed a basal diet (CON) or the basal diet supplemented with 5 × 1010 cfu kg-1L. reuteri LR1 (LR1) for a 14 d period. Untargeted metabolomic analysis of the liver showed that LR1 up-regulated 33 metabolites and most of them were related to AA metabolism. Quantitative proteomics found that differential proteins were mainly involved in a metabolic process in the ileal mucosa of LR1 vs. CON. Integrated metabolomic and proteomics analysis showed that the LR1's enhancement of AA metabolism in the gut-liver axis is mediated by the up-regulated intestinal AA transporters in the pathway of protein digestion and absorption. Moreover, qPCR results confirmed that LR1 increased (p < 0.05) mRNA abundances of AA transporters (PepT1, EAAT3, rBAT, B0AT1, and b0,+AT) in the ileal mucosa compared with CON. Furthermore, western blot analysis showed that LR1 activated the mammalian target of the rapamycin complex 1 (mTORC1) signaling pathway by increasing the phosphorylation of S6 and 70S6K1 in the gut-liver axis of weaned pigs. Together, these data indicated that dietary supplemented LR1 enhanced AA metabolism by up-regulating intestinal AA transporter expression and activating the mTORC1 signaling pathway in the gut-liver axis of weaned pigs.

p53, latent membrane protein 1, bcl-2, and prognosis in nasopharyngeal carcinoma: a meta-analysis.

The controversy of (p53) in nasopharyngeal carcinoma persists, despite the fact that many studies have been conducted on its correlation with latent membrane protein 1 (LMP1), bcl-2, and prognosis. To better understand this postulated relationship, a meta-analysis was performed based on existing relevant studies. A total of 19 individual studies with a total of 1189 patients were included in the meta-analysis. Overall, the results revealed a significant association of p53-positive status with a poor 5-year survival of nasopharyngeal carcinoma (NPC) patients as the risk difference (RD) was -0.17 (95% CI, -0.31, -0.03; P=0.02, Pheterogeneity =0.01).The overall odds ratio (OR) for LMP1 in the p53 positive group vs. negative group revealed that a significantly elevated risk of positive LMP1 in the former was achieved (OR 5.52 95% CI, 2.66-11.46; P<0.00001, Pheterogeneity =0.78). Similarly, a strong correlation between bcl-2 and p53 was found with an OR 6.85 (95% CI, 2.37-19.74; P=0.0004, Pheterogeneity =0.48). However, there did not appear to be any correlations with clinical parameters such as gender, tumor site, lymph node metastasis,pathological type and TNM stage. In conclusion, p53 expression is related to the survival of nasopharyngeal carcinoma. It can be considered as the auxiliary detection index in treatment and prognosis of nasopharyngeal carcinoma.

Identification of genes and analysis of prognostic values in nonsmoking females with non-small cell lung carcinoma by bioinformatics analyses.

BACKGROUND: This study was performed to identify disease-related genes and analyze prognostic values in nonsmoking females with non-small cell lung carcinoma (NSCLC). MATERIALS AND METHODS: Gene expression profile GSE19804 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed by using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. Then, the Search Tool for the Retrieval of Interacting Genes, Cytoscape, and Molecular Complex Detection were used to construct the protein-protein interaction (PPI) network and identify hub genes. Finally, the Kaplan-Meier plotter online tool was used for the overall survival analysis of hub genes. RESULTS: A cohort of 699 differentially expressed genes was screened, and they were mainly enriched in the terms of ECM-receptor interaction, focal adhesion, and cell adhesion molecules. A PPI network was constructed, and 15 hub genes were identified base on the subset of PPI network. Then, two significant modules were detected and several genes were found to be associated with the cell cycle pathway. Finally, nine hub genes' (UBE2C, DLGAP5, TPX2, CCNB2, BIRC5, KIF20A, TOP2A, GNG11, and ANXA1) expressions were found to be associated with the prognosis of the patients. CONCLUSION: Overall, we propose that the cell cycle pathway may play an important role in nonsmoking females with NSCLC and the nine hub genes may be further explored as potential targets for NSCLC diagnosis and treatment.

Cancer stem-like cell characteristics induced by EB virus-encoded LMP1 contribute to radioresistance in nasopharyngeal carcinoma by suppressing the p53-mediated apoptosis pathway.

Emerging evidence confirms that cancer stem cells (CSCs) are responsible for the chemoradioresistance of malignancies. EBV-encoded latent membrane protein 1 (LMP1) is associated with tumor relapse and poor prognosis of nasopharyngeal carcinoma (NPC). However, whether LMP1 induces the development of CSCs and the mechanism by which this rare cell subpopulation leads to radioresistance in NPC remain unclear. In the present study, LMP1-transformed NPC cells showed significant radioresistance compared to the empty vector control. We found that LMP1 up-regulated the expression of several stemness-related genes, increased the cell number of side population (SP) by flow cytometry analysis, enhanced the self-renewal properties of the cells in a spherical culture and enhanced the in vivo tumor initiation ability. We also found that LMP1 positively regulated the expression of the CSC marker CD44. The CD44(+/High) subpopulation of the LMP1-transformed NPC cells displayed more significant CSC characteristics than the CD44(-/Low) subpopulation of the LMP1-transformed NPC cells; these characteristics included the upregulation of stemness-related genes, in vitro self-renewal and in vivo tumor initiation ability. Importantly, the CD44(+/High) subpopulation displayed more radioresistance than the CD44(-/Low) subpopulation. Our results also demonstrated that phosphorylation of the DNA damage response (DDR) proteins, ATM, Chk1, Chk2 and p53, was inactivated in the LMP1-induced CD44(+/High) cells in response to DNA damage, and this was accompanied by a downregulation of the p53-targeted proapoptotic genes, which suggested that the inactivation of the p53-mediated apoptosis pathway was responsible for the radioresistance in the CD44(+/High) cells. Taken together, we found that LMP1 induced an increase in CSC-like CD44(+/High) cells, and we determined the molecular mechanism underlying the radioresistance of the LMP1-activated CSCs, highlighting the need of CSC-targeted radiotherapy in EBV-positive NPC.

Epstein-Barr Virus_Encoded LMP1 upregulates microRNA-21 to promote the resistance of nasopharyngeal carcinoma cells to cisplatin-induced Apoptosis by suppressing PDCD4 and Fas-L.

Approximately 30% of patients with Epstein-Barr virus (EBV)-positive advanced nasopharyngeal carcinoma (NPC) display chemoresistance to cisplatin-based regimens, but the underlying mechanisms are unclear. The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1), a functional homologue of the tumor necrosis factor receptor family, contributes substantially to the oncogenic potential of EBV through the activation of multiple signaling pathways, and it is closely associated with a poorer prognosis for NPC. Recent studies show that EBV infection can induce the expression of many cellular miRNAs, including microRNA-21, a biomarker for chemoresistance. However, neither a link between LMP1 expression and miR-21 upregulation nor their cross talk in affecting chemoresistance to cisplatin have been reported. Here, we observed that stable LMP1-transformed NPC cells were less sensitive to cisplatin treatment based on their proliferation, colony formation, the IC50 value of cisplatin and the apoptosis index. Higher levels of miR-21 were found in EBV-carrying and LMP1-positive cell lines, suggesting that LMP1 may be linked to miR-21 upregulation. These data were confirmed by our results that exogenous LMP1 increased miR-21 in both transiently and stably LMP1-transfected cells, and the knock down of miR-21 substantially reversed the resistance of the NPC cells to cisplatin treatment. Moreover, the proapoptotic factors programmed cell death 4 (PDCD4) and Fas ligand (Fas-L), which were negatively regulated by miR-21, were found to play an important role in the program of LMP1-dependent cisplatin resistance. Finally, we demonstrated that LMP1 induced miR-21 expression primarily by modulating the PI3K/AKT/FOXO3a signaling pathway. Taken together, we revealed for the first time that viral LMP1 triggers the PI3K/Akt/FOXO3a pathway to induce human miR-21 expression, which subsequently decreases the expression of PDCD4 and Fas-L, and results in chemoresistance in NPC cells.