Alterated gene expression in dilated cardiomyopathy after left ventricular assist device support by bioinformatics analysis.

Introduction: Heart transplantation is the best treatment for end-stage dilated cardiomyopathy (DCM). Left ventricular assist device (LVAD) support is becoming more prevalent and may delay heart transplantation. Gene expression of the left ventricular myocardium usually changes following LVAD implantation. In this study, we aimed to identify potential biomarkers to determine the prognosis of patients with DCM after receiving LVAD support. Methods: We extracted microarray datasets from Gene Expression Omnibus (GEO), including GSE430 and GSE21610. There were 28 paired DCM samples in the GSE430 and GSE21610 profiles. Differentially expressed genes (DEGs) were identified at LVAD implantation and heart transplantation. DEGs were annotated according to Gene Ontology (GO) and analyzed according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. A protein-protein interaction (PPI) network was constructed. The top 10 crucial genes were predicted using Cytoscape plugin CytoHubba in conformity with the network degree algorithm. The levels of gene expression and the diagnostic values of crucial genes were confirmed in the clinical datasets. Results: The 28 DEGs were clustered into the GSE datasets. GO annotations and KEGG pathway enrichment analyses revealed that inflammation might be involved. They were associated with correlative inflammation. Combined with PPI networks, these results revealed CytoHubba's top 10 hub genes, including CCL2, CXCL12, CXCL1, CTGF/CCN2, CX3CR1, POSTN, FKBP5, SELE, AIF1, and BMP2. Among them, CCL2, CXCL12, FKBP5, and BMP2 might be considered prognostic and diagnostic biomarkers after LVAD support and have confirmed their validity in clinical datasets. The area under the curve of the four main hub genes was more than 0.85, indicating high diagnostic ability and good prognosis for patients with DCM with LVAD implantation. However, a significant effect of CCL2, CXCL12, FKBP5, and BMP2 expression was not observed on the left ventricular end-diastolic diameter (LVEDD), left ventricular ejection fraction (LVEF), cardiac index (CI), or support time of LVAD. Conclusion: CCL2, CXCL12, FKBP5, and BMP2 could be potential gene biomarkers for patients with DCM after LVAD support. These findings provide critical clues for the therapeutic management of patients with DCM and LVADs. LVEDD, LVEF, CI, and support time of LVAD were not correlated with the expression of these hub genes.

PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida.

Pasteurella multocida can infect a wide range of host, including humans and animals of economic importance. Genomics studies on the pathogen have produced a large amount of omics data, which are deposited in GenBank but lacks a dedicated and comprehensive resource for further analysis and integration so that need to be brought together centrally in a coherent and systematic manner. Here we have collected the genomic data for 176 P. multocida strains that are categorized into 11 host groups and 9 serotype groups, and developed the open-access P. multocida Database (PamulDB) to make this resource readily available. The PamulDB implements and integrates Chado for genome data management, Drupal for web content management, and bioinformatics tools like NCBI BLAST, HMMER, PSORTb and OrthoMCL for data analysis. All the P. multocida genomes have been further annotated for search and analysis of homologous sequence, phylogeny, gene ontology, transposon, protein subcellular localization and secreted protein. Transcriptomic data of P. multocida are also selectively adopted for gene expression analysis. The PamulDB has been developing and improving to better aid researchers with identifying and classifying of pathogens, dissecting mechanisms of the pathogen infection and host response.

Genome sequence of Paenibacillus sp. strain Aloe-11, an endophytic bacterium with broad antimicrobial activity and intestinal colonization ability.

Paenibacillus sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic bacterium isolated from the root of Aloe chinensis in the southwest region of China, has excellent antibiotic activity and intestine colonization ability. Here, we present the 5.8-Mb draft genome sequence of Paenibacillus sp. strain Aloe-11.