Project description:We compiled the transcriptome by extracting mRNA, reverse transcription and Illumina sequencing, followed by assembly and annotation by comparison with public databases (including; Nr, SwissProt and COG). Quantitative data on the transcription abundance of each putative protein sequence is provided as assesed by the SOAPdenovo_trans assembly tool.
Project description:Molecular methods are increasingly used to identify pathogens that are difficult to cultivate. We report a case of disseminated infection with "Mycobacterium tilburgii," a proposed species that has never been cultivated. The case illustrates the diagnostic utility of sequence analysis of the 16S rRNA gene directly from clinical specimens.
Project description:Using a newly-developed workflow for quantitative newly synthesized proteome analysis (QuaNPA), featuring automated sample processing and multiplexed DIA (plexDIA) analysis, changes in the newly synthesized proteome of IFN-gamma treated Hela cells were monitored over time.
Project description:Angiogenesis is a critical process to form new blood vessels from preexisting vessels under physiologic and pathologic conditions and involves cellular and morphologic changes such as endothelial cell proliferation, migration, and vascular tube formation. Despite evidence that angiogenic factors, including vascular endothelial growth factor and Notch, control various aspects of angiogenesis, the molecular mechanisms underlying gene regulation in blood vessels and surrounding tissues are not fully understood. Importantly, recent studies demonstrate that Forkhead transcription factor Foxc2 directly regulates expression of various genes involved in angiogenesis, CXCR4, integrin beta3, Delta-like 4 (Dll4), and angiopoietin 2, thereby controlling angiogenic processes. Thus, Foxc2 is now recognized as a novel regulator of vascular formation and remodeling. This review summarizes current knowledge about the function of Foxc2 in angiogenesis and discusses prospects for future research in Foxc2-mediated pathologic angiogenesis in cardiovascular disease.
Project description:Sequencing newly synthesized transcriptome in addition to the regular transcriptome in single cells enable the study of gene expression temporal dynamics during rapid chromatin and gene regulation processes. However, current single-cell newly synthesized transcriptome assays require in-house technology expertise to achieve a high cellular throughput, preventing their widespread application. Here, we develop NOTE-seq to simultaneously profile regular and newly synthesized transcriptome in single cells. NOTE-seq combines 4-thiouridine labeling of newly synthesized RNA, thiol-alkylation-based chemical conversion, and the streamlined 10X Genomics platform, offering a high cellular throughput accessible to and convenient for regular biology labs without single-cell technology expertise. Using NOTE-seq, we investigate the temporal dynamics of gene expression during early-stage T-cell activation in human Jurkat T cells and mouse naïve T cells, characterize transcription factors and regulons, and discover Fli-1 as a master transcription factor for gene regulation upon T-cell activation. Interestingly, Fli-1 level in T cells is sensitive to the treatment of camptothecin, a topoisomerase inhibitor used in cancer chemotherapy, indicating its potential complication on the immune system.