Project description:We design and test a novel di-azido LASER reagent capable enrichment through attachment of biotin with strain-promoted azide alkyne cycloaddition (SPAAC). We term this approach in vivo click LASER or icLASER. Aligned with the goal of extending transcriptome-wide measurements of RNA structure and to develop an approach that takes advantage of combinatorial RNA structure probing,we then use this novel bi-functional probe to interrogate LASER reactivity transcriptome-wide, revealing the first solvent accessibility transcriptome map. We also directly compare icSHAPE (hydroxyl acylation; flexibility) and icLASER (solvent accessibility) to demonstrate the power of utilizing them together to predict RNA-protein interactions and RNA polyadenylation.Our results demonstrate that combinatorial RNA structure probing can be employed to compliment orthogonal methods to better understand RNA structure and processing in cells transcriptome-wide.
Project description:High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage
Project description:These E. coli strains were grown with various signaling molecules and the expression profiles were determined. Keywords: addition of quorum and host hormone signals
Project description:RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns under the phytotoxin treatment. To identify differentially expressed genes, we compared phytotoxins (toxoflavin and tropolone) transcriptome to methanol transcriptome as the solvent of phytotoxins. The expression of 2327 and 830 genes was differentially changed by toxoflavin and tropolone, respectively.
Project description:We constructed E. coli transcriptome under deoxynivalenol (DON) and nivalenol (NIV) condition from Fusarium spp. To identify differentially expressed genes in mycotoxin condition, we compared mycotoxin (DON and NIV) transcriptome to acetonitrile (ACN) transcriptome as the solvent of myxotoxin. As a result, 435-929 transcripts were identified from all conditions, respectively.
Project description:Cyadox(CYA), as a new species of Quinoxaline 1, 4-dioxides and olaquindox(OLA) both showed higher antibacterial activity under anaerobic incubation. Microarray was used for global gene expression studies, which were further confirmed by real-time PCR. Cyadox and olaquindox mainly stimulated the expression of DNA repair genes as a response to the DNA damage. The induced gene sbmC was found to provide partial protection against the antibiotics of gyrase inhibitors like the quinolones and the ruvAB helped remove the topoisomerase IV-DNA cleavage complex caused by some type IIA topoisomerase poison antibiotics. It was inferred that the radical intermediate of cyadox reduction under anaerobic condition was responsible for the poison effect of IIA topoisomerases, which brought about DNA double stand breaks and other DNA damages in E. coli.
Project description:Zika viruses (ZIKV) have pandemic potential, with infections that cause serious human diseases, including microcephaly and Guillain-Barre syndrome. The pathogenesis properties of ZIKV lineages vary widely, and defining the underlying mechanisms has been complicated by the use of different cell-based and animal models to test ZIKV infections. The goal of this work was to define differential pathogenesis mechanisms among mild and severe ZIKV infections through comparative infections, using a relevant human stem cell-derived cerebral organoid experimental model system. ZIKV RNA does not persist in organoid ventricle cells during mild Asian/American lineage ZIKV infections; however, viral RNA persisted in ventricle cells during severe African lineage infections. The data suggest that mild and severe ZIKV lineages are differentiated in pathogenesis by host antiviral, interferon, and stress responses that cause apoptosis and oxidative stress. Stress-related hydroxyl radical damage to the organoids was partially blocked by Trolox, a hydroxyl radical scavenger drug, suggesting potential therapeutic benefit.
Project description:The transcriptional profile of Escherichia coli O157 treated with small molecule inhibitors of type III secretion was determined. Four variations of the small molecule inhibitor were assessed for global changes in transcription by treating cells with 20uM of inhibitor or an equivalent volume of DMSO (inhibitor solvent). Keywords: treatment, dose, Cy3, Cy5, 2-colour
