Project description:To determine if MCPyV ST was recruited to chromatin together with MAX and the TRRAP complex, we performed chromatin immunoprecipitation (ChIP) using the validated antibodies to MCPyV ST produced in our lab, HA tagged ST, MAX and EP400 followed by next generation sequencing. De novo DNA motif analysis revealed that the canonical E-box MYC target sequence was the most frequently observed motif. Metagene analysis revealed that antibodies to MAX, EP400, ST (Ab5) and HA tagged ST showed strong enrichment in transcription start site (TSS). H3K4me3 ChIP-seq confirmed that the peaks enriched with antibodies to MAX, EP400 and ST all centered on the H3K4me3 peaks with a high degree of overlap.
Project description:Because ST embryos may be at risk of procedure related chromosomal or sub-chromosomal abnormalities, we biopsied and examined expanded blastocysts derived from ST and control embryos. We examined copy number variations (CNVs) by SNP array to explore possible subchromosomal abnormalities (deletion or duplication) in selected ST ESCs. De novo CNVs were detected in both ST and intact controls but none carried clinical significance (Table S3 in the Supplementary Appendix).
Project description:To identified Biotin-ST probe interacting proteins, we applied SPIDER assay by using Biotin-ST probe in cells lysates, and the enriched protein was identified by mass spectrometry to quantitatively find the targets of Biotin-ST interactors.
Project description:Interventions: Endoscopic decompression using modified ST hood (Replaced with conventional hood only if failure occurs with modified ST hood within a specified time).
Endoscopic decompression using conventional hood (Replaced with modified ST hood only if failure occurs with conventional hood within a specified time).
Primary outcome(s): Success rate and procedure time to pass the guide-wire through the colorectal stricture site.
Study Design: Parallel Randomized
Project description:we examined the glycoproteomics of N-glycosylation in untreated LNCaP (NC), ST-EPI, LT-EPI, ST-ENZ, and LT-ENZ groups using Tandem Mass Tag (TMT) labels by nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS).LNCaP-NC, SP-EPI, SP-ENZ, LP-EPI, and LP-ENZ cells each with two biological replicates were used for glycoproteomics analysis.
Project description:The aim of this study was to examine the effects of dietary supplementation of St John’s wort extract on azoxymethane-induced colorectal carcinogenesis in mice. Microarray data showed atttenuation of NF-kB and ERK-mediated pathway in colon epithelium by St. Jone's wort suggesting that the anti-inflammatory effect is a possible cancer-preventing mechanism induced by St. Jone's wort. Gene expression will be compared between mice with the control vs. St. Jone's wort.
Project description:Objective: Synovial fluid (SF) derived T-cells are frequently studied as a proxy for investigating the synovial tissue (ST) T-cell infiltrate in inflammatory arthritis. However, since ST is the primary site of inflammatory activity, there is debate as to whether SF provides a true reflection of the ST T-cell population. Methods: In this study, we used single cell RNA sequencing paired with single cell TCR sequencing to directly compare memory T-cells from paired samples of SF and ST from 6 patients with inflammatory arthritis to investigate their similarity in terms of T-cell receptor (TCR) repertoire and T-cell subset composition. Results: The TCR repertoires of SF and ST T-cells were strikingly similar, particularly for CD8+ T-cells. A median of 49% of the total CD8+ TCR repertoire in SF was shared with ST, compared to 20% shared with blood and 47% of the ST CD8+ TCR repertoire was shared with SF compared to 25% with blood. Furthermore, once the effect of collagenase digestion on gene expression by ST T-cells had been accounted for, the frequencies of specific CD8+ and CD4+ T-cell subsets were, in general, very similar in SF and ST and were distinct from blood. Conclusion: Our results suggest that T-cells migrate and equilibrate between SF and ST and maintain similar phenotypes in both sites. We conclude that SF is an appropriate proxy for investigating the T-cell infiltrate in inflamed synovium using single cell RNA sequencing, particularly in terms of investigating the TCR repertoire.
