Project description:Origin Recognition Complex Associated (ORCA) associates with repressive chromatin environments. We carried out H3K9me3 ChIP-seq to determine the affect of ORCA's loss on this repressive mark. Towards this end, we cultured U2OS osteosarcoma cells, performed control and ORCA knockdowns using siRNAs and then carried out H3K9me3 ChIP-seq to determine the regions in the genome which get affected upon ORCA knockdown. Examination of the levels of H3K9me3 in control and ORCA knockdown cells
Project description:Twenty-four patients were randomized to receive Orca-T alone (n=12) or Orca-T plus single-agent GVHD prophylaxis (n=12) to determine if Orca-T alone was non-inferior in preventing acute GVHD.
Project description:Origin Recognition Complex Associated (ORCA) associates with repressive chromatin environments. We carried out H3K9me3 ChIP-seq to determine the affect of ORCA's loss on this repressive mark. Towards this end, we cultured U2OS osteosarcoma cells, performed control and ORCA knockdowns using siRNAs and then carried out H3K9me3 ChIP-seq to determine the regions in the genome which get affected upon ORCA knockdown.
Project description:ORCA is an ORC associated protein that plays important roles in replication initiation as well as heterochromatin organization. We carried out ORCA ChIP-seq in U2OS cells synchronized at different stage of G1 phase to determine its genome wide localization. To understand the genomic features of ORCA binding regions, we also carried out Methylated DNA IP (MeDIP) followed by deep sequencing in U2OS cells to determine the genome wide localizatoin of methyl-CpG sites in U2OS cells and how ORCA bidning regions co-localize with this important repressive mark.
Project description:There are currently no published data documenting the presence of retroviruses in cetaceans, though the occurrences of cancers and immunodeficiency states suggest the potential. We examined tissues from adult killer whales and detected a novel gammaretrovirus by degenerate PCR. Reverse transcription-PCR also demonstrated tissue and serum expression of retroviral mRNA. The full-length sequence of the provirus was obtained by PCR, and a TaqMan-based copy number assay did not demonstrate evidence of productive infection. PCR on blood samples from 11 healthy captive killer whales and tissues from 3 free-ranging animals detected the proviral DNA in all tissues examined from all animals. A survey of multiple cetacean species by PCR for gag, pol, and env sequences showed homologs of this virus in the DNA of eight species of delphinids, pygmy and dwarf sperm whales, and harbor porpoises, but not in beluga or fin whales. Analysis of the bottlenose dolphin genome revealed two full-length proviral sequences with 97.4% and 96.9% nucleotide identity to the killer whale gammaretrovirus. The results of single-cell PCR on killer whale sperm and Southern blotting are also consistent with the conclusion that the provirus is endogenous. We suggest that this gammaretrovirus entered the delphinoid ancestor's genome before the divergence of modern dolphins or that an exogenous variant existed following divergence that was ultimately endogenized. However, the transcriptional activity demonstrated in tissues and the nearly intact viral genome suggest a more recent integration into the killer whale genome, favoring the latter hypothesis. The proposed name for this retrovirus is killer whale endogenous retrovirus.
