Project description:Investigation of transcripts (boundaries, expression level, etc.) using strand specific, paired-end RNA sequencing for T. maritima under multiple growth conditions. The new genome annotation has been approved by Genbank [CP004077, pending release of the manuscript].
Project description:Investigation of 5' transcripts using strand specific sequencing for T. maritima under logphase, maltose minimal media growth conditions
Project description:Investigation of transcripts (boundary, level, etc.) across the entire T. maritima genome in mulitple growth conditions, including logphase, late exponential, heat shock and hydrogen inhibited conditions. The new genome annotation has been approved by Genbank [CP004077, pending release of the manuscript].
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:This study aims to identify and functionally characterize miRNAs and their target genes in juvenile Nicotiana benthamiana plants using miRNA sequencing (miRNA-seq) and degradome sequencing. miRNA-seq will be employed to profile the miRNA repertoire, while degradome sequencing will be used to identify miRNA-mediated mRNA cleavage sites and validate target genes. The combined approach will elucidate the regulatory roles of miRNAs in the early developmental stages of Nicotiana benthamiana and provide insights into their functional characteristics
Project description:Investigation of 5' transcripts using strand specific sequencing for T. maritima under logphase, maltose minimal media growth conditions Two replicate samples were sequenced after isolating total RNA of cultures grown in maltose minimal media. Cells were harvested in logphase growth.
Project description:This study was conducted to identify the genes involved in the synthesis of membrane-spanning ether lipids in Thermotoga maritima MSB8.
Project description:Sesquiterpene lactones (STL) are lipophilic compounds synthesized as secondary metabolites in species across the plant kingdom, most notably in the family Asteraceae. One STL, found in North African Ambrosia maritima (A. maritima), and Caribbean Ambrosia hispida (A. hispida), is the compound ambrosin. Ambrosin exhibits several desirable pharmacologic characteristics, including compliance with the Rule of Five (RO5) pharmacokinetic profile. We have extracted ambrosin from A. maritima and A. hispida and demonstrated its cytotoxicity in bladder cancer and breast cancer cell lines in low micromolar ranges. Ambrosin also inhibited cancer stem cells and secondary spheroid formation of multiple bladder cancer and breast cancer cell lines. RNA Bru-Seq of ambrosin treated bladder cancer and breast cancer cells revealed a mitochondrial apoptotic gene signature as well as activation of glutathione metabolism, indicating the generation of reactive oxygen species (ROS). RNA Bru-Sequencing and drug target mapping also revealed potential antagonistic activity of ambrosin against the EGFR tyrosine kinase and Rho/Rac GTPases. Further studies showed that ambrosin inhibited EGFR auto-phosphorylation at tyrosine 1068 (Y1068) as well as the inhibition of Cdc42 GTPase and RhoC GTPase activity. These findings indicate novel mechanisms of action and justify further considerations for ambrosin pharmaco-development as a potential chemotherapeutic agent for advanced bladder cancer and triple negative breast cancer.
Project description:An eight chip study using total RNA recovered from separate wild-type cultures of Thermotoga maritima at mid-log with 3 different minimal sugar media.
