ABSTRACT: This data set was collected on a qexactive coupled to a Thermo vanquish. Data was collected in a DDA fashion in negative mode. The project itself revolved around compound 94NPD2, a compound that is similar to veraguamides
Project description:This data set was collected on a qexactive coupled to a thermo vanquish. Data was collected in a DDA fashion in positive mode. The project itself revolved around compound 94NPD2, a compound that is similar to veraguamides
Project description:To elucidate the antivirulent lactone U1 mode of action, next generation sequencing was applied to analyze the transcriptome of NCTC 8325 cells treated with either compound or DMSO as control. Overall design: Two biological replicates for compound treated and also two biological replicates for DMSO treated Staphylococcus aureus cultures were analysed.
Project description:To elucidate the antivirulent hydroxy amide (R*,R*)-3 mode of action, next generation sequencing was applied to analyze the transcriptome of NCTC 8325 cells treated with either compound or DMSO as control. Overall design: Two biological replicates for compound treated and also two biological replicates for DMSO treated Staphylococcus aureus cultures were analysed.
Project description:Natural Killer cells are innate lymphocytes, participate in immune surveillance and elimination of stressed or transformed cells and critically shape the inflammatory cytokine environment to interact with cells of the innate and adaptive immune system, including macrophages, dendritic and Tcells. By performing a focused compound library screening, further validated by knockdown approaches, we here identify Jumonji-type histone 3 lysine 27 (H3K27) demethylases as key regulators of cytokine production in various human NK cell subsets. The prototypic H3K27 demethylase inhibitor GSK-J4 increases global levels of the repressive H3K27me3 mark around transcription start sites including NK cell effector cytokines, and thereby reduces IFN-γ, TNFα, GM-CSF and IL-10 levels in IL-15 stimulated NK cells whilst sparing the cytotoxic killing capacity against cancer cells. The anti-inflammatory effect of GSK-J4 in highly inflammatory NK cell subsets, isolated from peripheral blood or tissue from rheumatoid arthritis patients, coupled with an inhibitory effect on formation of bone-resorbing osteoclasts, suggests a wider role and utility of histone demethylase inhibition in immunity and inflammation. Overall design: We constructed 6 RNA-seq libraries; two conditions in triplicate. NK cells were cultured in media in the presence of IL-15 stimulation then cultured in the presence of DMSO and GSK-J4 treated NK cells. RNA was collected at 24 hours.
Project description:We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Project description:We describe the development of a novel anti-leishmanial drug-like chemical series based on a pyrazolopyrimidine scaffold. The leading compound is efficacious in a mouse model of visceral leishmaniasis, and has suitable physicochemical, pharmacokinetic and toxicological properties for further development and has been declared a preclinical candidate. Detailed mode of action studies indicate that compounds from this series act principally by inhibiting the parasite protein kinases.
Project description:The zebrafish is a powerful model for the study of hematopoietic stem and progenitor cells (HSPC). We have developed a novel HSPC-specific transgenic line (Runx1+23:GFP). We have used this line in time-lapse live imaging studies to track the migration of HSPC during development. We have also performed a chemical genetic screen to find small molecules that modulate HSPC numbers during development. Treating embryos from 2-3 days post fertilization (2-3 dpf) then fixing for in situ staining with HSPC probes cmyb and runx1, we found the compound lycorine increased HSPC numbers. Applying this compound during time-lapse live imaging showed increased accumulation of Runx+ HSPC in the caudal hematopoietic tissue (CHT). Treatment from 2-3 dpf, then washing off the compound, had a sustained effect on the size of the HSPC with Runx+ numbers higher at 5 and 7 dpf. We have performed microarray analysis to elucidate the molecular changes within HSPC and endothelial cells after Lycorine treatment. We treated Runx1+23:GFP;kdrl:DsRed2 embryos from 2-3 dpf with 75 uM lycorine in 1% DMSO. We then dissociated the embryos and sorted the Runx+ GFP cells, the kdrl+ DsRed2 cells, and the non-fluorescent negative cells from the total embryo as a comparator population. Total RNA was amplified and biotin labled for hybridization on Affymetrix microarrays. 18 samples were collected and analyzed. There are 3 biological replicates. There are 3 cell type populations: 1) Runx+ HSPC; 2) kdrl+ endothelial cells; 3) non-fluorescent negative cells. There are cell populations from dissociated Lycorine-treated embryo pools, and control DMSO-treated embryo pools.
Project description:This study investigated the ability of two novel adjuvant formulations, QCDC (Quil A/cholesterol/DDA/Carbopol) and QCDCR (QCDC/Bay R1005), in combination with a recombinant profilin vaccine, to modulate host protective immunity and to alter new gene expression during experimental avian coccidiosis. Overall design: Four-condition experiment, Profilin only vs. Non-vaccination, Profilin only vs. Co-vaccination of QCDC plus profilin, Profilin only vs. Co-vaccination of QCDCR plus profilin, Biological replicates: 2 profilin only replicates, 2 Non-vaccination replicates, 2 QCDC plus profilin replicates, 2 QCDCR plus profilin replicates with dye-switching.
Project description:Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros and refers to the tissues around the hemogenic aorta. Cells that emerge from the endothelium and show hematopoietic traits can be distinguished by the expression of the c-kit receptor and finally acquire the CD45 marker. AGM regions were obtained from E11.5 embryos by dissection and digested with 0.1% collagenase. Cells were stained with anti-CD31, anti-ckit, anti-CD45 and anti-Ter119 antibodies. Sorting of the CD31+CD45-Ter119- population was performed, and cells were separated into c-kit+ and c-kit-. 3 replicates each of c-kit+ and c-kit- cells.