Project description:We recently reported that an orthologue of STING regulates infection by picorna-like viruses in drosophila. Here, we show that injection of flies with 2’3’-cGAMP can induce expression of dSTING-regulated genes. Analysis of the transcriptome of 2’3’-cGAMP injected flies reveals a complex pattern of response, with early and late induced genes. Our results reveal that dSTING regulates an NF-κB -dependent antiviral program, which predates the emergence of Interferon Regulatory Factors and interferons in vertebrates.
2020-05-31 | GSE140955 | GEO
Project description:Sequencing of plant-associated viruses and related viruses in the Havel River and Teltowkanal, Germany
| PRJNA1031393 | ENA
Project description:Sequencing of invertebrate viruses in water samples of Teltow Canal and Havel River, Germany
Project description:Liver sinusoidal endothelial cells (LSECs) from C57Bl/6J male mice obtained from Charles River Laboratory (Sulzfeld, Germany) were cultured on fibronectin coated plates in 5% oxygen atmosphere in AIM-V with serum-free supplements for 1h, 10h, or 48h. Data from quantitative proteomics using a tandem mass tag (TMT)6-plex strategy on an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific)), using a TMT SPS MS3 method (Navarrete-Perea, Yu et al. 2018).
Project description:With its 2.5 Mb DNA genome packed in amphora-shaped particles of bacterium-like dimension (1.2 µm in length, 0.5 µm in diameter), the Acanthamoeba-infecting Pandoravirus salinus remained the most spectacular and intriguing virus since its description in 2013. Following its isolation from shallow marine sediment off the coast of central Chile, that of its relative Pandoravirus dulcis from a fresh water pond near Melbourne, Australia, suggested that they were the first representatives of an emerging worldwide-distributed family of giant viruses. This was further suggested when P. inopinatum discovered in Germany, was sequenced in 2015. We now report the isolation and genome sequencing of three new strains (P. quercus, P.neocaledonia, P. macleodensis) from France, New Caledonia, and Australia. Using a combination of transcriptomic, proteomic, and bioinformatic analyses, we found that these six viruses share enough distinctive features to justify their classification in a new family, the Pandoraviridae, distinct from that of other large DNA viruses.
Project description:The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.
Project description:This study analysed the effect of maternal hyperthyroidism on the offspring’s white adipose tissue function. Hyperthyroidism during pregnancy was induced in wild type female C57BL/6NCrl (Charles River, Germany) at the age of three to four month with 0.5 mg/L T3 (3,3’,5-Triiodo-L-thyronine, T6397, Sigma Aldrich, Germany) in drinking water with 0.01% BSA from day of positive plug check until gestational day 18 (= day before birth). Adipose tissue samples were collected at the day of sacrifice (male offspring: 5-6 months, female offspring: 6-7 months), weighted, snap frozen on dry ice, and stored at -80 °C until nucleic acid extraction. Sex-specific gene expression profiling in the gWAT samples from the offspring of maternal T3 treatment experiment was performed using GeneChip Clariom S arrays (Affymetrix, Germany).
Project description:High throughput RNA sequencing For RNA sequencing, F. nucleatum was incubated with 1 mM or 5 mM metformin for 7 hours, when the bacterium were under logarithmic phase. Total RNA of F. nucleatum was stabilized with RNA protect Bacteria Reagent (QIAGEN, Germany) and extracted using a QIAGEN RNeasy kit (QIAGEN, Germany) following the manufacturer’s instructions.