ABSTRACT: Whole genome sequencing of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome
Project description:Whole genome sequencing of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome
Project description:Genomic analysis of 495 vancomycin resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark
Project description:Multi-analytical study of the materials and techniques used in the production of three Roman panel paintings produced in Egypt around 2000 years ago and stored at the Ny Carlsberg Glyptotek in Copenhagen (Denmark).
Project description:ATAC-seq was performed, mapped, and analyzed as previously described (PMID: 34446717: \\"ATAC-seq was performed on 50,000 cells per replicate as described in Buenrostro et al. (with modifications based on Corces et al.), on EpiSCs and PSM-differentiated cell populations at desired time-points. Libraries were generated using the Ad1_noMX and Ad2.1–2.16 barcoded primers64 and amplified for 10 total PCR cycles. Libraries were purified with AMPure XP beads to remove contaminating primer dimers and fragments >1,000 bp. Library quality was assessed using the Fragment analyzer and quantitated by Qubit assay. The libraries were sequenced with 50 bp paired-end reads on a Next-Seq 500 Sequencer (Illumina) at the DanStem Genomics Platform (University of Copenhagen, Copenhagen, Denmark).\\"). For all conditions, two biological replicate samples were collected from independent experiments. Library quality was assessed using the Fragment Analyzer and quantitated by Qubit assay. The libraries were sequenced with 50 bp paired-end reads on a NextSeq 500 Sequencer (Illumina) at the DanStem/reNEW Genomics Platform (University of Copenhagen, Copenhagen, Denmark). Prediction of cis-regulatory elements (CREs) and gene annotation was done using rGREAT (v4.0.4) [PMID: 20436461],[PMID: 36040971] or HOMER (v.4.7)[PMID: 20513432]
Project description:A small, shed antler fragment of a reindeer from Sjælland, Denmark has been dated to the Mid-Holocene, ca., 4700 cal B.C. Reindeer was an important component of the Lateglacial fauna in Denmark, and the species survived for ca. 1400 years into the Holocene. However, we consider it highly unlikely that this species inhabited Denmark during the Mid-Holocene, when dense forests characterized the vegetation and summer temperatures were somewhat higher than at present. We suggest that the reindeer antler came to Sjælland from Norway or Sweden as a result of trade, perhaps involving flint.
Project description:Total RNA was extracted from V. angularium susceptible and resistant rainbow trout, tissues (liver, spleen, gill), in different time points using GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). After measuring quantity (NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark)) and quality (gel electrophoresis) of RNA, cDNA was synthetised in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Primers and probes for total of 28 genes including three housekeeping genes were synthesized at TAG Copenhagen AS, Denmark. qPCR reactions were run by Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark) for all samples. The fold changes analysed by the simplified 2-ΔΔCq method. Fingerlings of rainbow trout (mean body weight of 12 g) were exposed (2 h bathing, 18°C) to the pathogen V. anguillarum serotype O1 in a solution of 1.5x107 cfu/ml and observed for 14 d. Disease signs appeared three days post exposure (dpe) whereafter morbidity progressed exponentially until 6 dpe reaching a total morbidity/mortality of 55% within 11 days. we sampled fish for immune gene expression analysis when they first showed clinical signs, fish without clinical signs at the same time point and finally fish surviving the exposure to the pathogen. The different immune gene expression profiles in the different groups were addressed when discussing possible resistance mechanisms in rainbow trout.
Project description:Anterior pituitary glands were isolated from 21 week old male rats either untreated or treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). Three biological replicates were prepared for untreated, control animals and four biological replicates were prepared for DES-treated animals. This was done for each of 3 inbred rat strains: ACI, Copenhagen, and Brown Norway. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. Comparisons of untreated vs. treated animals within a strain will allow identification of estrogen responsive genes. Comparisons between strains, either treated or untreated, will identify strain (i.e., genetic) differences in expression. Experiment Overall Design: 21 samples from anterior pituitary gland were analyzed. For each of 3 inbred rat strains (ACI, Copenhagen, and Brown Norway) there were 3 biological replicates of untreated, control animals, and 4 biological replicates of DES-treated animals.
