Project description:D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken. Two independent cultivations in a Chemostat have been performed. Each reactor was run for 3 light/dark-cycles of 12h/12h. Sampling started from the second cycle and continued to the third cycle.
Project description:Transcriptional effects in liver, lung and blood samples from mice after intratracheal challenge with either Streptococcus pneumoniae serotype 19 (lobar-pneumonia) or serotype 2 (sepsis) were monitored after 6 and 24 hours and compared to sham (vehicle control). We gratefully acknowledge the BMBF grant within the “Promoting global research excellence in severe sepsis” (PROGRESS) study (01KI07111). Three tissues x two serotypes x two time resolved treatment groups x four replicates, three tissues x Sham Control x three replicates.
Project description:Transcriptional effects in liver, lung, spleen and blood samples from mice challenged to Sham and Sepsis by Peritoneal Contamination and Infection (PCI) were monitored after 6 and 24 hours 4 Tissues x 2 Time Resolved Treatment Groups x 4 Replicates, 4 Tissues x Sham Control x 3 Replicates
Project description:We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse. We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome-wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions.
Project description:The aim of this study was to evaluate in a mouse prostate cancer xenograft model the effectiveness of cyclophosphamide metronomic regimen, as single agent or in combination with standard docetaxel therapy. We used a human prostate cancer cell line to establish tumours in mice and we treated the animals with the combination of 50 mg/kg of cyclophosphamide (per os) and 30 or 10 mg/kg of docetaxel (intraperitoneally) or with the two drugs alone. We found that metronomic cyclophosphamide alone is as efficient as docetaxel in blocking tumor growth (respectively 18% and 21% of the tumor volume reached by control group in 25 days of treatment). Immunohistochemical analysis on tumours and in vitro proliferation and FACS analyses revealed that cyclophosphamide acts downregulating cell proliferation, both in vitro and in vivo. Through microarray analysis we found the upregulation of p21 that probably together with an action on the micro-environment may explain the induction of apoptosis seen in tumor xenografts. Moreover, we found 107 genes differentially expressed upon treatment with the active metabolite of cyclophosphamide and associated with functions such as cellular movement, growth, and proliferation. Cells (2 x 10^6) were seeded in T150 flasks and then treated with vehicle (ctrl), with inactive cyclophosphamide (trt) or with 5.5 μM of active 4-Hydro peroxy cyclophosphamide (trtA) for 10, 24, and 48 hours.
Project description:Long-term culture associated changes need to be considered for quality control of cell preparations – especially in cellular therapy. Here we describe a simple method to track cellular aging based on continuous DNA-methylation changes at six specific CpG sites. This epigenetic signature can be used as a biomarker for various cell types to predict the state of cellular aging with regard to the number of passages or days of in vitro culture. 8 samples of human dermal fibroblasts. 4 samples of mesenchymal stem cells (MSC) from human adipose tissue.
Project description:Introduction. Glucocorticoids are critical drugs used to treat acute lymphoblastic leukemia, and response to glucocorticoids is highly predictive of outcome. Here we report a study evaluating the NOD/SCID xenograft mouse model to investigate glucocorticoid-induced gene expression. Methods. NOD/SCID mice were inoculated with ALL-3, a glucocorticoid-sensitive xenograft, and when highly engrafted were randomised to either dexamethasone 15mg/kg or vehicle control IP. Cells were harvested at 0, 8, 24 or 48 hours thereafter, RNA was extracted and hybridised onto Illumina WG-6_V3 chips. Results. The 8 hour dexamethasone-treated timepoint had the highest number of significantly differentially expressed genes with minimal changes seen across the time-matched controls. Replicate analysis revealed that using data from 3 replicates instead of 4 resulted in excellent recovery scores of >0.9 at timepoints with high signal. When assessed at the level of pathways, gene expression changes in the 8 hour xenograft samples were similar to patients treated with glucocorticoids. Conclusions. The NOD/SCID xenograft mouse model provides a reproducible experimental model system in which to investigate clinically-relevant mechanisms of in vivo glucocorticoid-induced gene regulation in ALL; the 8 hour timepoint provides the highest number of significantly differentially expressed genes; time-matched controls are redundant and excellent recovery scores can be obtained with 3 replicates. At 0, 8, 24 or 48 hours, NOD/SCID xenograft mice were treated with vehicle control, or dexamethasone. We used 4 biological replicates per time point (3 at the 48hour time point), each of which went onto an Illumina HumanWG-6_V3_0_R1_11282955_A microarray. Samples from each of the 7 groups were divided across a total of 5 microarray slides
Project description:In this study, we have analyzed DNA methylation changes upon aging of human dermal fibroblasts by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were isolated from skin samples donated by young (6-23 years) and elderly (60-73 years) patients undergoing surgical interventions. Strikingly, global DNA-methylation profiles of fibroblasts from the same anatomical site clustered closely together indicating that fibroblasts maintain positional memory even after in vitro culture. Skin samples from younger or elderly donors were treated with dispase (Roche Diagnostics, Mannheim, Germany) for 12 hours to separate the dermis from the epidermis. The dermis was digested with 0,2% collagenase and 1,5% BSA in collagenase buffer (100mM HEPES, 120mM NaCl, 50mM KCl, 1mM CaCl2, 5mM Glucose) for 45 minutes. Dermal remnants were removed by filtering the digest through a 100µm nylon strainer (Falcon, Becton Dickinson [BD], San Jose, USA). The cells were subsequently washed and expanded in standard medium consisting of DMEM (PAA; 1g/L glucose) supplemented with glutamine (PAA), penicillin/sptrepamycin (PAA) and 10% fetal calf serum (Biochrom, Berlin, Germany) in a humidified atmosphere at 5% CO2. Cells were always replated when grown to 80% confluency. For methylation profiles upon aging we have isolated DNA from the samples of passage 3 of younger and elderly donors. For methylation profiles upon long-term culture we have isolated DNA from the samples of early passage (P3) and late passage (P21)