Similar Datasets
Project description:MicroRNA sequencing of slow and rapid growing teratoma. Teratoma without a growth trend were included as controls. In total, 9 samples were analyzed for their expressed microRNAs by sequencing. YST and EC tissues were identified from the biobank of the Department of Urology (University Hospital Düsseldorf). Total RNA has been isolated and subsequently microRNA sequencing has been performed.
2024-04-28 | GSE251975 | GEO
Project description:Examination of E. coli transcripts present in bacteria in urine samples from 8 patients attending a urology clinic with symptoms of cystitis, as compared to transcripts present in the same E. coli strains during mid-exponential growth in filter-sterilized human urine in vitro.
2010-11-12 | GSE24478 | GEO
Project description:Staphylococcus aureus is a notorious biofilm-producing pathogen that is frequently isolated from implantable medical device infections. As biofilm ages, it becomes more tolerant to antimicrobial treatment leading to treatment failure and necessitating the costly removal of infected devices. In this study, we investigated what changes occur in the proteome of S. aureus biofilm grown for 3-days and 12-days in comparison with 24 h planktonic showed that proteins associated with bi-osynthetic processes, ABC transporter pathway, virulence proteins, and shikimate kinase pathway were significantly upregulated in 3-day biofilm, while proteins associated with sugar transporter, degradation, and stress response were downregulated. In 12-day biofilms, proteins associated with peptidoglycan biosynthesis, sugar transporters, and stress responses were upregulated, whereas proteins associated with ABC transporters, DNA replication, and adhesion proteins were down-regulated. Furthermore, we observed significant variations in the formation of biofilms result from changes in the level of metabolic activity in the different growth mode of biofilms that could be a significant factor of S. aureus biofilm maturation and persistence. Collectively, potential marker proteins were identified and further characterized to understand their exact role in S. aureus biofilm development which may shed light on possible new therapeutic regimes in the treatment of biofilm-related implant-associated infections.
2022-08-12 | PXD033499 | Pride
Project description:Ravindra Garde, Bashar Ibrahim & Stefan Schuster. Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms. Scientific Reports 10, 1 (2020).
Biofilms are composed of microorganisms attached to a solid surface or floating on top of a liquid surface. They pose challenges in the field of medicine but can also have useful applications in industry. Regulation of biofilm growth is complex and still largely elusive. Oscillations are thought to be advantageous for biofilms to cope with nutrient starvation and chemical attacks. Recently, a minimal mathematical model has been employed to describe the oscillations in Bacillus subtilis biofilms. In this paper, we investigate four different modifications to that minimal model in order to better understand the oscillations in biofilms. Our first modification is towards making a gradient of metabolites from the center of the biofilm to the periphery. We find that it does not improve the model and is therefore, unnecessary. We then use realistic Michaelis-Menten kinetics to replace the highly simple mass-action kinetics for one of the reactions. Further, we use reversible reactions to mimic the diffusion in biofilms. As the final modification, we check the combined effect of using Michaelis-Menten kinetics and reversible reactions on the model behavior. We find that these two modifications alone or in combination improve the description of the biological scenario.
2024-09-02 | BIOMD0000001053 | BioModels
Project description:Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
2024-09-02 | BIOMD0000000932 | BioModels
Project description:We examined the differential gene expression of Staphylococcus epidermidis and Staphylococcus epidermidis in dual species biofilms. Therefore, we performed RNA-Seq on single and dual species biofilms and we compared the gene expression levels in dual species biofilms to those in single species biofilms.
2016-05-27 | GSE79575 | GEO
Project description:The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate. The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms. Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene. These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms. Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea.
2010-07-20 | GSE22646 | GEO
Project description:We performed comparative analysis of transcriptomes of S. mutans in single biofilms and in mixed-biofilms with A. actinomycetemcomitans. We also compared the transcriptomic profiles of A. actinomycetemcomitans in single biofilms and A. actinomycetemcomitans in mixed biofilms with S. mutans. Finally we looked at the changes in gene expression in both organisms in time.
2017-03-31 | GSE75019 | GEO