Similar Datasets
Project description:Actinotignum schaalii strain:CCUG 27420 Genome sequencing
| PRJNA240634 | ENA
Project description:Actinotignum sanguinis strain:DSM 26039 Genome sequencing and assembly
| PRJNA451308 | ENA
Project description:Actinotignum massiliense, a Gram-positive, facultatively anaerobic coccoid rod, is a rare human pathogen able to infect the urinary tract and belongs to the order of Actinomycetales. We identified A. massiliense as a resident of microbial biofilms growing on indwelling urethral catheter surfaces that were isolated from two patients with neurogenic bladders. These catheter biofilms (CBs) also harbored common uropathogens such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense depends on other co-colonizing microbes for survival. We isolated the bacterium from an anaerobically grown culture of a clinical sample, identified the species by 16S rRNA gene sequencing and verified this result via shotgun proteomics. Bacterial proteomes were profiled from the in vitro grown strain and four clinical ‘in vivo’ samples. The quantified proteomes allowed us to infer metabolic pathways and virulence/survival factors of importance in the CB milieu. Two putative subtilisin-like proteases, two Rib/Esp surface antigen repeat-containing proteins, a papain-like cysteine protease and a metal/heme/oligopeptide uptake system were highly expressed in vivo, but less so in vitro. We predict these proteins to be critical for adhesion and growth in CBs attacked by the host’s innate immune system or to improve bacterial fitness. Mixed acid fermentation following uptake and metabolism of xylose and glucuronate, sugars highly represented in proteoglycans and glycoglycerolipids of the urothelial mucosa and, in the case of glucuronate, shed into urine via renal xenobiotic conjugates, is inferred to be a major pathway for A. massiliense to generate energy under microaerobic conditions in CBs. The bacteria also appear to have active pathways for storage and utilization of glycogen as a carbon resource. Finally, we identified a putative polyketide synthase which may generate a secondary metabolite that interacts with either the host or co-colonizing organisms to enable A. massiliense survival in CBs.
2019-11-12 | PXD011327 | Pride
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
2022-10-20 | E-MTAB-11946 | biostudies-arrayexpress
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
2022-08-07 | E-MTAB-12010 | biostudies-arrayexpress
Project description:The analysis identifies differentially occupied genomic regions of H2Bub1, H3K79me3, and H3K27ac by RNF40 silencing in HCC1806 cells
2023-07-20 | E-MTAB-12000 | biostudies-arrayexpress
Project description:This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse livers with such processes as replication, transcription, and interaction of DNA with proteins. Liver samples of 15-day old (P15) untreated C3H/HeOuJ mice were isolated and flash-frozen. ChIP-seq was performed to identify CTCF binding sites in livers of ten pooled individuals. The experiment was done with five biological replicates with a matched input library.
2023-04-29 | E-MTAB-11959 | biostudies-arrayexpress
Project description:Because antibiotics have been widely used to prevent severe losses due to infectious fishery diseases, the liberal application and overuse of antibiotics has led to the spread and evolution of bacterial resistance, food safety hazards, and environmental issues. The use of some antibiotics, including florfenicol and enrofloxacin, is allowed in aquaculture in China. Accordingly, to better address the concerns and questions associated with the impact of administered enrofloxacin and florfenicol to grass carp, here we investigated the immune response, bacterial diversity, and transcriptome of the intestine of C. idella treated with these oral antibiotics. The aim of this study was to provide an in-depth evaluation of the antibiotic-induced patterns and dynamics of the microbiota grass carp and the potential mechanism involved.
2022-08-08 | E-MTAB-12057 | biostudies-arrayexpress