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TraDIS in MG1655/pTF2

ABSTRACT: The secondary resistome to cefotaxime, chloramphenicol, gentamicin, cefotaxime-chloramphenicol, and cefotaxime-gentamicin combination treatments in CTX-M-1-producing Escherichia coli

PROVIDER: PRJEB52919 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10215827.fastq.gz	Fastqsanger.gz
	ERR10215828.fastq.gz	Fastqsanger.gz
	ERR10215829.fastq.gz	Fastqsanger.gz
	ERR10215830.fastq.gz	Fastqsanger.gz
	ERR9769130.fastq.gz	Fastqsanger.gz

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Comparative transcriptomic response analysis of Escherichia coli K-12 MG1655 to nine antibiotics

Project description:To investigate and compare transcriptomic changes of Escherichia coli K-12 MG1655, the bacterium was exposed to nine antibiotics (tetracycline, mitomycin C ,imipenem, ceftazidime, kanamycin, ciprofloxacin, polymyxin E, erythromycin, and chloramphenicol) , and RNA-Seq was performed to determine comparative transcriptomic changes.

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Treatment with Cefotaxime Affects Expression of Conjugation Associated Proteins and Conjugation Transfer Frequency of an IncI1 Plasmid in Escherichia coli

Project description:Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX). Analysis of the proteome by iTRAQ labeling and liquid chromatography tandem mass spectrometry revealed that Tra proteins were significantly up regulated in the presence of CTX. The up-regulation of the transfer machinery was confirmed at the transcriptional level for five selected genes. The CTX treatment did not cause induction of the SOS39 response as revealed by absence of significantly regulated SOS associated proteins in the proteome and no significant up-regulation of recA and sfiA genes. The frequency of plasmid conjugation, measured in an antibiotic free environment, increased significantly when the donor was pre-grown in broth containing CTX compared to growth without this drug, regardless of whether blaCTX-M-1 was located on the plasmid or in trans on the chromosome. The results shows that antibiotic treatment can affect expression of a plasmid conjugation machinery and subsequent DNA transfer.

2017-11-21 | PXD006679 | Pride

Project description:Combination exposure of amoxicillin and gentamicin

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Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose

Project description:Ribosome profiling was performed on E. coli wild type cells. All replicates were grown to an OD of ~0.4 in MOPS rich Media with 0.2% glucose supplemented, aerobically in shake flasks. Cultures were treated with chloramphenicol 2 min prior to harvest.

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Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose

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Cyclophosphamide enhances the anti-tumor potency of GITR engagement by increasing oligoclonal cytotoxic T cell fitness

Project description:Immune checkpoint blockade (ICB) therapy is a standard treatment option for many malignancies, but it is only effective in a subset of patients. Combination strategies to overcome resistance are promising areas of investigation. Targeting glucocorticoidinduced TNFR-related (GITR) protein with agonist antibodies has shown efficacy in preclinical models, but GITR engagement does not control growth of advanced poorly immunogenic murine tumors such as B16 melanoma and has not yielded benefit in clinical trials. The alkylating agent cyclophosphamide (CTX) preferentially depletes regulatory T cells (Tregs) and expands tumor-specific effector T cells (Teffs) via homeostatic proliferation. Additionally, CTX directly induces tumor cell death, thereby releasing antigen to prime Teffs in a lymphopenic environment where there are fewer Tregs. GITR agonism has a net inhibitory effect on Tregs and yet activates Teff. We therefore hypothesized that CTX treatment prior to GITR agonism would promote potent anti-tumor immunity. Here we show that the combination of CTX and GITR agonism robustly controls tumor growth in several clinically relevant mouse models. Mechanistically, we show that the combination therapy causes tumor cell death, clonal expansion of highly active and terminally differentiated CD8+ T cells, and depletion of regulatory T cells by AICD. Control of tumor growth was also associated with the presence of an expanded population of highly activated tumor-infiltrating oligoclonal CD8+ T cells that lead to a global contracted TCR repertoire. Our studies show that the combination of CTX and GITR agonism is a rational chemo-immunotherapeutic approach that warrants further clinical investigation.

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mRNA-seq analyses for the differentially expressed genes (DEGs) among Con, NF VM-astrocytes, Ctx-astrocytes, and control Ctx-NPCs

Project description:To gain further molecular insight into the observed astrocyte functions, we performed RNA-sequencing (RNA-seq) analysis of the differentiated Ctx-NPCs (control), Ctx-astrocytes and VM-astrocytes used in the co-culture and CM experiments. The genes that are differentially expressed (DEGs) in Ctx-astrocytes compared to differentiated Ctx-NPCs (FPKM>1, log2>1) significantly overlapped with DEGs in VM-astrocytes compared to differentiated Ctx-NPCs

2020-10-25 | GSE106216 | GEO

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