Expression profiling of E. coli in three media treated with antibiotics
Ontology highlight
ABSTRACT: RNA sequencing was performed on E. coli K12 MG1655 on three media (M9, CA-MHB, R10LB) treated with four antibiotics (Ciprofloxacin, Trimethoprim-sulfamethoxazole, Ceftriaxone, Meropenem) at their media-specific MIC90s
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655
Project description:Transcriptional profiling of E. coli MG1655 to Trimethoprim in i) LB media, ii) M9 minimal media and iii) M9 minimal media with supplements to study the association of gene expression with corresponding lethal and non-lethal growth conditions. Supplementation conditions in M9 media included addition of 50 microgram/ml of adenine, methionine, glycine or thymine in various combinations.
Project description:The response of antibiotic adapted resistant mutants of B. cenocepacia J2315 to antibiotic stress was investigated using expression profiling of three biological replicates and comparing the profiles to the J2315 parent control grown without antibiotics.<br>A reference design was used with Cy3 labeled genomic DNA of B. cenocepacia J2315 as common reference. Three test conditions with three biological replicates each were compared to three replicates of the control condition.<br>Test conditions: J2315-A grown in the presence of 250 ug per ml amikacin, J2315-M grown in the presence of 8 ug per ml meropenem and J2315-T grown in the presence of 60 ug per ml trimethoprim and 300 ug per ml sulfamethoxazole.<br>Control condition: J2315 parent strain grown without antibiotics.
Project description:Transcriptional profiling of E. coli MG1655 to Trimethoprim in i) LB media, ii) M9 minimal media and iii) M9 minimal media with supplements to study the association of gene expression with corresponding lethal and non-lethal growth conditions. Supplementation conditions in M9 media included addition of 50 microgram/ml of adenine, methionine, glycine or thymine in various combinations. For all growth conditions, TMP was added to E. coli in mid-log phase and samples were taken at regular intervals from 10 minutes to 120 minutes post treatment. 1 Biological replicate per time point.
Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol.
Project description:To assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the antibiotics trimethoprim and sulfamethoxazole. This will help to define more accurately those bacterial cell mechanisms that contribute to these phenomena and provide information that will contribute to the development of new antibiotics, or compounds or known antibiotics that synergise with those already in clinical use. Thus, this set of experiments confirmed that AZT, widely known for its antiviral activity, acts synergistically with trimehoprim.
Project description:Genomic and transcriptomic analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates
Project description:Circumventing or overwhelming the bacterial adaptation capabilities is key to combatting multidrug-resistant pathogens like Pseudomonas aeruginosa. In an effort to understand the physiological response of P. aeruginosa to clinically relevant antibiotics, we investigated the proteome after exposure to ciprofloxacin, levofloxacin, rifampicin, gentamicin, tobramycin, azithromycin, tigecycline, polymyxin B, colistin, ceftazidime, meropenem, and piperacillin/tazobactam. We further investigated the response to CHIR-90, which represents a promising class of lipopolysaccharide biosynthesis inhibitors currently under evaluation. Radioactive pulse-labeling of newly synthesized proteins followed by 2D-PAGE was used to monitor the acute response of P. aeruginosa to antibiotic treatment. Marker proteins were excised from non-radioactive gels and identified by mass spectrometry. The proteomic profiles provide insights into the cellular defense strategies for each antibiotic. A mathematical comparison of these response profiles based on upregulated marker proteins revealed similarities of responses to antibiotics acting on the same target area.
Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol. A six chip study under two separate culture conditions
Project description:Circumventing or overwhelming the bacterial adaptation capabilities is key to combatting multidrug-resistant pathogens like Pseudomonas aeruginosa. We investigated the physiological stress exerted by approved antibiotics (ciprofloxacin, levofloxacin, rifampicin, gentamicin, tobramycin, azithromycin, tigecycline, polymyxin B, colistin, ceftazidime, meropenem, piperacillin/tazobactam), experimental antibiotics (CHIR-090) and NSAIDs (acetylsalicylic acid (aspirin), diclofenac, ibuprofen), and studied the bacterial response on the proteome level. Radioactive pulse-labeling of newly synthesized proteins followed by 2D-PAGE was used to monitor the acute response of P. aeruginosa to antibiotic treatment. Subsequently, marker proteins were excised from non-radioactive gels and identified by mass spectrometry. We generated a reference library of P. aeruginosa proteomic responses and implemented a mathematical comparison of the profiles. Proteomic signatures were derived for clinically relevant target areas.
Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% maltose Keywords: Logical Set