Expression pattern of Pseudomonas aeruginosa biofilm-residing bacteria exposed to gentamicin or surface acoustic waves or gentamicin and surface acoustic waves combined
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ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa
PROVIDER: GSE28081 | GEO | 2011/09/01
SECONDARY ACCESSION(S): PRJNA139731
REPOSITORIES: GEO
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Project description:Expression pattern of Pseudomonas aeruginosa biofilm-residing bacteria exposed to gentamicin or surface acoustic waves or gentamicin and surface acoustic waves combined
| PRJNA139731 | ENA
Project description:Purpose: The goals of this study are to compare RNA-Seq transcriptomic data of P. aeruginosa PAO1 in response to chronic exposure of clindamycin and rifampicin eluted from antibiotic-impregnated catheters in a continuous biofilm culture condition. Methods: Transcriptomic profiles of P. aeruginosa PAO1 grown with catheters without antibiotic coating or with clindamycin/rifampicin coating were generated by deep sequencing, in quadruplicates, using Illumina NextSeq 550 sequencer with SE-75. FastQC and Trimmomatic (v0.39) were used for sequencing quality assessment. Raw read counts of the annotated genes were calculated using HTSeq-count. The log2 fold change and false discovery rate (FDR) were measured by edgeR. Genes with |log2FC| > 1.0 and FDR < 0.05 were considered as differential expression genes. Transcripts per million (TPM) was measured by Kallisto, which is an alignment free expression estimation tool. Results: P. aeruginosa PAO1 RNA sequencing using Illumina NextSeq 550 sequencer generated 5,205,190 of average number of reads with average read length of 65 bp and a mean coverage of 54X. Differentially regulated proteins of 877 in the planktonic cells were identified, 55 of which displayed up-regulation and 822 displayed down-regulation. On the other hand, 178 proteins were differentially expressed in the biofilm cells containing 152 up-regulated and 26 down-regulated. Conclusions: Our study represents the first detailed analysis of transcriptomes generated by RNA-seq technology after P. aeruginosa PAO1 planktonic and biofilm cells were continuously exposed to clindamycin/rifampicin-impregnated catheters. Our results show that RNA sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content of strain PAO1 cells. We conclude that RNA-seq based transcriptome characterization would help the understanding for the mechanism of antimicrobial resistance and virulence in P. aeruginosa after exposure of antimicrobial-coated catheter.
2020-07-01 | GSE153546 | GEO
Project description:Microactuation of free standing objects in fluids is currently dominated by the rotary propeller, giving rise to a range of potential applications in the military, aeronautic and biomedical fields. Previously, surface acoustic waves (SAWs) have been shown to be of increasing interest in the field of microfluidics, where the refraction of a SAW into a drop of fluid creates a convective flow, a phenomenon generally known as SAW streaming. We now show how SAWs, generated at microelectronic devices, can be used as an efficient method of propulsion actuated by localised fluid streaming. The direction of the force arising from such streaming is optimal when the devices are maintained at the Rayleigh angle. The technique provides propulsion without any moving parts, and, due to the inherent design of the SAW transducer, enables simple control of the direction of travel.
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Project description:Biofilms are ubiquitous in natural, medical, and engineering environments. While most antibiotics that primarily aim to inhibit cell growth may result in bacterial drug resistance, biofilm inhibitors do not affect cell growth and there is less chance of developing resistance. This work sought to identify novel, non-toxic and potent biofilm inhibitors from Streptomyces bacteria for reducing the biofilm formation of Pseudomonas aeruginosa PAO1. Out of 4300 Streptomyces strains, one species produced and secreted peptide(s) to inhibit P. aeruginosa biofilm formation by 93% without affecting the growth of planktonic cells. Global transcriptome analyses (DNA microarray) revealed that the supernatant of the Streptomyces 230 strain induced phenazine, pyoverdine, and pyochelin synthesis genes. Electron microscopy showed that the supernatant of Streptomyces 230 strain reduced the production of polymeric matrix in P. aeruginosa biofilm cells, while the Streptomyces species enhanced swarming motility of P. aeruginosa. Therefore, current study suggests that Streptomyces bacteria are an important resource of biofilm inhibitors as well as antibiotics.
2013-03-21 | GSE28194 | GEO
Project description:Chronic Pseudomonas biofilm infections are commonly associated in patients afflicted with cystic fibrosis (CF) leading to high degree of morbidity. In a murine tumor model we demonstrated that P. aeruginosa efficiently colonizes and forms biofilms in cancerous tissue post intra-venous injection. Several non-biofilm forming mutants have been identified and incorporated in the present study. Biofilm formation by wild type strains was evident in electron microscopy and immuno-histological studies. Efficacy of currently available CF infection treatment antibiotics such as ciprofloxacin, colistin and tobramycin were tested in this model. We found out that normal doses of these antibiotics were unable to eliminate wild type P. aeruginosa PA14. However, transposon mutants of P. aeruginosa PA14 (pqsA & Pel A) had strong influence on colonization. Subsequently high doses were effective against wild type P. aeruginosa PA14 biofilms.
2019-02-01 | GSE55000 | GEO
Project description:The experimental investigation of quantum devices incorporating mechanical resonators has opened up new frontiers in the study of quantum mechanics at a macroscopic level. It has recently been shown that surface acoustic waves (SAWs) can be piezoelectrically coupled to superconducting qubits, and confined in high-quality Fabry-Perot cavities in the quantum regime. Here we present measurements of a device in which a superconducting qubit is coupled to a SAW cavity, realising a surface acoustic version of cavity quantum electrodynamics. We use measurements of the AC Stark shift between the two systems to determine the coupling strength, which is in agreement with a theoretical model. This quantum acoustodynamics architecture may be used to develop new quantum acoustic devices in which quantum information is stored in trapped on-chip acoustic wavepackets, and manipulated in ways that are impossible with purely electromagnetic signals, due to the 105 times slower mechanical waves.In this work, Manenti et al. present measurements of a device in which a tuneable transmon qubit is piezoelectrically coupled to a surface acoustic wave cavity, realising circuit quantum acoustodynamic architecture. This may be used to develop new quantum acoustic devices.
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Project description:Stable and efficient guided waves are essential for information transmission and processing. Recently, topological valley-contrasting materials in condensed matter systems have been revealed as promising infrastructures for guiding classical waves, for they can provide broadband, non-dispersive and reflection-free electromagnetic/mechanical wave transport with a high degree of freedom. In this work, by designing and manufacturing miniaturized phononic crystals on a semi-infinite substrate, we experimentally realized a valley-locked edge transport for surface acoustic waves (SAWs). Critically, original one-dimensional edge transports could be extended to quasi-two-dimensional ones by doping SAW Dirac "semimetal" layers at the boundaries. We demonstrate that SAWs in the extended topological valley-locked edges are robust against bending and wavelength-scaled defects. Also, this mechanism is configurable and robust depending on the doping, offering various on-chip acoustic manipulation, e.g., SAW routing, focusing, splitting, and converging, all flexible and high-flow. This work may promote future hybrid phononic circuits for acoustic information processing, sensing, and manipulation.
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Project description:Extraordinary transmission of waves, i.e. a transmission superior to the amount predicted by geometrical considerations of the aperture alone, has to date only been studied in the bulk. Here we present a new class of extraordinary transmission for waves confined in two dimensions to a flat surface. By means of acoustic numerical simulations in the gigahertz range, corresponding to acoustic wavelengths λ ~ 3-50 μm, we track the transmission of plane surface acoustic wave fronts between two silicon blocks joined by a deeply subwavelength bridge of variable length with or without an attached cavity. Several resonant modes of the structure, both one- and two-dimensional in nature, lead to extraordinary acoustic transmission, in this case with transmission efficiencies, i.e. intensity enhancements, up to ~23 and ~8 in the two respective cases. We show how the cavity shape and bridge size influence the extraordinary transmission efficiency. Applications include new metamaterials and subwavelength imaging.
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Project description:The relevant length scales in sub-nanometer amplitude surface acoustic wave-driven acoustic streaming are demonstrated. We demonstrate the absence of any physical limitations preventing the downscaling of SAW-driven internal streaming to nanoliter microreactors and beyond by extending SAW microfluidics up to operating frequencies in the GHz range. This method is applied to nanoliter scale fluid mixing.
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