677 research outputs found
Functional analysis of pyochelin-/enantiopyochelin-related genes from a pathogenicity island of Pseudomonas aeruginosa strain PA14.
Genomic islands are foreign DNA blocks inserted in so-called regions of genomic plasticity (RGP). Depending on their gene content, they are classified as pathogenicity, symbiosis, metabolic, fitness or resistance islands, although a detailed functional analysis is often lacking. Here we focused on a 34-kb pathogenicity island of Pseudomonas aeruginosa PA14 (PA14GI-6), which is inserted at RGP5 and carries genes related to those for pyochelin/enantiopyochelin biosynthesis. These enantiomeric siderophores of P. aeruginosa and certain strains of Pseudomonas protegens are assembled by a thiotemplate mechanism from salicylate and two molecules of cysteine. The biochemical function of several proteins encoded by PA14GI-6 was investigated by a series of complementation analyses using mutants affected in potential homologs. We found that PA14_54940 codes for a bifunctional salicylate synthase/salicyl-AMP ligase (for generation and activation of salicylate), that PA14_54930 specifies a dihydroaeruginoic acid (Dha) synthetase (for coupling salicylate with a cysteine-derived thiazoline ring), that PA14_54910 produces a type II thioesterase (for quality control), and that PA14_54880 encodes a serine O-acetyltransferase (for increased cysteine availability). The structure of the PA14GI-6-specified metabolite was determined by mass spectrometry, thin-layer chromatography, and HPLC as (R)-Dha, an iron chelator with antibacterial, antifungal and antitumor activity. The conservation of this genomic island in many clinical and environmental P. aeruginosa isolates of different geographical origin suggests that the ability for Dha production may confer a selective advantage to its host
NrsZ: a novel, processed, nitrogen-dependent, small non-coding RNA that regulates Pseudomonas aeruginosa PAO1 virulence.
The opportunistic pathogen Pseudomonas aeruginosa PAO1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. Here, we report the discovery and characterization of a novel small non-coding RNA: NrsZ (nitrogen-regulated sRNA). We show that under nitrogen limitation, NrsZ is induced by the NtrB/C two component system, an important regulator of nitrogen assimilation and P. aeruginosa's swarming motility, in concert with the alternative sigma factor RpoN. Furthermore, we demonstrate that NrsZ modulates P. aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. This regulation takes place through the post-transcriptional control of rhlA, a gene essential for rhamnolipids synthesis. Interestingly, we also observed that NrsZ is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for NrsZ regulatory functions
Compressed sensing quantum process tomography for superconducting quantum gates
We apply the method of compressed sensing (CS) quantum process tomography
(QPT) to characterize quantum gates based on superconducting Xmon and phase
qubits. Using experimental data for a two-qubit controlled-Z gate, we obtain an
estimate for the process matrix with reasonably high fidelity compared
to full QPT, but using a significantly reduced set of initial states and
measurement configurations. We show that the CS method still works when the
amount of used data is so small that the standard QPT would have an
underdetermined system of equations. We also apply the CS method to the
analysis of the three-qubit Toffoli gate with numerically added noise, and
similarly show that the method works well for a substantially reduced set of
data. For the CS calculations we use two different bases in which the process
matrix is approximately sparse, and show that the resulting estimates of
the process matrices match each ther with reasonably high fidelity. For both
two-qubit and three-qubit gates, we characterize the quantum process by not
only its process matrix and fidelity, but also by the corresponding standard
deviation, defined via variation of the state fidelity for different initial
states.Comment: 16 pages, 11 figure
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Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa.
The opportunistic human pathogen Pseudomonas aeruginosa is able to utilize a wide range of carbon and nitrogen compounds, allowing it to grow in vastly different environments. The uptake and catabolism of growth substrates are organized hierarchically by a mechanism termed catabolite repression control (Crc) whereby the Crc protein establishes translational repression of target mRNAs at CA (catabolite activity) motifs present in target mRNAs near ribosome binding sites. Poor carbon sources lead to activation of the CbrAB two-component system, which induces transcription of the small RNA (sRNA) CrcZ. This sRNA relieves Crc-mediated repression of target mRNAs. In this study, we have identified novel targets of the CbrAB/Crc system in P. aeruginosa using transcriptome analysis in combination with a search for CA motifs. We characterized four target genes involved in the uptake and utilization of less preferred carbon sources: estA (secreted esterase), acsA (acetyl-CoA synthetase), bkdR (regulator of branched-chain amino acid catabolism) and aroP2 (aromatic amino acid uptake protein). Evidence for regulation by CbrAB, CrcZ and Crc was obtained in vivo using appropriate reporter fusions, in which mutation of the CA motif resulted in loss of catabolite repression. CbrB and CrcZ were important for growth of P. aeruginosa in cystic fibrosis (CF) sputum medium, suggesting that the CbrAB/Crc system may act as an important regulator during chronic infection of the CF lung
Deaf, Dumb, and Chatting Robots, Enabling Distributed Computation and Fault-Tolerance Among Stigmergic Robot
We investigate ways for the exchange of information (explicit communication)
among deaf and dumb mobile robots scattered in the plane. We introduce the use
of movement-signals (analogously to flight signals and bees waggle) as a mean
to transfer messages, enabling the use of distributed algorithms among the
robots. We propose one-to-one deterministic movement protocols that implement
explicit communication. We first present protocols for synchronous robots. We
begin with a very simple coding protocol for two robots. Based on on this
protocol, we provide one-to-one communication for any system of n \geq 2 robots
equipped with observable IDs that agree on a common direction (sense of
direction). We then propose two solutions enabling one-to-one communication
among anonymous robots. Since the robots are devoid of observable IDs, both
protocols build recognition mechanisms using the (weak) capabilities offered to
the robots. The first protocol assumes that the robots agree on a common
direction and a common handedness (chirality), while the second protocol
assumes chirality only. Next, we show how the movements of robots can provide
implicit acknowledgments in asynchronous systems. We use this result to design
asynchronous one-to-one communication with two robots only. Finally, we combine
this solution with the schemes developed in synchronous settings to fit the
general case of asynchronous one-to-one communication among any number of
robots. Our protocols enable the use of distributing algorithms based on
message exchanges among swarms of Stigmergic robots. Furthermore, they provides
robots equipped with means of communication to overcome faults of their
communication device
Improving the Coherence Time of Superconducting Coplanar Resonators
The quality factor and energy decay time of superconducting resonators have
been measured as a function of material, geometry, and magnetic field. Once the
dissipation of trapped magnetic vortices is minimized, we identify surface
two-level states (TLS) as an important decay mechanism. A wide gap between the
center conductor and the ground plane, as well as use of the superconductor Re
instead of Al, are shown to decrease loss. We also demonstrate that classical
measurements of resonator quality factor at low excitation power are consistent
with single-photon decay time measured using qubit-resonator swap experiments.Comment: 3 pages, 4 figures for the main paper; total 5 pages, 6 figures
including supplementary material. Submitted to Applied Physics Letter
Iron acquisition with the natural siderophore enantiomers pyochelin and enantio-pyochelin in Pseudomonas species.
The bacterial siderophore pyochelin is composed of salicylate and two cysteine-derived heterocycles, the second of which is modified by reduction and N-methylation during biosynthesis. In Pseudomonas aeruginosa, the first cysteine residue is converted to its D-isoform during thiazoline ring formation, whereas the second cysteine remains in its L-configuration. Stereochemistry is opposite in the Pseudomonas fluorescens siderophore enantio-pyochelin, in which the first ring originates from L-cysteine and the second ring from D-cysteine. Both siderophores promote growth of the producer organism during iron limitation and induce the expression of their biosynthesis genes by activating the transcriptional AraC-type regulator PchR. However, neither siderophore is functional as an iron carrier or as a transcriptional inducer in the other species, demonstrating that both processes are highly stereospecific. Stereospecificity of pyochelin/enantio-pyochelin-mediated iron uptake is ensured at two levels: (i) by the outer membrane siderophore receptors and (ii) by the cytosolic PchR regulators
Energy decay and frequency shift of a superconducting qubit from non-equilibrium quasiparticles
Quasiparticles are an important decoherence mechanism in superconducting
qubits, and can be described with a complex admittance that is a generalization
of the Mattis-Bardeen theory. By injecting non-equilibrium quasiparticles with
a tunnel junction, we verify qualitatively the expected change of the decay
rate and frequency in a phase qubit. With their relative change in agreement to
within 4% of prediction, the theory can be reliably used to infer quasiparticle
density. We describe how settling of the decay rate may allow determination of
whether qubit energy relaxation is limited by non-equilibrium quasiparticles.Comment: Main paper: 4 pages, 3 figures, 1 table. Supplementary material: 8
pages, 3 figure
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