The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization

Complexes between the quorum-sensing regulator TraR and its inducing ligand autoinducer (AAI) are soluble in Escherichia coli, whereas apo-TraR is almost completely insoluble. Here we show that the lack of soluble TraR is due in large part to rapid proteolysis, inasmuch as apo-TraR accumulated to high levels in an E. coli strain deficient in Clp and Lon proteases. In pulse labeling experiments, AAI protected TraR against proteolysis only when it was added before the radiolabel. This observation indicates that TraR proteins can productively bind AAI only during their own synthesis on polysomes, whereas fully synthesized apo-TraR proteins are not functional AAI receptors. Purified apo-TraR was rapidly degraded by trypsin to oligopeptides, whereas TraR–AAI complexes were more resistant to trypsin and were cleaved at discrete interdomain linkers, indicating that TraR requires AAI to attain its mature tertiary structure. TraR–AAI complexes eluted from a gel filtration column as dimers and bound DNA as dimers. In contrast, apo-TraR was monomeric, and incubation with AAI under a variety of conditions did not cause dimerization. We conclude that AAI is critical for the folding of nascent TraR protein into its mature tertiary structure and that full-length apo-TraR cannot productively bind AAI and is consequently targeted for rapid proteolysis.

Genetic evidence for direct sensing of phenolic compounds by the VirA protein of Agrobacterium tumefaciens.

The virulence (vir) genes of Agrobacterium tumefaciens are induced by low-molecular-weight phenolic compounds and monosaccharides through a two-component regulatory system consisting of the VirA and VirG proteins. However, it is not clear how the phenolic compounds are sensed by the VirA/VirG system. We tested the vir-inducing abilities of 15 different phenolic compounds using four wild-type strains of A. tumefaciens--KU12, C58, A6, and Bo542. We analyzed the relationship between structures of the phenolic compounds and levels of vir gene expression in these strains. In strain KU12, vir genes were not induced by phenolic compounds containing 4'-hydroxy, 3'-methoxy, and 5'-methoxy groups, such as acetosyringone, which strongly induced vir genes of the other three strains. On the other hand, vir genes of strain KU12 were induced by phenolic compounds containing only a 4'-hydroxy group, such as 4-hydroxyacetophenone, which did not induce vir genes of the other three strains. The vir genes of strains KU12, A6, and Bo542 were all induced by phenolic compounds containing 4'-hydroxy and 3'-methoxy groups, such as acetovanillone. By transferring different Ti plasmids into isogenic chromosomal backgrounds, we showed that the phenolic-sensing determinant is associated with Ti plasmid. Subcloning of Ti plasmid indicates that the virA locus determines which phenolic compounds can function as vir gene inducers. These results suggest that the VirA protein directly senses the phenolic compounds for vir gene activation.

Proteome analysis of extracellular proteins regulated by the las and rhl quorum sensing systems in Pseudomonas aeruginosa PAO1

The las and rhl quorum sensing (QS) systems regulate the expression of several genes in response to cell density changes in Pseudomonas aeruginosa. Many of these genes encode surface-associated or secreted virulence factors. Proteins from stationary phase culture supernatants were collected from wild-type and P. aeruginosa PAO1 mutants deficient in one or more of the lasRI, rhIRI and vfr genes and analysed using two-dimensional gel electrophoresis. All mutants released significantly lower amounts of protein than the wild-type. Protein spot patterns from each strain were compared using image analysis and visible spot differences were identified using mass spectrometry. Several previously unknown OS-regulated proteins were characterized, including an aminopeptidase (PA2939), an endoproteinase (PrpL) and a unique 'hypothetical' protein (PA0572), which could not be detected in the culture supernatants of Delta/as mutants, although they were unaffected in Deltarhl mutants. Chitin-binding protein (CbpD) and a hypothetical protein (PA4944) with similarity to host factor I (HF-1) could not be detected when any of the lasRI or rhIRI genes were disrupted. Fourteen proteins were present at significantly greater levels in the culture supernatants of OS mutants, suggesting that QS may also negatively control the expression of some genes. Increased levels of two-partner secretion exoproteins (PA0041 and PA4625) were observed and may be linked to increased stability of their cognate transporters in a CS-defective background. Known QS-regulated extracellular proteins, including elastase (lasB), LasA protease (lasA) and alkaline metalloproteinase (aprA) were also detected.

Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1

BACKGROUND: We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strain, V5 hxt1-7Delta, in which only HXT1-7 had been deleted. In this study, we compared the transcriptome of the resultant strain, V5.TM6*P, with that of its wild-type parent, V5, at different glucose concentrations. RESULTS: cDNA array analyses revealed that alterations in gene expression that occur when transitioning from a respiro-fermentative (V5) to a respiratory (V5.TM6*P) strain, are very similar to those in cells undergoing a diauxic shift. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4 (in complex with Hap2, 3, 5), Cat8 and Mig1, and used this in combination with verified binding consensus sequences to identify genes likely to be regulated by one or more of these. Of the induced genes in our dataset, 77% had binding sites for the Hap complex, with 72% having at least two. In addition, 13% were found to have a binding site for Cat8 and 21% had a binding site for Mig1. Unexpectedly, both the up- and down-regulation of many of the genes in our dataset had a clear glucose dependence in the parent V5 strain that was not present in V5.TM6*P. This indicates that the relief of glucose repression is already operable at much higher glucose concentrations than is widely accepted and suggests that glucose sensing might occur inside the cell. CONCLUSION: Our dataset gives a remarkably complete view of the involvement of genes in the TCA cycle, glyoxylate cycle and respiratory chain in the expression of the phenotype of V5.TM6*P. Furthermore, 88% of the transcriptional response of the induced genes in our dataset can be related to the potential activities of just three proteins: Hap4, Cat8 and Mig1. Overall, our data support genetic remodelling in V5.TM6*P consistent with a respiratory metabolism which is insensitive to external glucose concentrations.

Refractive index sensing properties of long-period fibre grating with sol-gel derived coatings

Long-period fibre gratings (LPGs) have previously been used to detect quantities such as temperature, strain and refractive index (RI). The responsivity to surrounding refractive index means that, potentially, LPGs could be realised as optical biosensors for applications in biochemical and biomedical application areas. We report here to our best knowledge the first investigation on refractive index sensing properties of LPGs with sol-gel derived titanium and silicon oxide coatings. It is revealed that the RI sensitivity of an LPG is affected by both the thickness and the index value of the coating; the coating with higher index and thickness will enhance the LPG RI sensitivity significantly. The surrounding refractive index induced LPG resonance shift has been evaluated over the LPGs’ most sensitive RI region from 1.42 to 1.44. We have identified that, in this region, the uncoated LPG has an RI sensitivity of (-673.0±0.4)nm/uri (unit of refractive index) while the LPG coated with titanium oxide exhibits a sensitivity as high as (-1067.15±0.04)nm/uri.

Discrimination between strain and temperature effects using first and second-order diffraction from a long period grating

We study the effects of temperature and strain on the spectra of the first and second-order diffraction attenuation bands of a single long-period grating (LPG) in step-index fibre. The primary and second-order attenuation bands had comparable strength with the second-order bands appearing in the visible and near-infra red parts of the spectrum. Using first and second-order diffraction to the eighth cladding mode a sensitivity matrix was obtained with limiting accuracy given by cross-sensitivity of ~1.19% of the measurement. The sensing scheme presented as a limiting temperature and strain resolution of ±0.7 °C and ~±25 µ.

A comparison of the sensing characteristics of long period gratings written in three different types of fiber

This paper compares the environmental sensing behaviour of long period gratings written in three fibers with different refractive index profiles: step, W and a progressive three layered fiber. The measurands considered are temperature, refractive index, axial strain and bending, and the spectral behaviour of individual attenuation bands were observed and, where possible, compared to theoretical predictions. Significant differences in the behaviour of the three fiber types were found.

Fibre bragg gratings for microwave photonics and sensing

This thesis presents details on the fabrication of microwave transversal filters using fibre Bragg grating arrays and the building of fibre Bragg grating based magnetic-field sensors. Some theoretical background about fibre Bragg gratings, photosensitivity, fibre Bragg grating sensors and filters are presented. Fibre Bragg grating sensors in other industrial applications are highlighted. Some sensing principles are also introduced. Experimental work is carried out to demonstrate a magnetic-field sensor using an established fibre Bragg grating strain sensor. System performance and trade-off are discussed. The most important part of this thesis is on the fabrication of photonic transversal filter using fibre Bragg grating arrays. In order to improve the filter performance, a novel tap multiplexing structure is presented. Further improving approaches such as apodisation are also investigated. The basis of nonrecirculating filter, some structure and performance are introduced.

Exploitation of fibre characteristics in temperature sensing and radio-over-fibre applications

The development of sensing devices is one of the instrumentation fields that has grown rapidly in the last decade. Corresponding to the swift advance in the development of microelectronic sensors, optical fibre sensors are widely investigated because of their advantageous properties over the electronics sensors such as their wavelength multiplexing capability and high sensitivity to temperature, pressure, strain, vibration and acoustic emission. Moreover, optical fibre sensors are more attractive than the electronics sensors as they can perform distributed sensing, in terms of covering a reasonably large area using a single piece of fibre. Apart from being a responsive element in the sensing field, optical fibre possesses good assets in generating, distributing, processing and transmitting signals in the future broadband information network. These assets include wide bandwidth, high capacity and low loss that grant mobility and flexibility for wireless access systems. Among these core technologies, the fibre optic signal processing and transmission of optical and radio frequency signals have been the subjects of study in this thesis. Based on the intrinsic properties of single-mode optical fibre, this thesis aims to exploit the fibre characteristics such as thermal sensitivity, birefringence, dispersion and nonlinearity, in the applications of temperature sensing and radio-over-fibre systems. By exploiting the fibre thermal sensitivity, a fully distributed temperature sensing system consisting of an apodised chirped fibre Bragg grating has been implemented. The proposed system has proven to be efficient in characterising grating and providing the information of temperature variation, location and width of the heat source applied in the area under test.To exploit the fibre birefringence, a fibre delay line filter using a single high-birefringence optical fibre structure has been presented. The proposed filter can be reconfigured and programmed by adjusting the input azimuth of launched light, as well as the strength and direction of the applied coupling, to meet the requirements of signal processing for different purposes in microwave photonic and optical filtering applications. To exploit the fibre dispersion and nonlinearity, experimental investigations have been carried out to study their joint effect in high power double-sideband and single-sideband modulated links with the presence of fibre loss. The experimental results have been theoretically verified based on the in-house implementation of the split-step Fourier method applied to the generalised nonlinear Schrödinger equation. Further simulation study on the inter-modulation distortion in two-tone signal transmission has also been presented so as to show the effect of nonlinearity of one channel on the other. In addition to the experimental work, numerical simulations have also been carried out in all the proposed systems, to ensure that all the aspects concerned are comprehensively investigated.

Sensitivity of LPGs in PCFs fabricated by an electric arc to temperature, strain, and external refractive index

Sensing properties of long-period gratings (LPGs) fabricated in photonic crystal fibers by an electric arc are explained and quantified by semianalytical and numerical models. In particular, the grating's insensitivity to temperature and simultaneous sensitivity to strain and refractive index are simulated. The modeling procedure is generalized so that it can be applied to a wide range of LPGs in various fibers.

Effectively simultaneous temperature and strain measurement utilising a dual-grating sensor formed by type IA and type IIA FBGs

In this paper, we report a systematic investigation of the dependence of both temperature and strain sensitivities on the jiber Bragg grating (FBG) type, including the wellknown Type I, Type IIA, and a new type which we have designated Type 1.4, using both hydrogen-Ji-ee and hydrogenated B/Ge codoped jibers. We have identijed distinct sensitivity characteristics for each grating type, and we have utilised them to implement a novel dual-grating, duul-parameter sensor device. Three dual-grating sensing schemes with different combinations of gruting types have been constructed and compared. The Type IA-Type IIA combination exhibits the best pe$ormance and is superior to that of previously reported gruting-based structures. The characteristics of the measurement errors in such dualgrating sensor systems is also presented in detail.

Measurements of polarimetric sensitivity to hydrostatic pressure, strain and temperature in birefringent dual-core microstructured polymer fiber

We experimentally characterized a birefringent microstructured polymer fiber of specific construction, which allows for single mode propagation in two cores separated by a pair of large holes. The fiber exhibits high birefringence in each of the cores as well as relatively weak coupling between the cores. Spectral dependence of the group and the phase modal birefringence was measured using an interferometric method. We have also measured the sensing characteristics of the fiber such as polarimetric sensitivity to hydrostatic pressure, strain and temperature. Moreover, we have studied the effect of hydrostatic pressure and strain on coupling between the cores.

High-frequency fiber Bragg grating sensing interrogation system using Sagnac-loop-based microwave photonic filtering

A novel high-frequency fiber Bragg grating (FBG) sensing interrogation system by using fiber Sagnac-loop-based microwave photonic filtering is proposed and experimentally demonstrated. By adopting the microwave photonic filtering, the wavelength shift of sensing FBG can be converted into amplitude variation of the modulated electronic radio-frequency (RF) signal. In the experiment, the strain applied onto the sensing FBG has been demodulated by measuring the intensity of the recovered RF signal, and by modulating the RF signal with different frequencies, different interrogation sensitivities can be achieved.

Sol–gel derived coating applied to long-period gratings for enhanced refractive index sensing properties

Long-period fibre gratings (LPGs) have previously been used to detect quantities such as temperature, strain, and refractive index (RI). We report here, to the best of our knowledge, the first investigation on refractive index sensing properties of LPGs with sol–gel derived titanium and silicon oxide coatings. It is revealed that the RI sensitivity of an LPG is affected by both the thickness and the index value of the coating; a coating with higher index and thickness will enhance the LPG RI sensitivity significantly. The surrounding refractive index induced LPG resonance shift has been evaluated over the LPGs' most sensitive RI region from 1.42 to 1.44. We have identified that, in this region, the uncoated LPG has an RI sensitivity of (-673.0 ± 0.4) nm/uri (unit of refractive index) while the LPG coated with titanium oxide exhibits a sensitivity as high as (-1067.15 ± 0.04) nm/uri. The experimental results also reveal that, even in the RI insensitive region around 1.33, there still is a marked enhancement in RI sensitivity of the sol–gel coated LPG compared to the uncoated one. This is potentially significant as coated LPGs may be extended to low RI gas and semi-liquidized based sensing applications.

Fibre Bragg gratings in polymer optical fibre for applications in sensing

This thesis presents the potential sensing applications of fibre Bragg gratings in polymer optical fibres. Fibre Bragg gratings are fabricated in different kinds of polymer optical fibres, including Poly methyl methacrylate (PMMA) and TOPAS cyclic olefin copolymer based microstructured polymer optical fibres and PMMA based step-index photosensitive polymer optical fibre, using the 325nm continuous wave ultraviolet laser and phase mask technique. The thermal response of fabricated microstructured polymer optical fibre Bragg gratings has been characterized. The PMMA based single mode microstructured polymer optical fibre Bragg gratings exhibit negative non-linear Bragg wavelength shift with temperature, including a quasi-linear region. The thermal sensitivity of such Bragg gratings in the linear region is up to -97pm/°C. A permanent shift in the grating wavelength at room temperature is observed when such gratings are heated above a threshold temperature which can be extended by annealing the fibre before grating inscription. The largest positive Bragg wavelength shift with temperature in transmission is observed in TOPAS based few moded microstructured polymer optical fibre Bragg gratings and the measured temperature sensitivity is 250±0.5pm/°C. Gluing method is developed to maintain stable optical coupling between PMMA based single mode step index polymer optical fibre Bragg gratings and single mode step index silica optical fibre. Being benefit from this success, polymer optical fibre Bragg gratings are able to be characterised for their temperature, humidity and strain sensitivity, which are -48.2±1pm/°C, 38.3±0.5pm per %RH and 1.33±0.04 pm/µ??respectively. These sensitivities have been utilised to achieve several applications. The strain sensitivity of step index polymer optical fibre Bragg grating devices has been exploited in the potential application of the strain condition monitoring of heavy textiles and when being attached to textile specimens with certain type of adhesives. These polymer fibre Bragg grating devices show better strain transfer and lower structure reinforcement than silica optical fibre Bragg grating devices. The humidity sensitivity of step index polymer optical fibre Bragg grating devices is applied to detecting water in jet fuel and is proved to be able to measure water content of less than 20 ppm in Jet fuel. A simultaneous temperature and humidity sensor is also made by attaching a polymer fibre Bragg grating to a silica optical fibre Bragg grating and it shows better humidity measurement accuracy than that of electronic competitors.