Characterization of EhaJ, a new autotransporter protein from enterohemorrhagic and enteropathogenic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are diarrheagenic pathotypes of E. coli that cause gastrointestinal disease with the potential for life-threatening sequelae. While certain EHEC and EPEC virulence mechanisms have been extensively studied, the factors that mediate host colonization remain to be properly defined. Previously, we identified four genes (ehaA, ehaB, ehaC, and ehaD) from the prototypic EHEC strain EDL933 that encode for proteins that belong to the autotransporter (AT) family. Here we have examined the prevalence of these genes, as well as several other AT-encoding genes, in a collection of EHEC and EPEC strains. We show that the complement of AT-encoding genes in EHEC and EPEC strains is variable, with some AT-encoding genes being highly prevalent. One previously uncharacterized AT-encoding gene, which we have termed ehaJ, was identified in 12/44 (27%) of EHEC and 2/20 (10%) of EPEC strains. The ehaJ gene lies immediately adjacent to a gene encoding a putative glycosyltransferase (referred to as egtA). Western blot analysis using an EhaJ-specific antibody indicated that EhaJ is glycosylated by EgtA. Expression of EhaJ in a recombinant E. coli strain, revealed EhaJ is located at the cell surface and in the presence of the egtA glycosyltransferase gene mediates strong biofilm formation in microtiter plate and flow cell assays. EhaJ also mediated adherence to a range of extracellular matrix proteins, however this occurred independent of glycosylation. We also demonstrate that EhaJ is expressed in a wild-type EPEC strain following in vitro growth. However, deletion of ehaJ did not significantly alter its adherence or biofilm properties. In summary, EhaJ is a new glycosylated AT protein from EPEC and EHEC. Further studies are required to elucidate the function of EhaJ in colonization and virulence.

Potentiation of ciprofloxacin action against Gram-negative bacterial biofilms by a nitroxide

We previously showed that soluble nitroxides (nitric oxide analogues) mimicked the well-established ability of nitric oxide to cause biofilm dispersal and further showed that these compounds could prevent biofilm formation. Here, we investigated the effect of the nitroxide carboxy-TEMPO in combination with sub μg/ml concentrations of ciprofloxacin on pre-formed flow cell biofilms formed by Gram-negative bacteria. Combination therapy led to substantial eradication of existing biofilms formed by Pseudomonas aeruginosa PA14 (99.3%) and Escherichia coli O157 (93%).

A Network Model of Static Foam Drainage

On the basis of a more realistic tetrakaidecahedral structure of foam bubbles, a network model of static foam drainage has been developed. The model considers the foam to be made up of films and Plateau borders. The films drain into the adjacent Plateau borders, which in turn form a network through which the liquid moves from the foam to the liquid pool. From the structure, a unit flow cell was found, which constitutes the foam when stacked together both horizontally and vertically. Symmetry in the unit flow cell indicates that the flow analysis of a part of it can be employed to obtain the drainage for the whole foam. Material balance equations have been written for each segment of this subsection, ensuring connectivity, and solved with the appropriate boundary and initial conditions. The calculated rates of drainage, when compared with the available experimental results, indicate that the model predicts the experimental results well.

Differential reflectance modulation sensing with diffractive microstructures

We present a method for differential ratiometric measurement of reflectance change due to molecular adsorption using a diffractive microstructure fabricated on a reflectance contrast enhancing substrate for bulk refractometry and surface molecular binding detection applications. The differential method suppresses signal fluctuations due to thermal or concentration gradients in the sample flow cell by more than 40x and enables the real-time measurement of molecular interactions on the surface with a noise floor of about 70 pm. (V)C 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4766190]

On-chip integrated label-free optical biosensing

This thesis investigates the design and implementation of a label-free optical biosensing system utilizing a robust on-chip integrated platform. The goal has been to transition optical micro-resonator based label-free biosensing from a laborious and delicate laboratory demonstration to a tool for the analytical life scientist. This has been pursued along four avenues: (1) the design and fabrication of high-$Q$ integrated planar microdisk optical resonators in silicon nitride on silica, (2) the demonstration of a high speed optoelectronic swept frequency laser source, (3) the development and integration of a microfluidic analyte delivery system, and (4) the introduction of a novel differential measurement technique for the reduction of environmental noise.

The optical part of this system combines the results of two major recent developments in the field of optical and laser physics: the high-$Q$ optical resonator and the phase-locked electronically controlled swept-frequency semiconductor laser. The laser operates at a wavelength relevant for aqueous sensing, and replaces expensive and fragile mechanically-tuned laser sources whose frequency sweeps have limited speed, accuracy and reliability. The high-$Q$ optical resonator is part of a monolithic unit with an integrated optical waveguide, and is fabricated using standard semiconductor lithography methods. Monolithic integration makes the system significantly more robust and flexible compared to current, fragile embodiments that rely on the precarious coupling of fragile optical fibers to resonators. The silicon nitride on silica material system allows for future manifestations at shorter wavelengths. The sensor also includes an integrated microfluidic flow cell for precise and low volume delivery of analytes to the resonator surface. We demonstrate the refractive index sensing action of the system as well as the specific and nonspecific adsorption of proteins onto the resonator surface with high sensitivity. Measurement challenges due to environmental noise that hamper system performance are discussed and a differential sensing measurement is proposed, implemented, and demonstrated resulting in the restoration of a high performance sensing measurement.

The instrument developed in this work represents an adaptable and cost-effective platform capable of various sensitive, label-free measurements relevant to the study of biophysics, biomolecular interactions, cell signaling, and a wide range of other life science fields. Further development is necessary for it to be capable of binding assays, or thermodynamic and kinetics measurements; however, this work has laid the foundation for the demonstration of these applications.

The effect of low solubility organic acids on the hygroscopicity of sodium halide aerosols

In order to accurately assess the influence of fatty acids on the hygroscopic and other physicochemical properties of sea salt aerosols, hexanoic, octanoic or lauric acid together with sodium halide salts (NaCl, NaBr and NaI) have been chosen to be investigated in this study. The hygroscopic properties of sodium halide sub-micrometre particles covered with organic acids have been examined by Fourier-transform infrared spectroscopy in an aerosol flow cell. Covered particles were generated by flowing atomized sodium halide particles (either dry or aqueous) through a heated oven containing the gaseous acid. The obtained results indicate that gaseous organic acids easily nucleate onto dry and aqueous sodium halide particles. On the other hand, scanning electron microscopy (SEM) images indicate that lauric acid coating on NaCl particles makes them to aggregate in small clusters. The hygroscopic behaviour of covered sodium halide particles in deliquescence mode shows different features with the exchange of the halide ion, whereas the organic surfactant has little effect in NaBr particles, NaCl and NaI covered particles experience appreciable shifts in their deliquescence relative humidities, with different trends observed for each of the acids studied. In efflorescence mode, the overall effect of the organic covering is to retard the loss of water in the particles. It has been observed that the presence of gaseous water in heterogeneously nucleated particles tends to displace the cover of hexanoic acid to energetically stabilize the system.

The adsorption of dopamine on gold and its interactions with iron(III) ions studied by microcantilevers

The adsorption of dopamine (DA) molecules on gold and their interactions with Fe3+ were studied by a microcantilever in a flow cell. The microcantilever bent toward the Au side with the adsorption of DA due to the change Of Surface stress induced by the intermolecular hydrogen bonds of DA or the charge transfer effect between adsorbates and the Substrate. The interaction process between DA adsorbates and Fe3+ was revealed by the deflection curves of microcantilever. As indicated by the appearance of a variation during the decline of curves, two steps were observed in the curve at relative high concentrations of Fe3+. In this case, Fe3+ reacted with DA molecules only in the outer layers and the complexes removed with solution. Then Fe3+ reacted further with DA molecules forming the surface complex in the first layer next to the gold. At this stage, the stability Of Surface complexes was time dependent, i.e., unstable initially and stable finally. This may be due to the surface complexes change from mono-dentate to bi-dentate complexes. In another case, i.e., at relative low concentration of Fe3+, only the first step was observed as indicated by the absence of a variation.

Kinetics and mechanism of Yb(III) extraction and separation from Y(III) with mixtures of bis(2,4,4-trimethylpentyl)phosphinic acid and 2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester

The ytterbium(III) extraction kinetics and mechanism with mixtures of bis(2,4,4-trimethylpentyl)phosphinic acid (Cyanex272) and 2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester (P507) dissolved in heptane have been investigated by constant interfacial cell with laminar flow. The effects of the stirring rate, temperature, extractant concentration, and pH on the extraction with mixtures of Cyanex272 and P507 have been studied. The results are compared with those of the system with Cyanex272 or P507 alone. It is concluded that the Yb(III) extraction rate is enhanced with mixtures extractant of Cyanex272 and P507 according to their values of the extraction rate constant, which is due to decreasing the activation energy of the mixtures. At the same time, the mixtures exhibits no synergistic effects for Y(III), which provides better possibilities for Yb(III) and Y(III) separations at a proper conditions than anyone alone. Moreover, thermodynamic extraction separation Yb(III) and Y(III) by the mixtures has been discussed, which agrees with kinetics results. Extraction rate equations have also been obtained, and through the approximate solutions of the flux equation, diffusion parameters and thickness of the diffusion film have been calculated.

Mass-transfer kinetics of ytterbium extraction with sec-nonylphenoxy acetic acid

The extraction kinetics of ytterbium with sec-nonylphenoxy acetic acid (CA-100) in heptane have been investigated using a constant interfacial area cell with laminar flow. The influence of stirring speed and temperature on the rate indicated that the extraction rate was controlled by the experiment conditions. The plot of interfacial area on the rate showed a linear relationship. This fact together with the low solubility in water and strong surface activity of CA-100 at heptane-water interfaces made the interface the most probable locale for the chemical reactions. The influences of extractant concentration and hydrogen ion concentration on the extraction rate were investigated, and the forward and reverse rate equations for the ytterbium extraction with CA-100 were also obtained. Based on the experimental data, the apparent forward extraction rate constant was calculated. Interfacial reaction models were proposed that agree well with the rate equations obtained from experimental data.

Electrochemiluminescence of tris(2,2 '-bipyridine)ruthenium(II) immobilized in poly(p-styrenesulfonate)-silica-Triton X-100 composite thin-films

The electrochemiluminescence (ECL) of tris(2,2'-bipyridine)ruthenium(ii) [Ru(bpy)(3)(2+)] immobilized in poly(p-styrenesulfonate) (PSS)-silica-Triton X-100 composite films was investigated. The cooperative action of PSS, sol-gel and Triton X-100 attached Ru(bpy)(3)(2+) to the electrode strongly, and the presence of Triton X-100 prevented drying fractures of the sol-gel films during gelation and even on repeated wet-dry cycles. The modified electrode was used for the ECL detection of oxalate, tripropylamine (TPA) and NADH in a flow injection analysis (FIA) system with a newly designed flow cell. The detection scheme exhibited good stability, short response time and high sensitivity. Detection limits were 0.1, 0.1 and 0.5 mu mol L-1 for oxalate, TPA and NADH, respectively, and the linear concentration range extended from 0.001 to 1 mmol L-1 for the three analytes. Applications of the flow cell in ECL and electrochemical detection, as well as the immobilization of reagents based on the cooperative action, are suggested.

Chemiluminescent determination of glucose with a modified carbon paste electrode

A flow injection analysis detection method for glucose is presented which is based on the oxidation of glucose by glucose oxidase followed by chemiluminescent detection of hydrogen peroxide. Both glucose oxidase and hematin, a chemiluminescent reaction catalyst, were bulk-immobilized conveniently by direct mixing with carbon paste, which allows renewal of the electrode surface by simply polishing or cutting to expose a new and fully active surface in the case of fouling. Luminol in reagent solution passed through the flow cell and reacted with hydrogen peroxide produced by the enzyme reactor in the presence of the catalyst to yield light. An applied potential of -0.4 V avoided the electrode fouling effectively. The log-log plot of the emitted light intensity vs glucose concentration was linear over the range of 1-100 mmol L-1 with a correlation coefficient of 0.992. Application of this method to other chemiluminescent and bioluminescent systems is suggested. (C) 1999 Academic Press.

In situ FTIR spectroelectrochemistry of a microarray electrode

A thin-layer microdisk array electrode (TLMDAE) was designed for in situ reflectance FTIR spectroelectrochemical studies. A theoretical estimation, cyclic voltammetry, chronoamperometry and in situ IR measurements demonstrate that this novel design of array electrode results in advantages such as reduced ohmic potential drop, small cell constant and facility for diffusional exchange between thin layer and bulk solution. It has been suggested that the enhanced edge diffusion on the TLMDAE leads to a reduced accumulation of species in the thin layer. (C) 1997 Elsevier Science S.A.

Broadband optical cavity absorption spectroscopy in the near-ultraviolet: applications in atmospheric chemistry

A novel spectroscopic method, incoherent broadband cavity enhanced absorption spectroscopy (IBBCEAS), has been modified and extended to measure absorption spectra in the near-ultraviolet with high sensitivity. The near-ultraviolet region extends from 300 to 400 nm and is particularly important in tropospheric photochemistry; absorption of near-UV light can also be exploited for sensitive trace gas measurements of several key atmospheric constituents. In this work, several IBBCEAS instruments were developed to record reference spectra and to measure trace gas concentrations in the laboratory and field. An IBBCEAS instrument was coupled to a flow cell for measuring very weak absorption spectra between 335 and 375 nm. The instrument was validated against the literature absorption spectrum of SO2. Using the instrument, we report new absorption cross-sections of O3, acetone, 2-butanone, and 2-pentanone in this spectral region, where literature data diverge considerably owing to the extremely weak absorption. The instrument was also applied to quantifying low concentrations of the short-lived radical, BrO, in the presence of strong absorption by Br2 and O3. A different IBBCEAS system was adapted to a 4 m3 atmosphere simulation chamber to record the absorption cross-sections of several low vapour pressure compounds, which are otherwise difficult to measure. Absorption cross-sections of benzaldehyde and the more volatile alkyl nitrites agree well with previous spectra; on this basis, the cross-sections of several nitrophenols are reported for the first time. In addition, the instrument was also used to study the optical properties of secondary organic aerosol formed following the photooxidation of isoprene. An extractive IBBCEAS instrument was developed for detecting HONO and NO2 and had a sensitivity of about 10-9 cm-1. This instrument participated in a major international intercomparison of HONO and NO2 measurements held in the EUPHORE simulation chamber in Valencia, Spain, and results from that campaign are also reported here.

Studies on factors relating to the development of defects in commercial cheese

Defects in commercial cheese result in a downgrading of the final cheese and a consequential economic loss to the cheese producer. Developments of defects in cheese are often not fully understood and therefore not controllable by the producer. This research investigated the underlying factors in the development of split and secondary fermentation defect and of pinking defects in commercial Irish cheeses. Split defect in Swiss-type cheese is a common defect associated with eye formation and manifests as slits and cracks visible in the cut cheese loaf (Reinbold, 1972; Daly et al., 2010). No consensus exists as to the definitive causes of the defect and possible factors which may contribute to the defect were reviewed. Models were derived to describe the relationship between moisture, pH, and salt levels and the distance from sample location to the closest external block surface during cheese ripening. Significant gradients within the cheese blocks were observed for all measured parameters in cheeses at 7 day post/after manufacture. No significant pH gradient was found within the blocks on exit from hot-room ripening and at three months post exit from the hot-room. Moisture content reached equilibrium within the blocks between exit from hot-room and 3 months after exit from hot-room while salt and salt-to-moisture levels had not reached equilibrium within the cheese blocks even at three months after exit from hot-room ripening. A characterisation of Swiss-type cheeses produced from a seasonal milk supply was undertaken. Cheeses were sampled on two days per month of the production year, at three different times during the manufacturing day, at internal and external regions of the cheese block and at four ripening time points (7 days post manufacture, post hot-room, 14 days post hot-room and 3 months in a cold room after exit from hot-room). Compositional, biochemical and microbial indices were determined, and the results were analysed as a splitplot with a factorial arrangement of treatments (season, time of day, area) on the main plot and ripening time on the sub-plot. Season (and interactions) had a significant effect on pH and salt-in-moisture levels (SM), mean viable counts of L. helveticus, propionic acid and non-starter lactic acid bacteria, levels of primary and secondary proteolysis and cheese firmness. Levels of proteolysis increased significantly during hot-room ripening but also during cold room storage, signifying continued development of cheese ripening during cold storage (> 8°C). Rheological parameters (e.g. springiness and cohesiveness) were significantly affected by interactions between ripening and location within cheese blocks. Time of day of manufacture significantly affected mean cheese calcium levels at 7 days post manufacture and mean levels of arginine and mean viable counts of NSLAB. Cheeses produced during the middle of the production day had the best grading scores and were more consistent compared to cheeses produced early or late during day of manufacture. Cheeses with low levels of S/M and low values of resilience were associated with poor grades at 7 days post manufacture. Chesses which had high elastic index values and low values of springiness in the external areas after exit from hot-room ripening also obtained good commercial grades. Development of a pink colour defect is an intermittent defect in ripened cheese which may or may not contain an added colourant, e.g., annatto. Factors associated with the defect were reviewed. Attempts at extraction and identification of the pink discolouration were unsuccessful. The pink colour partitioned with the water insoluble protein fraction. No significant difference was observed between ripened control and defect cheese for oxygen levels and redox potential or for the results of elemental analysis. A possible relationship between starter activity and defect development was established in cheeses with added coulourant, as lower levels of residual galactose and lactose were observed in defective cheese compared to control cheese free of the defect. Swiss-type cheese without added colourant had significantly higher levels of arginine and significantly lower lactate levels. Flow cell cytometry indicated that levels of bacterial cell viability and metabolic state differed between control and defect cheeses (without added colourant). Pyrosequencing analysis of cheese samples with and without the defect detected the previously unreported bacteria in cheese, Deinococcus thermus (a potential carotenoid producer). Defective Swiss-type cheeses had elevated levels of Deinococcus thermus compared to control cheeses, however the direct cause of pink was not linked to this bacterium alone. Overall, research was undertaken on underlying factors associated with the development of specific defects in commercial cheese, but also characterised the dynamic changes in key microbial and physicochemical parameters during cheese ripening and storage. This will enable the development of processing technologies to enable seasonal manipulation of manufacture protocols to minimise compositional and biochemical variability and to reduce and inhibit the occurrence of specific quality defects.

Microscopic Examination of Biofilm Destruction by Atmospheric Pressure Plasma

Objective: The aim of this study is to examine microscopically the destruction of bacterial biofilms mediated by atmospheric pressure non-thermal plasma (APNTP) at cellular level as well as at the level of biofilm structure as a whole. Methods: 3-day old bacterial biofilms were grown on polycarbonate coupons in a dual channel flow cell and were treated with an in-housed designed atmospheric pressure non-thermal plasma jet for up to 4 minutes of exposure before being examined by both confocal laser scanning microscopy (CLSM), preceded by Live/Dead bacterial viability staining, and scanning electron microscopy (SEM). Results: Differential live/dead staining followed by confocal microscopy examination revealed that biofilm eradication by APNTP was mediated by varying levels of both cell killing and physical removal. Relative extent of each mechanism was dependent on plasma operating conditions, bacterial species, growth conditions and biofilm thickness. On the other hand, SEM examination of plasma-exposed biofilms revealed a series of morphological changes exhibited by biofilm cells ranging from increased roughness of cell surface to complete cell lysis. Conclusions: Interesting mechanistic insights have been revealed by microscopic examination of plasma-treated bacterial biofilms that, when coupled with more specific biochemical studies, will not only contribute significantly to our understanding of the mechanism of plasma mediated biofilm destruction but also will help in better application-guided development of this novel anti-biofilm approach.