Jan Mrázek

Low-fouling surface plasmon resonance biosensor for multi-step detection of foodborne bacterial pathogens in complex food samples.

Recent outbreaks of foodborne illnesses have shown that foodborne bacterial pathogens present a significant threat to public health, resulting in an increased need for technologies capable of fast and reliable screening of food commodities. The optimal method of pathogen detection in foods should: (i) be rapid, specific, and sensitive; (ii) require minimum sample preparation; and (iii) be robust and cost-effective, thus enabling use in the field. Here we report the use of a SPR biosensor based on ultra-low fouling and functionalizable poly(carboxybetaine acrylamide) (pCBAA) brushes for the rapid and sensitive detection of bacterial pathogens in crude food samples utilizing a three-step detection assay. We studied both the surface resistance to fouling and the functional capabilities of these brushes with respect to each step of the assay, namely: (I) incubation of the sensor with crude food samples, resulting in the capture of bacteria by antibodies immobilized to the pCBAA coating, (II) binding of secondary biotinylated antibody (Ab2) to previously captured bacteria, and (III) binding of streptavidin-coated gold nanoparticles to the biotinylated Ab2 in order to enhance the sensor response. We also investigated the effects of the brush thickness on the biorecognition capabilities of the gold-grafted functionalized pCBAA coatings. We demonstrate that pCBAA-compared to standard low-fouling OEG-based alkanethiolate self-assemabled monolayers-exhibits superior surface resistance regarding both fouling from complex food samples as well as the non-specific binding of S-AuNPs. We further demonstrate that a SPR biosensor based on a pCBAA brush with a thickness as low as 20 nm was capable of detecting E. coli O157:H7 and Salmonella sp. in complex hamburger and cucumber samples with extraordinary sensitivity and specificity. The limits of detection for the two bacteria in cucumber and hamburger extracts were determined to be 57 CFU/mL and 17 CFU/mL for E. coli and 7.4 × 10(3) CFU/mL and 11.7 × 10(3)CFU/mL for Salmonella sp., respectively. In addition, we demonstrate the simultaneous detection of E. coli and Salmonella sp. in hamburger sample using a multichannel SPR biosensor having appropriate functional coatings.

Detection of aromatic hydrocarbons in air and water by using xerogel layers coated on PCS fibers excited by an inclined collimated beam

This paper deals with experimental results on the sensitivity of silica optical fibers coated with detection xerogel membranes to benzene and toluene both in gaseous mixtures and in aqueous solutions. For this purpose thin polysiloxane and methyl-group-doped polysiloxane xerogel membranes are applied on straight segments of PCS fibers. The interaction of these membranes with hydrocarbons is investigated on the basis of changes of the output optical power from the fibers excited by an inclined collimated beam. The results obtained show that the hydrophobic methyl-group-doped xerogel layers exhibit higher sensitivity to hydrocarbons both in the gaseous phase and in solutions. The detection limits are about 230 ppm vol. for toluene in air and about 9 mg/l for toluene in water. Both the membranes show lower sensitivity to benzene than to toluene.

Biased distribution of adenine and thymine in gene nucleotide sequences

We analyzed occurrences of bases in 20,352 introns, exons of 25,574 protein-coding genes, and among the three codon positions in the protein-coding sequences. The nucleotide sequences originated from the whole spectrum of organisms from bacteria to primates. The analysis revealed the following: (1) In most exons, adenine dominates over thymine. In other words, adenine and thymine are distributed in an asymmetric way between the exon and the complementary strand, and the coding sequence is mostly located in the adenine-rich strand. (2) Thymine dominates over adenine not only in the strand complementary to the exon but also in introns. (3) A general bias is further revealed in the distribution of adenine and thymine among the three codon positions in the exons, where adenine dominates over thymine in the second and mainly the first codon position while the reverse holds in the third codon position. The product (A1/T1) × (A2/T2) × (T3/A3) is smaller than one in only a few analyzed genes.

Detection of toluene dissolved in water by using PCS fibers excited by an inclined collimated beam

This paper reports results on the sensitivity of straight polymer-clad silica (PCS) detection fibers with short sensing parts coated with polysiloxane polymers to toluene dissolved in water. The detection was based on refractive index changes of the polymers induced by the penetration of toluene into them. These changes were detected by measuring changes of the output power from the detection fibers excited by an inclined collimated beam at 630 nm. Commercially available Cablelite 950-701 and two types of polymethylphenylsiloxane polymers developed at the Romanian Academy were tested as materials for the fabrication of the detection part in the fiber cladding. These parts were prepared by application of polymer layers onto a bare silica core by a dip-coating technique. Layers with thicknesses of about 20 mm were prepared. Examples of angular distributions of the output power determined for the detection polymers in contact with air, time response curves measured with the detection parts brought into contact with aqueous solutions of toluene under different hydrodynamic conditions, and sensitivity curves are shown in the paper. The best detection limit of about 10 mg/l of toluene, reversibility and linearity of the fiber response in a range 0‐100 mg/l could be achieved with fibers coated with Cablelite 950-701 polymer. # 2003 Elsevier Science B.V. All rights reserved.

In vivo optical detection of pH in microscopic tissue samples of Arabidopsis thaliana.

Minimally invasive in vivo measurement of pH in microscopic biological samples of μm or μl size, e.g. plant cells, tissues and saps, may help to explain complex biological processes. Consequently, techniques to achieve such measurements are a focus of interest for botanists. This paper describes a technique for the in vivo measurement of pH in the range pH5.0 to pH7.8 in microscopic plant tissue samples of Arabidopsis thaliana based on a ratiometric fluorescence method using low-loss robust tapered fiber probes. For this purpose tapered fiber probes were prepared and coated with a detection layer containing ion-paired fluorescent pH-transducer 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (c-HPTS). A fluorescence ratiometric approach was employed based on excitation at 415 nm and 450 nm and on the comparison of the fluorescence response at 515 nm. The suitability of tapered fiber probes for local detection of pH between 5.0 and 7.8 was demonstrated. A pH sensitivity of 0.15 pH units was achieved within the pH ranges 5.0-5.9 and 7.1-7.8, and this was improved to 0.04 pH units within the pH range 5.9-7.1. Spatial resolution of the probes was better than 20 μm and a time response within 15-20s was achieved. Despite the minute dimensions of the tapered fiber probes the setup developed was relatively robust and compact in construction and performed reliably. It has been successfully employed for the in vivo local determination of pH of mechanically resistant plant tissues of A. thaliana of microscopic scale. The detection of momentary pH gradients across the intact plant seems to be a good tool for the determination of changes in pH in response to experimental treatments affecting for example enzyme activities, availability of mineral nutrients, hormonal control of plant development and plant responses to environmental cues.

Optical fibre biosensors for oxygen and glucose monitoring

An optical fibre biosensor that uses an oxygen sensitive coating; Ruthenium complex [Dichlorotris(1,10-phenantroline)-ruthenium(II) hydrate], incorporated into an adhesive inorganic-organic hybrid polymer coating (ORMOCER) is described. The Ruthenium/ ORMOCER layer is used with optical fibres to form an extrinsic or intrinsic sensor. It can be applied to a microscope slide or lens to be interrogated by optical fibres, or form a cladding layer for an evanescent field optical fibre sensor. The Ruthenium complex is caused to fluoresce by a high brightness blue LED at 470 nm and the excitation light at 600nm is detected by a photomultiplier tube used as a photon counter, to measure fluorescence lifetime. The fluorescence is quenched by oxygen depletion within the layer, which can be linked to glucose by incorporation of suitable enzymes. The detection threshold is 0.7mg(O2)/litre, and the sensitivity is 70 ns/mg per litre.

Dielectric annular core fiber for optical sensing

The paper deals with a special type of sensing optical fiber, the annular core fiber. This fiber is composed of a narrow annular low-loss glass optical core and glass optical cladding which are applied onto the inner wall of a silica capillary. In the paper transmission characteristics are determined theoretically from the solution of the Helmholtz equation as well as experimentally from measurements of the near field and angular distributions of the output power from the fiber excited by an inclined collimated beam. The sensitivity of the fiber to gaseous toluene is determined under the excitation of the fiber by an inclined beam at 670 nm, when refractive-index changes in the evanescent field are responsible for the sensitivity. These measurements are compared with those carried out with reference capillary silica fibers and PCS fibers. It is shown that the annular core fibers have the highest sensitivity in comparison with the reference fibers. A detection limit of 0.06 % can be determined from the sensitivity measurements.

The influence of nanostructured optical fiber core matrix on the optical properties of EDFA

In this contribution we demonstrate the effect of the nanostructured optical fiber core matrix, doped with erbium and Al2O3, on the resulting optical properties. Several optical fibers with nanostructured cores were drawn from preforms prepared by different techniques, i.e., by conventional doping from solution of erbium and aluminium chlorides, by deposition of the dispersed alumina nanoparticles with either Er3+ ions or Er2O3. Reference bulk samples were prepared by the solid-state approach and thermally treated by similar way as optical fibers. Prepared optical fibers and bulk samples were investigated by the absorption spectroscopy. Reference samples were analyzed by the X-ray diffraction for the determination of the crystalline properties of formed nanostructures. It was found that nanocrystals inside the optical fiber core matrix improves the homogeneity and decreases the basic optical attenuation. Nanostructured alumina inside the fiber core matrix enhances the absorption properties of Er3+ ions.

Special optical fibers doped with nanocrystalline holmium-yttrium titanates (HoxY1-x)2Ti2O7 for fiber-lasers

The paper deals with the preparation and characterization of the silica optical fibers doped with nanocrystalline holmium-yttrium titanates (HoxY1-x)2Ti2O7 with optimized luminescence properties. The sol-gel approach was employed to prepare colloidal solution of (HoxY1-x)2Ti2O7 precursors. The concentration of Ho3+ ions in the compounds was varied up to x=0.4. Prepared sols were calcined at 1000 °C forming xerogels which were characterized by X-ray diffraction to confirm their structure. The xerogels were analyzed by the mean of steady-state luminescence technique to optimize the concentration of Ho3+ ions in the compound. The most intensive emission at 2050 nm was observed for the compound (Ho5Y95)2Ti2O7. Sol of the corresponding composition was soaked into the porous silica frit deposed inside the silica substrate tube which was collapsed into preform and drawn into optical fiber. Single mode optical fiber with the core diameter 12 μm and outer diameter 125 μm was prepared. Numerical aperture of prepared fiber was 0.16. The concentration of Ho3+ ions in the fiber core was 0.03 at %. Background attenuation of prepared fiber at 850 nm was smaller than 0.5 dB⋅m-1.

Capillary optical fibers modified by xerogel layers for chemical detection

Xerogel layers have been used in the development of fiber-optic chemical sensors with the aim of enhancing the interaction of detected chemicals with light waves transmitted in the fiber. In most of fiber-optic sensors xerogels layers have been applied onto the fibers. This paper shows an alternative approach, in which xerogel detection layers are applied onto the walls of holes of silica capillaries. Single capillaries as well as multiple capillaries of microstructure fibers were used as substrates for the application of xerogel layers. Sensitivities of the prepared layers to vapours of water and toluene were determined experimentally. In these experiments, light was coupled into the capillaries and the xerogel layers were brought into contact with gaseous mixtures of the chemicals and nitrogen. Spectral changes of the output light from the capillaries were measured in a wavelength range from 1300 to 1800 nm. Results of these measurements are shown and compared with those obtained for layers applied onto silica fibers. These results show that capillary fibers modified by xerogel layers offer novel means for increasing the detection sensitivity.