Immunochemical detection of glyoxal DNA damage

The relevance of reactive oxygen species (ROS) in the pathogenesis of inflammatory diseases is widely documented. Immunochemical detection of ROS DNA adducts has been developed, however, recognition of glyoxal-DNA adducts has not previously been described. We have generated a polyclonal antibody that has shown increased antibody binding to ROS-modified DNA in comparison to native DNA. In addition, dose-dependent antibody binding to DNA modified with ascorbate alone was shown, with significant inhibition by desferrioxamine, catalase, and ethanol. Minimal inhibition was observed with uric acid, 1,10-phenanthroline and DMSO. However, antibody binding in the presence of EDTA increased 3500-fold. The involvement of hydrogen peroxide and hydroxyl radical in ascorbate-mediated DNA damage is consistent with ascorbate acting as a reducing agent for DNA-bound metal ions. Glyoxal is known to be formed during oxidation of ascorbate. Glyoxylated DNA, that previously had been proposed as a marker of oxidative damage, was recognised in a dose dependent manner using the antibody. We describe the potential use of our anti-ROS DNA antibody, that detects predominantly Fenton-type mediated damage to DNA and report on its specificity for the recognition of glyoxal-DNA adducts.

From marine ecology to crime analysis: improving the detection of serial sexual offences using a taxonomic similarity measure

Jaccard has been the choice similarity metric in ecology and forensic psychology for comparison of sites or offences, by species or behaviour. This paper applies a more powerful hierarchical measure - taxonomic similarity (s), recently developed in marine ecology - to the task of behaviourally linking serial crime. Forensic case linkage attempts to identify behaviourally similar offences committed by the same unknown perpetrator (called linked offences). s considers progressively higher-level taxa, such that two sites show some similarity even without shared species. We apply this index by analysing 55 specific offence behaviours classified hierarchically. The behaviours are taken from 16 sexual offences by seven juveniles where each offender committed two or more offences. We demonstrate that both Jaccard and s show linked offences to be significantly more similar than unlinked offences. With up to 20% of the specific behaviours removed in simulations, s is equally or more effective at distinguishing linked offences than where Jaccard uses a full data set. Moreover, s retains significant difference between linked and unlinked pairs, with up to 50% of the specific behaviours removed. As police decision-making often depends upon incomplete data, s has clear advantages and its application may extend to other crime types. Copyright © 2007 John Wiley & Sons, Ltd.

Detection of bacterial DNA in cardiac vegetations by PCR after the completion of antimicrobial treatment for endorcarditis

PCR with broad-range primers for prokaryotic 16S rRNA genes was used to identify bacterial DNA in tissue from patients undergoing valve replacements following a previous episode of infective endocarditis (IF). Of eight valves investigated, bacterial DNA was detected in three from patients for whom IE had been treated by antibiotic therapy 5, 12 and 18 months previously. The demonstration of bacterial DNA within resected heart valves suggests either recurrence of infection, treatment failure or the persistence of bacterial debris within the cardiac vegetation. There may also be implications for routine use of PCR in the diagnosis of infection. © 2004 Copyright by the European Society of Clinical Microbiology and Infectious Diseases.

The combination of smart hydrogels and fibre optic sensor technology for analyte detection

The subject of investigation of the present research is the use of smart hydrogels with fibre optic sensor technology. The aim was to develop a costeffective sensor platform for the detection of water in hydrocarbon media, and of dissolved inorganic analytes, namely potassium, calcium and aluminium. The fibre optic sensors in this work depend upon the use of hydrogels to either entrap chemotropic agents or to respond to external environmental changes, by changing their inherent properties, such as refractive index (RI). A review of current fibre optic technology for sensing outlined that the main principles utilised are either the measurement of signal loss or a change in wavelength of the light transmitted through the system. The signal loss principle relies on changing the conditions required for total internal reflection to occur. Hydrogels are cross-linked polymer networks that swell but do not dissolve in aqueous environments. Smart hydrogels are synthetic materials that exhibit additional properties to those inherent in their structure. In order to control the non-inherent properties, the hydrogels were fabricated with the addition of chemotropic agents. For the detection of water, hydrogels of low refractive index were synthesized using fluorinated monomers. Sulfonated monomers were used for their extreme hydrophilicity as a means of water sensing through an RI change. To enhance the sensing capability of the hydrogel, chemotropic agents, such as pH indicators and cobalt salts, were used. The system comprises of the smart hydrogel coated onto an exposed section of the fibre optic core, connected to the interrogation system measuring the difference in the signal. Information obtained was analysed using a purpose designed software. The developed sensor platform showed that an increase in the target species caused an increase in the signal lost from the sensor system, allowing for a detection of the target species. The system has potential applications in areas such as clinical point of care, water detection in fuels and the detection of dissolved ions in the water industry.

Water detection in jet fuel using a polymer optical fibre Bragg grating

Water is a common impurity of jet fuel, and can exist in three forms: dissolved in the fuel, as a suspension and as a distinct layer at the bottom of the fuel tank. Water cannot practically be eliminated from fuel but must be kept to a minimum as large quantities can cause engine problems, particularly when frozen, and the interface between water and fuel acts as a breeding ground for biological contaminants. The quantities of dissolved or suspended water are quite small, ranging from about 10 ppm to 150 ppm. This makes the measurement task difficult and there is currently a lack of a convenient, electrically passive system for water-in-fuel monitoring; instead the airlines rely on colorimetric spot tests or simply draining liquid from the bottom of fuel tanks. For all these reason, people have explored different ways to detect water in fuel, however all these approaches have problems, e.g. they may not be electrically passive or they may be sensitive to the refractive index of the fuel. In this paper, we present a simple, direct and sensitive approach involving the use of a polymer optical fibre Bragg grating to detect water in fuel. The principle is that poly(methyl methacrylate) (PMMA) can absorb moisture from its surroundings (up to 2% at 23 °C), leading to both a swelling of the material and an increase in refractive index with a consequent increase in the Bragg wavelength of a grating inscribed in the material.

Simultaneous measurement of temperature and external refractive index by use of a hybrid grating in D fiber with enhanced sensitivity by HF etching

We propose a dual-parameter optical sensor device achieved by UV inscription of a hybrid long-period grating-fiber Bragg grating structure in D fiber. The hybrid configuration permits the detection of the temperature from the latter's response and measurement of the external refractive index from the former's response. In addition, the host D fiber permits effective modification of the device's sensitivity by cladding etching. The grating sensor has been used to measure the concentrations of aqueous sugar solutions, demonstrating its potential capability to detect concentration changes as small as 0.01%.

Protein oxidative modifications:new mass spectrometry approaches to detection in biological samples

In inflammatory diseases, release of oxidants leads to oxidative damage to proteins. The precise nature of oxidative damage to individual proteins depends on the oxidant involved. Chlorination and nitration are markers of modification by the myeloperoxidase-H2O2-Cl- system and nitric oxide-derived oxidants, respectively. Although these modifications can be detected by western blotting, currently no reliable method exists to identify the specific sites damage to individual proteins in complex mixtures such as clinical samples. We are developing novel LCMS2 and precursor ion scanning methods to address this. LC-MS2 allows separation of peptides and detection of mass changes in oxidized residues on fragmentation of the peptides. We have identified indicative fragment ions for chlorotyrosine, nitrotyrosine, hydroxytyrosine and hydroxytryptophan. A nano-LC/MS3 method involving the dissociation of immonium ions to give specific fragments for the oxidized residues has been developed to overcome the problem of false positives from ions isobaric to these immonium ions that exist in unmodified peptides. The approach has proved able to identify precise protein modifications in individual proteins and mixtures of proteins. An alternative methodology involves multiple reaction monitoring for precursors and fragment ions are specific to oxidized and chlorinated proteins, and this has been tested with human serum albumin. Our ultimate aim is to apply this methodology to the detection of oxidative post-translational modifications in clinical samples for disease diagnosis, monitoring the outcomes of therapy, and improved understanding of disease biochemistry.

Aptamer-based surface plasmon sensor for thrombin detection

A series of surface plasmonic fibre devices were fabricated using multiple coatings deposited on a lapped section of a single mode fibre and post-fabrication UV laser irradiation processing with a phase mask, producing a surface relief grating structure. These devices showed high spectral sensitivity in the aqueous index regime ranging up to 4000 nm/RIU for wavelength and 800 dB/RIU for intensity. The devices were then coated with human thrombin binding aptamer. Several concentrations of thrombin in buffer solution were made, ranging from 1nM to 1µM. All the concentrations were detectable by the devices demonstrating that sub-nM concentrations may be monitored.

Optical sensor based on hybrid LPG/FBG in D-fiber for simultaneous refractive index and temperature measurement

A dual-parameter optical sensor has been realized by UV-writing a long-period and a Bragg grating structure in D-fiber. The hybrid configuration permits the detection of the temperature from the latter and measuring the external refractive index from the former responses, respectively. The employment of the D-fiber allows as effective modification and enhancement of the device sensitivity by cladding etching. The grating sensor has been used to measure the concentrations of aqueous sugar solutions, demonstrating the potential capability to detect concentration changes as small as 0.01%.

An overview of Total Factor Productivity estimations adjusted for pollutant outputs:an application to sugarcane farming

The conventional Total Factor Productivity (TFP) measurement does not incorporate the effects of undesirable outputs, which are harmful to the environment. Using sugarcane farming in Kenya, this paper illustrates the differences between the conventional Malmquist index measures where the environment variable is not adjusted and environment-adjusted measures using both hyperbolic and directional distance functions. The mean TFP change estimates for the conventional Malmquist index, adjusted hyperbolic index and Luenberger indicator were 3.13%, 0.11% and 2.21%, respectively. The conventional non-adjusted measure lies between the two adjusted measures of hyperbolic index and Luenberger indicator. © 2012 Inderscience Enterprises Ltd.

Simultaneous measurement of temperature and external refractive index by use of a hybrid grating in D fiber with enhanced sensitivity by HF etching

We propose a dual-parameter optical sensor device achieved by UV inscription of a hybrid long-period grating-fiber Bragg grating structure in D fiber. The hybrid configuration permits the detection of the temperature from the latter's response and measurement of the external refractive index from the former's response. In addition, the host D fiber permits effective modification of the device's sensitivity by cladding etching. The grating sensor has been used to measure the concentrations of aqueous sugar solutions, demonstrating its potential capability to detect concentration changes as small as 0.01%.

Water detection in jet fuel using a polymer optical fibre Bragg grating

Water is a common impurity of jet fuel, and can exist in three forms: dissolved in the fuel, as a suspension and as a distinct layer at the bottom of the fuel tank. Water cannot practically be eliminated from fuel but must be kept to a minimum as large quantities can cause engine problems, particularly when frozen, and the interface between water and fuel acts as a breeding ground for biological contaminants. The quantities of dissolved or suspended water are quite small, ranging from about 10 ppm to 150 ppm. This makes the measurement task difficult and there is currently a lack of a convenient, electrically passive system for water-in-fuel monitoring; instead the airlines rely on colorimetric spot tests or simply draining liquid from the bottom of fuel tanks. For all these reason, people have explored different ways to detect water in fuel, however all these approaches have problems, e.g. they may not be electrically passive or they may be sensitive to the refractive index of the fuel. In this paper, we present a simple, direct and sensitive approach involving the use of a polymer optical fibre Bragg grating to detect water in fuel. The principle is that poly(methyl methacrylate) (PMMA) can absorb moisture from its surroundings (up to 2% at 23 °C), leading to both a swelling of the material and an increase in refractive index with a consequent increase in the Bragg wavelength of a grating inscribed in the material.

Refractive index sensitivity characteristics near the dispersion turning point of the multimode microfiber-based Mach–Zehnder interferometer

The turning point of the refractive index (RI) sensitivity based on the multimode microfiber (MMMF) in-line Mach–Zehnder interferometer (MZI) is observed. By tracking the resonant wavelength shift of the MZI generated between the HE11 and HE12 modes in the MMMF, the surrounding RI (SRI) could be detected. Theoretical analysis demonstrates that the RI sensitivity will reach ±∞ on either side of the turning point due to the group effective RI difference (퐺) approaching zero. Significantly, the positive sensitivity exists in a very wide fiber diameter range, while the negative sensitivity can be achieved in a narrow diameter range of only 0.3 μm. Meanwhile, the experimental sensitivities and variation trend at different diameters exhibit high consistency with the theoretical results. High RI sensitivity of 10777.8 nm/RIU (RI unit) at the fiber diameter of 4.6 μm and the RI around 1.3334 is realized. The discovery of the sensitivity turning points has great significance on trace detection due to the possibility of ultrahigh RI sensitivity.

Detection of organic aromatic compounds in paraffin by a long-period fiber grating optical sensor with optimized sensitivity

A long-period grating (LPG) sensor is used to detect small variations in the concentration of an organic aromatic compound (xylene) in a paraffin (heptane) solution. A new design procedure is adopted and demonstrated to maximize the sensitivity of LPG (wavelength shift for a change in the surrounding refractive index, (dλ/dn3)) for a given application. The detection method adopted is comparable to the standard technique used in industry (high performance liquid chromatograph and UV spectroscopy) which has a relative accuracy between ∼±0.5% and 5%. The minimum detectable change in volumetric concentration is 0.04% in a binary fluid with the detection system presented. This change of concentration relates to a change in refractive index of Δn ∼ 6 × 10-5. © 2001 Elsevier Science B.V.

Optical sensor based on hybrid LPG/FBG in D-fiber for simultaneous refractive index and temperature measurement

A dual-parameter optical sensor has been realized by UV-writing a long-period and a Bragg grating structure in D-fiber. The hybrid configuration permits the detection of the temperature from the latter and measuring the external refractive index from the former responses, respectively. The employment of the D-fiber allows as effective modification and enhancement of the device sensitivity by cladding etching. The grating sensor has been used to measure the concentrations of aqueous sugar solutions, demonstrating the potential capability to detect concentration changes as small as 0.01%.