Comparison and evaluation of the specificity and binding capacity of commercial and in house affinity columns used in sample preparation for analysis of growth-promoting drugs

Immunoaffinity chromatography (IAC) and affinity chromatography (AC:) are widely used for extraction of drugs from biological samples. Fifteen column types were purchased from five different manufacturers and;their ability to bind specific drugs including beta-agonists and anabolic steroids over a range of analyte concentrations in fortified bovine urine samples was assessed. The performance data obtained from these columns were compared with columns produced in this laboratory (in house columns). The in house columns gave the highest recoveries, ranging from 92 to 100% at the 1 ng spiking concentration, for five of the seven analytes assessed. Forty percent (11 of 27) of all the commercial column assessments recorded recoveries of less than 50% even when the lowest spiking concentration was applied (1 ng). For one manufacturer, only one of seven different columns purchased delivered extraction efficiencies greater than 50%. The extraction efficiencies of the clenbuterol columns were the highest with all commercially prepared columns showing at least 50% binding of radiolabelled tracer. Recoveries of alpha-nortestosterone were the lowest. The variability of these products with respect to quality control requires constant monitoring.

Feasibility of a Clinical Chemical Analysis Approach to Predict Misuse of Growth Promoting Hormones in Cattle

A study was performed to determine if targeted metabolic profiling of cattle sera could be used to establish a predictive tool for identifying hormone misuse in cattle. Metabolites were assayed in heifers (n ) 5) treated with nortestosterone decanoate (0.85 mg/kg body weight), untreated heifers (n ) 5), steers (n ) 5) treated with oestradiol benzoate (0.15 mg/kg body weight) and untreated steers (n ) 5). Treatments were administered on days 0, 14, and 28 throughout a 42 day study period. Two support vector machines (SVMs) were trained, respectively, from heifer and steer data to identify hormonetreated animals. Performance of both SVM classifiers were evaluated by sensitivity and specificity of treatment prediction. The SVM trained on steer data achieved 97.33% sensitivity and 93.85% specificity while the one on heifer data achieved 94.67% sensitivity and 87.69% specificity. Solutions of SVM classifiers were further exploited to determine those days when classification accuracy of the SVM was most reliable. For heifers and steers, days 17-35 were determined to be the most selective. In summary, bioinformatics applied to targeted metabolic profiles generated from standard clinical chemistry analyses, has yielded an accurate, inexpensive, high-throughput test for predicting steroid abuse in cattle.

Mass spectrometric analysis of muscle samples to detect potential antibiotic growth promoter misuse in broiler chickens

Mass spectrometric methods were developed and validated for the analysis in chicken muscle of a range of antibiotic growth promoters: spiramycin, tylosin, virginiamycin and bacitracin, and separately for two marker metabolites of carbadox (quinoxaline-2-carboxylic acid and 1,4-bisdesoxycarbadox), and a marker metabolite of olaquindox (3-methyl-quinoxaline-2-carboxylic acid). The use of these compounds as antibiotic growth promoters has been banned by the European Commission. This study aimed to develop methods to detect their residues in muscle samples as a means of checking for the use of these drugs during the rearing of broiler chickens. When fed growth-promoting doses for 6 days, spiramycin (31.4 mu g kg(-1)), tylosin (1.0 mu g kg(-1)), QCA (6.5 mu g kg(-1)), DCBX (71.2 mu g kg(-1)) and MQCA (0.2 mu g kg(-1)) could be detected in the muscle 0 days after the withdrawal of fortified feed. Only spiramycin could consistently be detected beyond a withdrawal period of 1 day. All analytes showed stability commercial cooking process, therefore raw or cooked muscle could be used for monitoring purposes.

Clinical and testing protocols for the analysis of epidermal growth factor receptor mutations in East Asian patients with non-small cell lung cancer:a combined clinical-molecular pathological approach

Several randomized phase III studies in advanced stage non-small cell lung cancer (NSCLC) confirmed the superior response rate and progression-free survival of using epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor as first-line therapy compared with chemotherapy in patients with activating EGFR mutations. Despite the need for EGFR mutation tests to guide first-line therapy in East Asian NSCLC, there are no current standard clinical and testing protocols.

Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2–3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128 000 bp and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20 000 bp) in the Hurd Deep, an enigmatic trench in the English Channel.

Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495

Aminobacter lissarensis CC495 is an aerobic facultative methylotroph capable of growth on glucose, glycerol, pyruvate and methylamine as well as the methyl halides methyl chloride and methyl bromide. Previously, cells grown on methyl chloride have been shown to express two polypeptides with apparent molecular masses of 67 and 29 kDa. The 67 kDa protein was purified and identified as a halomethane:bisulfide/halide ion methyltransferase. This study describes a single gene cluster in A. lissarensis CC495 containing the methyl halide utilisation genes cmuB, cmuA, cmuC, orf 188, paaE and hutI The genes correspond to the same order and have a high similarity to a gene cluster found in Aminobacter ciceronei IMB-1 and Hyphomicrobium chloromethanicum strain CM2 indicating that genes encoding methyl halide degradation are highly conserved in these strains. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier, B.V. All rights reserved.

Solid-state analysis of low-melting 1,3-dialkylimidazolium hexafluorophosphate salts (ionic liquids) by combined x-ray crystallographic and computational analyses

The interactions of ions in the solid state for a series of representative 1,3-dialkylimidazolium hexafluorophosphate salts (either ionic liquids or closely related) have been examined by crystallographic analysis, combined with the theoretical estimation of crystal-packing densities and lattice-interaction energies. Efficient close-packing of the ions in the crystalline states is observed, but there was no compelling evidence for specific directional hydrogen-bonding to the hexafluorophosphate anions or the formation of interstitial voids. The close-packing efficiency is supported by the theoretical calculation of ion volumes, crystal lattice energies, and packing densities, which correlated well with experimental data. The crystal density of the salts can be predicted accurately from the summation of free ion volumes and lattice energies calculated. Of even more importance for future work, on these and related salts, the solid-state density of 1,3-dialkylimidazolium hexafluorophosphate salts can be predicted with reasonable accuracy purely on the basis of on ab initio free ion volumes, and this allows prediction of lattice energies without necessarily requiring the crystal structures.

A meta-analysis of latitudinal variations in life-history traits of roach, Rutilus rutilus, over its geographical range: linear or non-linear relationships?

1. We collated information from the literature on life history traits of the roach (a generalist freshwater fish), and analysed variation in absolute fecundity, von Bertalanffy parameters, and reproductive lifespan in relation to latitude, using both linear and non-linear regression models. We hypothesized that because most life history traits are dependent on growth rate, and growth rate is non-linearly related with temperature, it was likely that when analysed over the whole distribution range of roach, variation in key life history traits would show non-linear patterns with latitude.

Analysis of information leakage from encrypted Skype conversations

Voice over IP (VoIP) has experienced a tremendous growth over the last few years and is now widely used among the population and for business purposes. The security of such VoIP systems is often assumed, creating a false sense of privacy. This paper investigates in detail the leakage of information from Skype, a widely used and protected VoIP application. Experiments have shown that isolated phonemes can be classified and given sentences identified. By using the dynamic time warping (DTW) algorithm, frequently used in speech processing, an accuracy of 60% can be reached. The results can be further improved by choosing specific training data and reach an accuracy of 83% under specific conditions. The initial results being speaker dependent, an approach involving the Kalman filter is proposed to extract the kernel of all training signals.

After the Party the Hangover?: An Analysis of ‘Post-Celtic Tiger’ Ireland in the Light of the February 2011 elections’

The election of February 2011 was dominated by the International Monetary Fund/European Central Bank bailout of November 2010, the state of the public finances, the ongoing Irish banking crisis, and the disastrous state of the economy with rising unemployment, emigration and collapsing international competiveness. After years of phenomenal economic growth (at least as measured by orthodox economic measurements such as gross domestic product (GDP) and foreign direct investment), known as the 'Celtic Tiger‘, during which a bloated construction industry accounted for a quarter of GDP and Irish banks sank nearly a third of their lending in construction projects, Ireland has entered a 'post-Celtic Tiger‘ era. This article offers a critical analysis outlining some political, economic and cultural issues of this election as heralding a decisive stage in the 'post-Celtic Tiger' development of the Republic of Ireland, and suggests that what is required at this present historical moment is that a different development model be articulated by the Irish state and wider society.

Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation

The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63.

Numerical analysis of stiffener runout sections

The recent trend of incorporating more composite material in primary aircraft structures has highlighted the vulnerability of stiffened aerostructures to through-thickness stresses, which may lead to delamination and debonding at the skin-stiffener interface, leading to collapse. Stiffener runout regions are particularly susceptible to this problem and cannot be avoided due to the necessity to terminate stiffeners at rib intersections or at cutouts, interrupting the stiffener load path. In this paper, experimental tests relating to two different stiffener runout specimens are presented and the failure modes of both specimens are discussed in detail. A thinner-skinned specimen showed sudden and unstable crack propagation, while a thicker-skinned specimen showed initially unstable but subsequent stable crack growth. Detailed finite element models of the two specimens are developed, and it is shown how such models can explain and predict the behaviour and failure mode of stiffener runouts. The models contain continuum shell elements to model the skin and stiffener, while cohesive elements using a traction-separation law are placed at the skin-stiffener interface to effectively model the debonding which promotes structural failure.