Validation of Next Generation Sequencing Technologies in Comparison to Current Diagnostic Gold Standards for BRAF, EGFR and KRAS Mutational Analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.

Synthesis of surfactant-free electrostatically stabilized gold nanoparticles by plasma-induced liquid chemistry

Plasma-induced non-equilibrium liquid chemistry is used to synthesize gold nanoparticles (AuNPs) without using any reducing or capping agents. The morphology and optical properties of the synthesized AuNPs are characterized by transmission electron microscopy (TEM) and ultraviolet-visible spectroscopy. Plasma processing parameters affect the particle shape and size and the rate of the AuNP synthesis process. Particles of different shapes (e. g. spherical, triangular, hexagonal, pentagonal, etc) are synthesized in aqueous solutions. In particular, the size of the AuNPs can be tuned from 5 nm to several hundred nanometres by varying the initial gold precursor (HAuCl4) concentration from 2.5 mu M to 1 mM. In order to reveal details of the basic plasma-liquid interactions that lead to AuNP synthesis, we have measured the solution pH, conductivity and hydrogen peroxide (H2O2) concentration of the liquid after plasma processing, and conclude that H2O2 plays the role of the reducing agent which converts Au+3 ions to Au-0 atoms, leading to nucleation growth of the AuNPs.

Fabrication and optical properties of gold nanotube arrays

Arrays of gold nanotubes with polypyrrole cores were grown on glass substrates by electrodeposition into thin film porous alumina templates. Measurements of optical transmission revealed strong extinction peaks related to plasmonic resonances, which were sensitive to the polarization state and angle of incidence. On prolonging the electrodeposition of gold, the polypyrrole core became fully encapsulated and this had a dramatic effect on the optical properties of the arrays, which was rationalized by finite element simulation of the local field intensities resulting from plasmon excitation.

The controlled fabrication and geometry tunable optics of gold nanotube arrays

Arrays of vertically aligned gold nanotubes are fabricated over several square centimetres which display a geometry tunable plasmonic extinction peak at visible wavelengths and at normal incidence. The fabrication method gives control over nanotube dimensions with inner core diameters of 15–30 nm, wall thicknesses of 5–15 nm and nanotube lengths of up to 300 nm. It is possible to tune the position of the extinction peak through the wavelength range 600–900 nm by varying the inner core diameter and wall thickness. The experimental data are in agreement with numerical modelling of the optical properties which further reveal highly localized and enhanced electric fields around the nanotubes. The tunable nature of the optical response exhibited by such structures could be important for various label-free sensing applications based on both refractive index sensing and surface-enhanced Raman scattering.

Fabrication and optical properties of large-scale arrays of gold nanocavities based on rod-in-a-tube coaxials

Centimeter sized arrays of gold coaxial rod-in-a tube cavities have been fabricated using anodized aluminum oxide as a template. The etching process used to create the cavities enables the production of extremely small gaps between tube and rod, on the order of 5 nm, smaller than those created by standard fabrication techniques. Normal incidence spectroscopy reveals two extinction peaks in the visible and near infrared wavelength range associated with resonant plasmonic modes excited in the structure. Numerical simulations show that the modes are associated with in-phase and out-of-phase hybridization of transverse dipolar excitations in the nanorod and in the tube.

Application of halohydrocarbons for the re-dispersion of gold particles

Methods to control the dispersion of gold in supported heterogeneous catalysts are very valuable due to the strong nanoparticle size dependence on their activity and selectivity towards many reactions. Additionally, the ability to disperse large, inactive gold nanoparticles to smaller nanoparticles provides an opportunity to reactivate, stabilise and increase the lifetime of gold catalysts making them more practical for industrial applications. Previously it has been demonstrated that the use of gas phase iodomethane (J. Am. Chem. Soc., 2009, 131, 6973; Angew. Chem., Int. Ed., 2011, 50, 8912) was able to re-disperse gold from >20 nm particles to dimers and trimers. In the current work, we show that this technique can be applied using less hazardous halohydrocarbons treatments, both in the gas phase and the liquid phase. The ability of these individual halohydrocarbons to re-disperse gold as well as the extent to which leaching occurs is assessed.

Ranakinestatin-PPF from the Skin Secretion of the Fukien Gold-Striped Pond Frog, Pelophylax plancyi fukienensis: A Prototype of a Novel Class of Bradykinin B2 Receptor Antagonist Peptide from Ranid Frogs

The defensive skin secretions of many amphibians are a rich source of bradykinins and bradykinin-related peptides (BRPs). Members of this peptide group are also common components of reptile and arthropod venoms due to their multiple biological functions that include induction of pain, effects on many smooth muscle types, and lowering systemic blood pressure. While most BRPs are bradykinin receptor agonists, some have curiously been found to be exquisite antagonists, such as the maximakinin gene-related peptide, kinestatin—a specific bradykinin B₂-receptor antagonist from the skin of the giant fire-bellied toad, Bombina maxima. Here, we describe the identification, structural and functional characterization of a heptadecapeptide (DYTIRTRLHQGLSRKIV), named ranakinestatin-PPF, from the skin of the Chinese ranid frog, Pelophylax plancyi fukienensis, representing a prototype of a novel class of bradykinin B₂-receptor specific antagonist. Using a preconstricted preparation of rat tail arterial smooth muscle, a single dose of 10⁻⁶ M of the peptide effectively inhibited the dose-dependent relaxation effect of bradykinin between 10⁻¹¹ M and 10⁻⁵ M and subsequently, this effect was pharmacologically-characterized using specific bradykinin B₁- (desArg-HOE140) and B₂-receptor (HOE140) antagonists; the data from which demonstrated that the antagonism of the novel peptide was mediated through B₂-receptors. Ranakinestatin—PPF—thus represents a prototype of an amphibian skin peptide family that functions as a bradykinin B₂-receptor antagonist herein demonstrated using mammalian vascular smooth muscle.

Unraveling the synergy between gold nanoparticles and chromium- hydrotalcites in aerobic oxidation of alcohols

The combination of gold nanoparticles (AuNPs) with chromium-substituted hydrotalcite (Cr-HT) supports makes very efficient heterogeneous catalysts (Au/Cr-HT) for aerobic alcohol oxidation under soluble-base-free conditions. The Au-support synergy increases with increasing Cr content of the support and decreasing AuNP size. In situ UV-Raman, X-ray absorption and photoelectron spectroscopic studies firmly establish that the strong Au-Cr synergy is related to a Cr ↔ Cr redox cycle at the Au/Cr-HT interface, where O activation takes place accompanied by electron transfer from Cr-HT to Au. The interfacial Cr species can be reduced by surface Au-H hydride and negative-charged Au species to close the catalytic cycle. A study of kinetic isotope effect indicates that alcohol O-H cleavage is facilitated by the presence of Cr, making a-C-H bond cleavage step more rate-controlling. Accordingly, a dual synergistic effect of Au/Cr-HT catalysts on the activation of O2 and alcohol reactants is proposed.

Optical and magneto-optical properties of gold core cobalt shell magnetoplasmonic nanowire arrays

In this work we present core–shell nanowire arrays of gold coated with a nanometric layer of cobalt. Despite the extremely small Co volume, these core–shell nanowires display large magneto-optical activity and plasmonic resonance determined by the geometry of the structure. Therefore, we are able to tune both the plasmonic and magneto-optical response in the visible range. Through optical and ellipsometric measurements in transmission, and applying a magnetic field to the sample, it is possible to modulate the value of the phase angle (Del {Δ}) between the S and P polarised components. It was found that the core–shell sample produced an order of magnitude larger variation in Del with changing magnetic field direction, compared with hollow cobalt tubes. The enhancement of magneto optical properties through the plasmonic nature of the gold core is complemented with the ability to induce magnetic influence over optical properties via an externally applied field. Moreover, we demonstrate for the first time the ability to use the remanent magnetisation of the Co, in conjunction with the optical properties defined by the Au, to observe remanent optical states in this uniquely designed structure. This new class of magnetoplasmonic metamaterial has great potential in a wide range of applications, from bio-sensing to data storage due to the tuneable nature of multiple resonance modes and dual functionality.

The distribution of COPD in UK general practice using the new GOLD classification

The new Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2011 document recommends a combined assessment of chronic obstructive pulmonary disease (COPD) based on current symptoms and future risk.

A large database of primary-care COPD patients across the UK was used to determine COPD distribution and characteristics according to the new GOLD classification. 80 general practices provided patients with a Read code diagnosis of COPD. Electronic and hand searches of patient medical records were undertaken, optimising data capture.

Data for 9219 COPD patients were collected. For the 6283 patients with both forced expiratory volume in 1 s (FEV1) and modified Medical Research Council scores (mean¡SD age 69.2¡10.6 years, body mass index 27.3¡6.2 kg?m-2), GOLD 2011 group distributions were: A (low risk and fewer symptoms) 36.1%, B (low risk and more symptoms) 19.1%, C (high risk and fewer symptoms) 19.6% and D (high risk and more symptoms) 25.3%. This is in contrast with GOLD 2007 stage classification: I (mild) 17.1%, II (moderate) 52.2%, III (severe) 25.5% and IV (very severe) 5.2%. 20% of patients with FEV1 o50% predicted had more than two exacerbations in the previous 12 months. 70% of patients with FEV1 ,50% pred had fewer than two exacerbations in the previous 12 months.

This database, representative of UK primary-care COPD patients, identified greater proportions of patients in the mildest and most severe categories upon comparing 2011 versus 2007 GOLD classifications. Discordance between airflow limitation severity and exacerbation risk was observed.

Application of AAO Matrix in Aligned Gold Nanorod Array Substrates for Surface-Enhanced Fluorescence and Raman Scattering

In this paper, we probed surface-enhanced Raman scattering (SERS) and surface-enhanced fluorescence (SEF) from probe molecule Rhodamine 6G (R6G) on self-standing Au nanorod array substrates made using a combination of anodization and potentiostatic electrodeposition. The initial substrates were embedded within a porous alumina template (AAO). By controlling the thickness of the AAO matrix, SEF and SERS were observed exhibiting an inverse relationship. SERS and SEF showed a non-linear response to the removal of AAO matrix due to an inhomogeneous plasmon activity across the nanorod which was supported by FDTD calculations. We showed that by optimizing the level of AAO thickness, we could obtain either maximized SERS, SEF or simultaneously observe both SERS and SEF together.

Gold nanoparticle cellular uptake, toxicity and radiosensitisation in hypoxic conditions

Background and purpose: Gold nanoparticles (GNPs) are novel agents that have been shown to cause radiosensitisation in vitro and in vivo. Tumour hypoxia is associated with radiation resistance and reduced survival in cancer patients. The interaction of GNPs with cells in hypoxia is explored.

Materials and methods: GNP uptake, localization, toxicity and radiosensitisation were assessed in vitro under oxic and hypoxic conditions.

Results: GNP cellular uptake was significantly lower under hypoxic than oxic conditions. A significant reduction in cell proliferation in hypoxic MDA-MB-231 breast cancer cells exposed to GNPs was observed. In these cells significant radiosensitisation occurred in normoxia and moderate hypoxia. However, in near anoxia no significant sensitisation occurred.

Conclusions: GNP uptake occurred in hypoxic conditions, causing radiosensitisation in moderate, but not extreme hypoxia in a breast cancer cell line. These findings may be important for the development of GNPs for cancer therapy.