A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples

The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED) designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes

DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma

The significance of chromosome 3p gene alterations in lung cancer is poorly understood. This study set out to investigate promoter methylation in the deleted in lung and oesophageal cancer 1 (DLEC1), MLH1 and other 3p genes in 239 non-small cell lung carcinomas (NSCLC). DLEC1 was methylated in 38.7%, MLH1 in 35.7%, RARβ in 51.7%, RASSF1A in 32.4% and BLU in 35.3% of tumours. Any two of the gene alterations were associated with each other except RARβ. DLEC1 methylation was an independent marker of poor survival in the whole cohort (P=0.025) and in squamous cell carcinoma (P=0.041). MLH1 methylation was also prognostic, particularly in large cell cancer (P=0.006). Concordant methylation of DLEC1/MLH1 was the strongest independent indicator of poor prognosis in the whole cohort (P=0.009). However, microsatellite instability and loss of MLH1 expression was rare, suggesting that MLH1 promoter methylation does not usually lead to gene silencing in lung cancer. This is the first study describing the prognostic value of DLEC1 and MLH1 methylation in NSCLC. The concordant methylation is possibly a consequence of a long-range epigenetic effect in this region of chromosome 3p, which has recently been described in other cancers

Towards a Framework for Understanding Fairtrade Purchase Intention in the Mainstream Environment of Supermarkets

© 2014, Springer Science+Business Media Dordrecht. Despite growing interest in ethical consumer behaviour research, ambiguity remains regarding what motivates consumers to purchase ethical products. While researchers largely attribute the growth of ethical consumerism to an increase in ethical consumer concerns and motivations, widened distribution (mainstreaming) of ethical products, such as fairtrade, questions these assumptions. A model that integrates both individual and societal values into the theory of planned behaviour is presented and empirically tested to challenge the assumption that ethical consumption is driven by ethical considerations alone. Using data sourced from fairtrade shoppers across the UK, structural equation modelling suggests that fairtrade purchase intention is driven by both societal and self-interest values. This dual value pathway helps address conceptual limitations inherent in the underlying assumptions of existing ethical purchasing behaviour m odels and helps advance understanding of consumers’ motivation to purchase ethical products

The one dimensional Kondo lattice model at partial band filling

The Kondo lattice model introduced in 1977 describes a lattice of localized magnetic moments interacting with a sea of conduction electrons. It is one of the most important canonical models in the study of a class of rare earth compounds, called heavy fermion systems, and as such has been studied intensively by a wide variety of techniques for more than a quarter of a century. This review focuses on the one dimensional case at partial band filling, in which the number of conduction electrons is less than the number of localized moments. The theoretical understanding, based on the bosonized solution, of the conventional Kondo lattice model is presented in great detail. This review divides naturally into two parts, the first relating to the description of the formalism, and the second to its application. After an all-inclusive description of the bosonization technique, the bosonized form of the Kondo lattice hamiltonian is constructed in detail. Next the double-exchange ordering, Kondo singlet formation, the RKKY interaction and spin polaron formation are described comprehensively. An in-depth analysis of the phase diagram follows, with special emphasis on the destruction of the ferromagnetic phase by spin-flip disorder scattering, and of recent numerical results. The results are shown to hold for both antiferromagnetic and ferromagnetic Kondo lattice. The general exposition is pedagogic in tone.Comment: Review, 258 pages, 19 figure

van der Waals Interactions in Material Modelling

Van der Waals (vdW) interactions stem from electronic zero-point fluctuations and are often critical for the correct description of structure, stability, and response properties of molecules and materials, including biomolecules, nanomaterials, and material interfaces. Here, we give a conceptual as well as mathematical overview of the current state of modeling vdW interactions,focusing in particular on the consequences of different approximations for practical applications. We present a systematic classification of approximate first-principles models based on the adiabatic-connection fluctuation-dissipation theorem, namely the nonlocal density functionals, interatomic methods, and methods based on the random-phase approximation. The applicability of these methods to different types of materials and material properties is discussed in connection with availability of theoretical and experimental benchmarks. We conclude with a roadmap of the open problems that remain to be solved to construct a universal, efficient, and accurate vdW model for realistic material modeling

Canonical BMP–Smad Signalling Promotes Neurite Growth in Rat Midbrain Dopaminergic Neurons

Ventral midbrain (VM) dopaminergic (DA) neurons project to the dorsal striatum via the nigrostriatal pathway to regulate voluntary movements, and their loss leads to the motor dysfunction seen in Parkinson’s disease (PD). Despite recent progress in the understanding of VM DA neurogenesis, the factors regulating nigrostriatal pathway development remain largely unknown. The bone morphogenetic protein (BMP) family regulates neurite growth in the developing nervous system and may contribute to nigrostriatal pathway development. Two related members of this family, BMP2 and growth differentiation factor (GDF)5, have neurotrophic effects, including promotion of neurite growth, on cultured VM DA neurons. However, the molecular mechanisms regulating their effects on DA neurons are unknown. By characterising the temporal expression profiles of endogenous BMP receptors (BMPRs) in the developing and adult rat VM and striatum, this study identified BMP2 and GDF5 as potential regulators of nigrostriatal pathway development. Furthermore, through the use of noggin, dorsomorphin and BMPR/Smad plasmids, this study demonstrated that GDF5- and BMP2-induced neurite outgrowth from cultured VM DA neurons is dependent on BMP type I receptor activation of the Smad 1/5/8 signalling pathway