A high-throughput and sensitive method to measure Global DNA Methylation: Application in Lung Cancer

<p>Abstract</p> <p>Background</p> <p>Genome-wide changes in DNA methylation are an epigenetic phenomenon that can lead to the development of disease. The study of global DNA methylation utilizes technology that requires both expensive equipment and highly specialized skill sets.</p> <p>Methods</p> <p>We have designed and developed an assay, <it>CpG</it>lobal, which is easy-to-use, does not utilize PCR, radioactivity and expensive equipment. <it>CpG</it>lobal utilizes methyl-sensitive restriction enzymes, HRP Neutravidin to detect the biotinylated nucleotides incorporated in an end-fill reaction and a luminometer to measure the chemiluminescence. The assay shows high accuracy and reproducibility in measuring global DNA methylation. Furthermore, <it>CpG</it>lobal correlates significantly with High Performance Capillary Electrophoresis (HPCE), a gold standard technology. We have applied the technology to understand the role of global DNA methylation in the natural history of lung cancer. World-wide, it is the leading cause of death attributed to any cancer. The survival rate is 15% over 5 years due to the lack of any clinical symptoms until the disease has progressed to a stage where cure is limited.</p> <p>Results</p> <p>Through the use of cell lines and paired normal/tumor samples from patients with non-small cell lung cancer (NSCLC) we show that global DNA hypomethylation is highly associated with the progression of the tumor. In addition, the results provide the first indication that the normal part of the lung from a cancer patient has already experienced a loss of methylation compared to a normal individual.</p> <p>Conclusion</p> <p>By detecting these changes in global DNA methylation, <it>CpG</it>lobal may have a role as a barometer for the onset and development of lung cancer.</p

Henipavirus RNA in African Bats

BACKGROUND: Henipaviruses (Hendra and Nipah virus) are highly pathogenic members of the family Paramyxoviridae. Fruit-eating bats of the Pteropus genus have been suggested as their natural reservoir. Human Henipavirus infections have been reported in a region extending from Australia via Malaysia into Bangladesh, compatible with the geographic range of Pteropus. These bats do not occur in continental Africa, but a whole range of other fruit bats is encountered. One of the most abundant is Eidolon helvum, the African Straw-coloured fruit bat. METHODOLOGY/PRINCIPAL FINDINGS: Feces from E. helvum roosting in an urban setting in Kumasi/Ghana were tested for Henipavirus RNA. Sequences of three novel viruses in phylogenetic relationship to known Henipaviruses were detected. Virus RNA concentrations in feces were low. CONCLUSIONS/SIGNIFICANCE: The finding of novel putative Henipaviruses outside Australia and Asia contributes a significant extension of the region of potential endemicity of one of the most pathogenic virus genera known in humans

Beyond equilibrium climate sensitivity

ISSN:1752-0908ISSN:1752-089

A review of ground-penetrating radar studies related to peatland stratigraphy with a case study on the determination of peat thickness in a northern boreal fen in Quebec, Canada

Ground-penetrating radar (GPR) is a non-intrusive geophysical observation method based on propagation and reflection of high-frequency electromagnetic waves in the shallow subsurface. The vertical cross-sectional images obtained allow the identification of thickness and lithologic horizons of different media, without destruction. Over the last decade, several studies have demonstrated the potential of GPR. This paper presents a review of recent GPR applications to peatlands, particularly to determine peat stratigraphy. An example study of acquisition and comparison of peatland soil thickness of a fen-dominated watershed located in the James Bay region of Quebec, using (1) a meter stick linked to a GPS RTK and (2) a GSSI GPR, is given. A coefficient of determination (r(2) ) of 56% was obtained between the ordinary krigings performed on data gathered using both techniques. Disparities occurred mainly in the vicinity of ponds which can be explained by the attenuation of GPR signal in open water. Despite these difficulties - the higher time required for analysis and the error margin - it seems more appropriate to use a GPR, instead of a graduated rod linked to a GPS, to measure the peat depths on a site like the one presented in this study. Manual measurements, which are user-dependent in the context of variable mineral substrate densities and with the presence of obstacles in the substrate, may be more subjective