DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight

Alterations in cytosine-5 DNA methylation are frequently observed in most types of human cancer. Although assays utilizing PCR amplification of bisulfite-converted DNA are widely employed to analyze these DNA methylation alterations, they are generally limited in throughput capacity, detection sensitivity, and or resolution. Digital PCR, in which a DNA sample is analyzed in distributive fashion over multiple reaction chambers, allows for enumeration of discrete template DNA molecules, as well as sequestration of non-specific primer annealing templates into negative chambers, thereby increasing the signal-to-noise ratio in positive chambers. Here, we have applied digital PCR technology to bisulfite-converted DNA for single-molecule high-resolution DNA methylation analysis and for increased sensitivity DNA methylation detection. We developed digital bisulfite genomic DNA sequencing to efficiently determine single-basepair DNA methylation patterns on single-molecule DNA templates without an interim cloning step. We also developed digital MethyLight, which surpasses traditional MethyLight in detection sensitivity and quantitative accuracy for low quantities of DNA. Using digital MethyLight, we identified single-molecule, cancer-specific DNA hypermethylation events in the CpG islands of RUNX3, CLDN5 and FOXE1 present in plasma samples from breast cancer patients

Effects of 126 dimensional Higgs scalar on Bottom-Tau unification and quasi-infrared fixed point

In the presence of ${\bf 126 + \bar{126}}$ Higgs multiplets in a SO(10) theory, the fermion masses get contributions from an induced vacuum expectation value (VEV) of a $SU(2)_L$ doublet residing in ${\bf 126}$ which differentiates between quarks and leptons by a relative sign leading to a significant correction to the prediction of the mass ratio of the bottom quark and the tau lepton for ranges of the mass of this extra doublet. We perform a two-loop renormalization group analysis of the minimal version of the one-step supersymmetric SO(10) model to display this and re-calculate the corrections to the top quark mass in the presence of such an induced VEV. We show that these effects make the infra-red fixed point scenario consistent with experimental results.Comment: revised version with same conclusions. To appear in Phys. Rev.

Intermediate Scales in SUSY SO(10), b-\tau unification and Hot Dark Matter Neutrinos

Considerations of massive neutrinos, baryogenesis as well as fermion mass textures in the grand unified theory framework provide strong motivations for supersymmetric(SUSY) SO(10) as the theory beyond the standard model. If one wants to simultaneously solve the strong CP problem via the Peccei-Quinn mechanism, the most natural way to implement it within the framework of the SUSY SO(10) model is to have an intermediate scale ($v_{BL}$) (corresponding to B-L symmetry breaking) around the invisible axion scale of about 10$^{11}$ - 10$^{12}$ GeV. Such a scale is also desirable if $\nu_{\tau}$ is to constitute the hot dark matter (HDM) of the universe. In this paper, we discuss examples of superstring inspired SUSY SO(10) models with intermediate scales that are consistent with the low energy precision measurements of the standard model gauge couplings. The hypothesis of $b-\tau$ unification which is a successful prediction of many grand unified theories is then required of these models and the resulting prediction of $b$-quark mass is used as a measure of viability of these schemes. Detailed analysis of a model with a $v_{BL}\simeq 10^{11}$ GeV, which satisfies both the requirements of invisible axion and $\nu_{\tau}$ as HDM is presented and shown to lead to $m_b\simeq 4.9$ GeV in the one-loop approximation.Comment: Latex file; 20 pages; Four figures available on reques

Refined brain tumor diagnostics and stratified therapies: the requirement for a multidisciplinary approach

Individualized therapies are popular current concepts in oncology and first steps towards stratified medicine have now been taken in neurooncology through implementation of stratified therapeutic approaches. Knowledge about the molecular basis of brain tumors has expanded greatly in recent years and a few molecular alterations are studied routinely because of their clinical relevance. However, no single targeted agent has yet been fully approved for the treatment of glial brain tumors. In this review, we argue that multidisciplinary and integrated approaches are essential for translational research and the development of new treatments for patients with malignant gliomas, and we present a conceptual framework in which to place the components of such an interdisciplinary approach. We believe that this ambitious goal can be best realized through strong cooperation of brain tumor centers with local hospitals and physicians; such an approach enables close dialogue between expert subspecialty clinicians and local therapists to consider all aspects of this increasingly complex set of diseases