Nucleation at Finite Temperature: A Gauge-Invariant Perturbative Framework.

We present a gauge-invariant framework for bubble nucleation in theories with radiative symmetry breaking at high temperature. As a procedure, this perturbative framework establishes a practical, gauge-invariant computation of the leading order nucleation rate, based on a consistent power counting in the high-temperature expansion. In model building and particle phenomenology, this framework has applications such as the computation of the bubble nucleation temperature and the rate for electroweak baryogenesis and gravitational wave signals from cosmic phase transitions.

Thermodynamics of a Two-Step Electroweak Phase Transition.

New field content beyond that of the standard model of particle physics can alter the thermal history of electroweak symmetry breaking in the early Universe. In particular, the symmetry breaking may have occurred through a sequence of successive phase transitions. We study the thermodynamics of such a scenario in a real triplet extension of the standard model, using nonperturbative lattice simulations. Two-step electroweak phase transition is found to occur in a narrow region of allowed parameter space with the second transition always being first order. The first transition into the phase of nonvanishing triplet vacuum expectation value is first order in a non-negligible portion of the two-step parameter space. A comparison with two-loop perturbative calculation is provided and significant discrepancies with the nonperturbative results are identified.

Nonperturbative Analysis of the Electroweak Phase Transition in the Two Higgs Doublet Model.

We perform a nonperturbative study of the electroweak phase transition (EWPT) in the two Higgs doublet model (2HDM) by deriving a dimensionally reduced high-temperature effective theory for the model, and matching to known results for the phase diagram of the effective theory. We find regions of the parameter space where the theory exhibits a first-order phase transition. In particular, our findings are consistent with previous perturbative results suggesting that the primary signature of a first-order EWPT in the 2HDM is m_{A_{0}}>m_{H_{0}}+m_{Z}.

Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity.

Here we provide the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly similar RNA variants, a reverse-transcriptase primer whose sequence matches a specific variant selectively primes only that variant, whereas mismatch priming to the alternative variant is suppressed by virtue of hybridization and subsequent extension of the perfectly matched ExBP on that alternative variant template to form a cDNA-RNA hybrid. This hybrid will render the alternative RNA template unavailable for mismatch priming initiated by the specific primer in a hot-start protocol of reverse transcription when the temperature decreases to a level where such mismatch priming could occur. The ExBP-based reverse transcription assay detected BRAF and KRAS mutations in at least 1000-fold excess of wild-type RNA and detection was linear over a 4-log dynamic range. This novel strategy not only reveals the presence or absence of rare mutations with an exceptionally high selectivity, but also provides a convenient tool for accurate determination of RNA variants in different settings, such as quantification of allele-specific expression.

Targeted gene-expression analysis by genome-controlled reverse transcription-PCR.

BACKGROUND: For gene-expression analysis, which is anticipated to play an important role in classification of tumors and premalignant conditions, PCR-based quantitative assays must have increased diagnostic quantitative accuracy and reproducibility and enable analysis of gene expression in formalin-fixed paraffin-embedded (FFPE) tissue samples. METHODS: We developed a reverse transcription-PCR-based quantitative assay that modifies the cDNA sequence to increase the melting temperature of short (56-64 bp) PCR amplicons, enabling their quantification in-tube by homogeneous melting-curve analysis. We used this method to analyze the expression of 8 genes, 7 potential colon cancer markers, and 1 control in samples obtained from 3 colon carcinoma cell lines, endoscopic biopsy from 8 patients undergoing gastroscopy for Barrett esophagus, and archival FFPE and frozen tissue from 20 patients who underwent surgery for colon carcinoma. RESULTS: The detection limit of the assay, when optimized for FFPE samples, was 100 copies of cDNA, and the dynamic range was 3 orders of magnitude. A prototype assay containing a panel of 8 genes displayed good reproducibility compared with the commercially available TaqMan assay (interassay CVs, 5%-20% vs 7%-43%, respectively). Gene-expression analysis was performed successfully in 26 (96%) of 27 endoscopic biopsy specimens, 30 (86%) of 35 archival FFPE samples, and 20 (100%) of 20 archival frozen samples. CONCLUSIONS: This new technology combines the reproducibility of competitive PCR with accurate quantitative detection by in-tube melting-curve analysis, enabling efficient analysis of mRNA profiles in samples with small numbers of cells or small amounts of tissue, as well as in archival FFPE tissues.