Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

BACKGROUND: Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. RESULTS: We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC) in peripheral blood mononuclear cells); the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. CONCLUSION: Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting

Tunneling of massive and charged particles from noncommutative Reissner-Nordstr\"{o}m black hole

Massive charged and uncharged particles tunneling from commutative Reissner-Nordstrom black hole horizon has been studied with details in literature. Here, by adopting the coherent state picture of spacetime noncommutativity, we study tunneling of massive and charged particles from a noncommutative inspired Reissner-Nordstrom black hole horizon. We show that Hawking radiation in this case is not purely thermal and there are correlations between emitted modes. These correlations may provide a solution to the information loss problem. We also study thermodynamics of noncommutative horizon in this setup.Comment: 10 pages, 2 figure

Background field quantization and non-commutative Maxwell theory

We quantize non-commutative Maxwell theory canonically in the background field gauge for weak and slowly varying background fields. We determine the complete basis for expansion under such an approximation. As an application, we derive the Wigner function which determines the leading order high temperature behavior of the perturbative amplitudes of non-commutative Maxwell theory. To leading order, we also give a closed form expression for the distribution function for the non-commutative $U (1)$ gauge theory at high temperature.Comment: 9 pages, title slightly modified, to appear in Physics Letters

Interleukin-7 deficiency in rheumatoid arthritis: consequences for therapy-induced lymphopenia

We previously demonstrated prolonged, profound CD4+ T-lymphopenia in rheumatoid arthritis (RA) patients following lymphocyte-depleting therapy. Poor reconstitution could result either from reduced de novo T-cell production through the thymus or from poor peripheral expansion of residual T-cells. Interleukin-7 (IL-7) is known to stimulate the thymus to produce new T-cells and to allow circulating mature T-cells to expand, thereby playing a critical role in T-cell homeostasis. In the present study we demonstrated reduced levels of circulating IL-7 in a cross-section of RA patients. IL-7 production by bone marrow stromal cell cultures was also compromised in RA. To investigate whether such an IL-7 deficiency could account for the prolonged lymphopenia observed in RA following therapeutic lymphodepletion, we compared RA patients and patients with solid cancers treated with high-dose chemotherapy and autologous progenitor cell rescue. Chemotherapy rendered all patients similarly lymphopenic, but this was sustained in RA patients at 12 months, as compared with the reconstitution that occurred in cancer patients by 3–4 months. Both cohorts produced naïve T-cells containing T-cell receptor excision circles. The main distinguishing feature between the groups was a failure to expand peripheral T-cells in RA, particularly memory cells during the first 3 months after treatment. Most importantly, there was no increase in serum IL-7 levels in RA, as compared with a fourfold rise in non-RA control individuals at the time of lymphopenia. Our data therefore suggest that RA patients are relatively IL-7 deficient and that this deficiency is likely to be an important contributing factor to poor early T-cell reconstitution in RA following therapeutic lymphodepletion. Furthermore, in RA patients with stable, well controlled disease, IL-7 levels were positively correlated with the T-cell receptor excision circle content of CD4+ T-cells, demonstrating a direct effect of IL-7 on thymic activity in this cohort

GATA-2 and GATA-3 regulate trophoblast-specific gene expression in vivo.

We previously demonstrated that the zinc finger transcription factors GATA-2 and GATA-3 are expressed in trophoblast giant cells and that they regulate transcription from the mouse placental lactogen I gene promoter in a transfected trophoblast cell line. We present evidence here that both of these factors regulate transcription of the placental lactogen I gene, as well as the related proliferin gene, in trophoblast giant cells in vivo. Placentas lacking GATA-3 accumulate placental lactogen I and proliferi

Non-Perturbative String Equations for Type 0A

Well-defined non-perturbative formulations of the physics of string theories, sometimes with D-branes present, were identified over a decade ago, from a careful study of double scaled matrix models. Following recent work which recasts some of those old results in the context of type 0 string theory, a study is made of a much larger family of models, which are proposed as type 0A models of the entire superconformal minimal series coupled to gravity. This gives many further examples of important physical phenomena, including non-perturbative descriptions of transitions between D-branes and fluxes, tachyon condensation, and holography. In particular, features of a large family of non-perturbatively stable string equations are studied, and results are extracted which pertain to type 0A string theory, with D-branes and fluxes, in this large class of backgrounds. For the entire construction to work, large parts of the spectrum of the supergravitationally dressed superconformal minimal models and that of the gravitationally dressed bosonic conformal minimal models must coincide, and it is shown how this happens. The example of the super-dressed tricritical Ising model is studied in some detail.Comment: 29 pages LaTe

Two-Dimensional Unoriented Strings And Matrix Models

We investigate unoriented strings and superstrings in two dimensions and their dual matrix quantum mechanics. Most of the models we study have a tachyon tadpole coming from the RP^2 worldsheet which needs to be cancelled by a renormalization of the worldsheet theory. We find evidence that the dual matrix models describe the renormalized theory. The singlet sector of the matrix models is integrable and can be formulated in terms of fermions moving in an external potential and interacting via the Calogero-Moser potential. We show that in the double-scaling limit the latter system exhibits particle-hole duality and interpret it in terms of the dual string theory. We also show that oriented string theories in two dimensions can be continuously deformed into unoriented ones by turning on non-local interactions on the worldsheet. We find two unoriented superstring models for which only oriented worldsheets contribute to the S-matrix. A simple explanation for this is found in the dual matrix model.Comment: 36 pages, harvmac, 2 eps figure

Scattered Results in 2D String Theory

The nonperturbative $1\to N$ tachyon scattering amplitude in 2D type 0A string theory is computed. The probability that $N$ particles are produced is a monotonically decreasing function of $N$ whenever $N$ is large enough that statistical methods apply. The results are compared with expectations from black hole thermodynamics.Comment: 22 pages, 5 figures, harvmac. v2: minor comments added, typos correcte

D-branes at multicritical points

The moduli space of c=1 conformal field theories in two dimensions has a multicritical point, where a circle theory is equivalent to an orbifold theory. We analyse all the conformal branes in both descriptions of this theory, and find convincing evidence that the full brane spectrum coincides. This shows that the equivalence of the two descriptions at this multicritical point extends to the boundary sector. We also perform the analogous analysis for one of the multicritical points of the N=1 superconformal field theories at c=3/2. Again the brane spectra are identical for both descriptions, however the identification is more subtle.Comment: 32 pages, 2 figure

Comments on 2D Type IIA String and Matrix Model

We consider a type IIA-like string theory with RR-flux in two dimension and propose its matrix model dual. This string theory describes a Majorana fermion in the two dimensional spacetime. We also discuss its scattering amplitudes both in the world-sheet theory and in the matrix model.Comment: 21 pages, Harvmac, to appear in JHEP, relation to 2d superstring constructed by D. Kutasov hep-th/9110041 is clarifie