Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes

The aim of this study was to develop new strategies for analyzing molecular signatures of disease states approaching real-time using single pair fluorescence resonance energy transfer (spFRET) to rapidly detect point mutations in unamplified genomic DNA. In addition, the detection process was required to discriminate between normal and mutant (minority) DNAs in heterogeneous populations. The discrimination was carried out using allele-specific primers, which flanked the point mutation in the target gene and were ligated using a thermostable ligase enzyme only when the genomic DNA carried this mutation. The allele-specific primers also carried complementary stem structures with end-labels (donor/acceptor fluorescent dyes, Cy5/Cy5.5, respectively), which formed a molecular beacon following ligation. We coupled ligase detection reaction (LDR) with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the molecular beacon probes formed upon ligation. LDR-spFRET provided the necessary specificity and sensitivity to detect single-point mutations in as little as 600 copies of human genomic DNA directly without PCR at a level of 1 mutant per 1000 wild type sequences using 20 LDR thermal cycles. We also demonstrate the ability to rapidly discriminate single base differences in the K-ras gene in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA (600 copies). Real-time LDR-spFRET detection of point mutations in the K-ras gene was accomplished in PMMA microfluidic devices using sheath flows.     

Slow Light Excitation in Tapered 1D Photonic Crystals: Theory

Slow light (SL) states corresponding to wavelength regions near the bandgap edge of grated structures are known to show strong field enhancement. Such states may be excited efficiently by well-optimized adiabatic transitions in grated structures, e.g., by slowly turning on the modulation depth. To study adiabatic excitations, a detailed research in 1D is performed to obtain insight into the relation between the device parameters and properties like enhancement and modal reflection. The results enable the design of an adiabatic device for efficient excitation of SL states in 1D. The effect of small wavelength variations as well as small fluctuations in the modulation depth of the grating has been investigated.     

Analytic approach to dielectric optical bent slab waveguides

A rigorous classical analytic frequency domain model of confined optical wave propagation along 2D bent slab waveguides and curved dielectric interfaces is investigated, based on a piecewise ansatz for bend mode profiles in terms of Bessel and Hankel functions. This approach provides a clear picture of the behaviour of bend modes, concerning their decay for large radial arguments or effects of varying bend radius. Fast and accurate routines are required to evaluate Bessel functions with large complex orders and large arguments. Our implementation enabled detailed studies of bent waveguide properties, including higher order bend modes and whispering gallery modes, their interference patterns, and issues related to bend mode normalization and orthogonality properties.     

Time-resolved X-ray spectroscopy of hot spots in an X-pinch

The plasma parameters in hot spots of an X-pinch are determined by using time-resolved data from X-ray spectroscopy in experiments on the implosion of crossed Ti wires in the XP device with a current of 480 kA and pulse duration of 100 ns. The electron densities and temperatures calculated from these data are in the ranges (0.8–3)×10²³cm^–3 and 1–2.5 keV, respectively. An analysis performed shows that the plasma processes are highly nonequilibrium.     

An infrared renormalization group limit cycle in QCD

We use effective field theories to show that small increases in the up and down quark masses would move QCD very close to the critical renormalization group trajectory for an infrared limit cycle in the three-nucleon system. We conjecture that QCD can be tuned to the critical trajectory by adjusting the quark masses independently. At the critical values of the quark masses, the binding energies of the deuteron and its spin-singlet partner would be tuned to zero and the triton would have infinitely many excited states with an accumulation point at the 3-nucleon threshold. The ratio of the binding energies of successive states would approach a universal constant that is close to 515.     

One-dimensional PtO2 at Pt steps: formation and reaction with CO

Using core-level spectroscopy and density functional theory we show that a one-dimensional (1D) oxide structure forms at the steps of the Pt(332) surface after exposure. The 1D oxide is found to be stable in an oxygen pressure range, where bulk oxides are only metastable, and is therefore argued to be a precursor to the Pt oxidation. As an example of the consequences of such a precursor exclusively present at the steps, we investigate the reaction of CO with oxygen covered Pt(332). Albeit more strongly bound, the oxidic oxygen is found to react more easily with CO than oxygen chemisorbed on the Pt terraces.     

Structure and reactivity of surface oxides on Pt(110) during catalytic CO oxidation

We present the first structure determination by surface x-ray diffraction during the restructuring of a model catalyst under reaction conditions, i.e., at high pressure and high temperature, and correlate the restructuring with a change in catalytic activity. We have analyzed the Pt(110) surface during CO oxidation at pressures up to 0.5 bar and temperatures up to 625 K. Depending on the pressure ratio, we find three well-defined structures: namely, (i) the bulk-terminated Pt(110) surface, (ii) a thin, commensurate oxide, and (iii) a thin, incommensurate oxide. The commensurate oxide only appears under reaction conditions, i.e., when both and CO are present and at sufficiently high temperatures. Density functional theory calculations indicate that the commensurate oxide is stabilized by carbonate ions (CO3(2-)). Both oxides have a substantially higher catalytic activity than the bulk-terminated Pt surface.