Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays

We have combined molecular beacon (MB) probes with barcoded metal nanowires to enable no-wash, sealed chamber, multiplexed detection of nucleic acids. Probe design and experimental parameters important in nanowire-based MB assays are discussed. Loop regions of 24 bases and 5 base pair stem regions in the beacon probes gave optimal performance. Our results suggest that thermodynamic predictions for secondary structure stability of solution-phase MB can guide probe design for nanowire-based assays. Dengue virus-specific probes with predicted solution-phase DeltaG of folding in 500 mM buffered NaCl of approximately -4 kcal/mol performed better than those with DeltaG > -2 or < -6 kcal/mol. Buffered 300-500 mM NaCl was selected after comparison of several buffers previously reported for similar types of assays, and 200-500 mM NaCl was found to be the optimal ionic strength for the hybridization temperatures (25 and 50 degrees C) and probe designs used here. Target binding to the surface as a function of solution concentration fit a Sips isotherm with Kd = 1.7 +/- 0.3 nM. The detection limit was approximately 100 pM, limited by incomplete quenching. Single base mismatches could be discriminated from fully complementary targets. Oligonucleotide target sequences specific for human immunodeficiency, hepatitis C, and severe acute respiratory viruses were assayed simultaneously in a no-wash, sealed chamber, multiplexed experiment in which each of three probe sequences was attached to a different pattern of encoded nanowires. Finally, we demonstrated that probe-coated nanowires retain their selectivity and sensitivity in a triplexed assay after storage for over 3 months.     

Photodissociation of the BrO radical using velocity map ion imaging: excited state dynamics and accurate D0(0)(BrO) evaluation

We have studied the photodissociation dynamics of expansion-cooled BrO radical both above (278-281.5 nm) and below (355 nm) the A (2)Pi(3/2) state threshold using velocity map ion imaging. A recently developed late-mixing flash pyrolytic reactor source was utilized to generate an intense BrO radical molecular beam. The relative electronic product branching ratios at 355 nm and from 278 to 281.5 nm were determined. We have investigated the excited state dynamics based on both the product branching and the photofragment angular distributions. We find that above the O((1)D(2)) threshold the contribution of the direct excitation to states other than the A (2)Pi(3/2) state and the role of curve crossing is considerably larger in BrO compared to that observed for ClO, in agreement with recent theoretical studies. The measurement of low velocity photofragments resulting from photodissociation just above the O((1)D(2)) threshold provides an accurate and direct determination of the A (2)Pi(3/2) state dissociation threshold of 35418+/-35 cm(-1), leading to a ground state bond energy of D(0)(0)(BrO)=55.9+/-0.1 kcal/mol.     

Morphology of Photopolymerized End-linked Poly(ethylene glycol) Hydrogels by Small Angle X-ray Scattering

Due to the biocompatibility of poly(ethylene glycol) (PEG), PEG-based hydrogels have attracted considerable interest for use as biomaterials in tissue engineering applications. In this work, we show that PEG-based hydrogels prepared by photopolymerization of PEG macromonomers functionalized with either acrylate or acrylamide end-groups generate networks with crosslink junctions of high functionality. Although the crosslink functionality is not well controlled, the resultant networks are sufficiently well ordered to generate a distinct correlation peak in the small angle x-ray scattering (SAXS) related to the distance between crosslink junctions within the PEG network. The crosslink spacing is a useful probe of the PEG chain conformation within the hydrogel and ranges from approximately 6 to 16 nm, dependent upon both the volume fraction of polymer and the molecular weight of the PEG macromonomers. The presence of a peak in the scattering of photopolymerized PEG networks is also correlated with an enhanced compressive modulus in comparison to PEG networks reported in the literature with much lower crosslink functionality that exhibit no scattering peak. This comparison demonstrates that the method used to link together PEG macromonomers has a critical impact on both the nanoscale structure and the macroscopic properties of the resultant hydrogel network.     

Phosphatidylcholines and -ethanolamines can be easily mistaken in phospholipid mixtures: a negative ion MALDI-TOF MS study with 9-aminoacridine as matrix and egg yolk as selected example

Phospholipids (PL) are increasingly analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). As in the case of polar molecules, however, the careful selection of the matrix is crucial for optimum results. 9-Aminoacridine (9-AA) was recently suggested as the matrix of choice to analyze PL mixtures because of (a) the improved sensitivity and (b) the reduction of suppression effects compared to other matrices. However, the distinction of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in the negative ion mode is obscured as PC is also detectable as –CH₃⁺ ion if 9-AA is used as matrix. This may result in the erroneous assignment of PC as a PE species. Using an organic extract from hen egg yolk as example it will be shown that the contribution of PC must be taken into consideration if the negative ion mass spectra are used to evaluate the fatty acyl compositions of PE mixtures. 9-AA can as well be used in hyphenated thin-layer chromatography (TLC)-MALDI-TOF MS where PC and PE are chromatographically well separated for unequivocal assignments.      

Linguistic contributions to speech-on-speech masking for native and non-native listeners: language familiarity and semantic content

This study examined whether speech-on-speech masking is sensitive to variation in the degree of similarity between the target and the masker speech. Three experiments investigated whether speech-in-speech recognition varies across different background speech languages (English vs Dutch) for both English and Dutch targets, as well as across variation in the semantic content of the background speech (meaningful vs semantically anomalous sentences), and across variation in listener status vis-a?-vis the target and masker languages (native, non-native, or unfamiliar). The results showed that the more similar the target speech is to the masker speech (e.g., same vs different language, same vs different levels of semantic content), the greater the interference on speech recognition accuracy. Moreover, the listener's knowledge of the target and the background language modulate the size of the release from masking. These factors had an especially strong effect on masking effectiveness in highly unfavorable listening conditions. Overall this research provided evidence that that the degree of target-masker similarity plays a significant role in speech-in-speech recognition. The results also give insight into how listeners assign their resources differently depending on whether they are listening to their first or second language.     

Large deviations principle for the cubic NLS equation

In this paper, we present a probabilistic study of rare phenomena of the cubic nonlinear Schrödinger equation on the torus in a weakly nonlinear setting. This equation has been used as a model to numerically study the formation of rogue waves in deep sea. Our results are twofold: first, we introduce a notion of criticality and prove a Large Deviations Principle (LDP) for the subcritical and critical cases. Second, we study the most likely initial conditions that lead to the formation of a rogue wave, from a theoretical and numerical point of view. Finally, we propose several open questions for future research.