Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA

Atmospheric pressure (AP) MALDI has been combined with Fourier transform mass spectrometry (FTMS) to obtain the unambiguous characterization of RNA samples modified by solvent accessibility reagents used in structural studies of RNA and protein-RNA complexes. The formation of cation adducts typical of MS analysis of nucleic acids was effectively reduced by extensive washing of the anionic analytes retained onto the probe surface by strong interactions with a cationic layer of poly(diallyldimethylammonium chloride) (PADMAC). This rapid desalting procedure allowed for the detection of DNA and RNA samples in high femtomole quantities distributed over a 4 x 4 mm sample well. AP MALDI-FTMS was shown to provide high-resolution spectra for analytes as large as approximately 6.4 kDa with little or no evidence of metastable decomposition. The absence of significant metastable decay observed for precursor ions selected for tandem experiments offered a further measure of the low energy content typical of ions generated by AP MALDI. This feature proved to be very beneficial in the characterization of chemically modified RNA samples, which become particularly prone to base losses upon alkylation. The high resolution offered by FTMS enabled the application of a data-reduction algorithm capable of rejecting any signal devoid of plausible isotopic distribution, thus facilitating the analysis of complex analyte mixtures produced by nuclease treatment of RNA substrates. Proper selection of nucleases and digestion conditions can ensure the production of hydrolytic fragments of manageable size, which could extend the range of applicability of this bottom-up strategy to the structural investigation of very large RNA and protein-RNA complexes.     

Amplifying fluorescent polymer sensors for the explosives taggant 2,3-dimethyl-2,3-dinitrobutane (DMNB)

Structural and electronic effects on the efficiency of DMNB detection with fluorescent conjugated polymers are described.     

New synthesis of (Z,E)-2,7-bis(4-cyanobenzylidene)cycloheptan-1-one under stereospecific constraints induced by host-guest interactions

A selective, efficient, and fast access to (Z,E)-2,7-bis(4-cyanobenzylidene)cycloheptan-1-one (BCBCH), precursor of the synthetic antagonist of tissue-plasminogen activator (t-PA), is reported using a solid/solid aldolisation-crotonisation reaction on a supramolecular complex under microwave irradiation. The underlying mechanism is investigated from the crystal structure of the intermediate host-guest complex formed between permethylated gamma-cyclodextrin and (Z)-2-(4-cyanobenzylidene)cycloheptan-1-one.     

Feasibility of diffusion-NMR surface-to-volume measurements tested by calculations and computer simulations

It has been demonstrated previously that the surface-to-volume ratio S/V can be determined from the derivative of the time-dependent diffusion coefficient D(t), in the limit t --> 0. Several questions arise concerning the practicality of determining S/V by NMR. In particular, how large are the errors generated by (1) working outside the t --> 0 limit and (2) measuring D outside the b --> 0 limit, both for narrow and full-width gradient pulses? Here b is gamma2G2delta2Delta for narrow pulses and gamma2G2t3/12 for broad pulses. These questions are addressed by random-walk computer simulations and numerical calculations in geometries relevant to small-airways of lung. The results demonstrate that one can work well outside the t --> 0 and b --> 0 limits, provided 10-20% accuracy in the measured S/V is sufficient. Emphasis is placed on the useful range of times t for which NMR determinations of lung S/V are feasible.     

Hartmann wave-front measurement at 13.4 nm with lambdaEUV/120 accuracy

We report, for the first time to our knowledge, experimental demonstration of wave-front analysis via the Hartmann technique in the extreme ultraviolet range. The reference wave front needed to calibrate the sensor was generated by spatially filtering a focused undulator beam with 1.7- and 0.6-microm-diameter pinholes. To fully characterize the sensor, accuracy and sensitivity measurements were performed. The incident beam's wavelength was varied from 7 to 25 nm. Measurements of accuracy better than lambdaEUV/120 (0.11 nm) were obtained at lambdaEUV = 13.4 nm. The aberrations introduced by an additional thin mirror, as well as wave front of the spatially unfiltered incident beam, were also measured.     

perpendicular organization of macromolecules: synthesis and alignment studies of a soluble poly(iptycene)

We describe herein a polymeric material that prefers to align perpendicular to a stretch-aligned polymer host in the solid state. Poly(iptycene) poly-1 was synthesized from monomer 1 under hyperbaric techniques via a Diels-Alder polymerization. Polarized excitation spectra of the anthracene end groups in this material in a stretch-aligned, solution-cast poly(vinyl chloride) (PVC) film showed that the poly(iptycene) prefers to align normal (counter aspect ratio) to the stretching direction of the PVC. This is explained by a "threading" mechanism, whereby the PVC intercalates through the internal free volume presented by poly-1, similar to effects observed in small molecule iptycenes under similar conditions.     

Cyclic maps in rational homotopy theory

The notion of a cyclic map g:AX is a natural generalization of a Gottlieb element in _n(X). We investigate cyclic maps from a rational homotopy theory point of view. We show a number of results for rationalized cyclic maps which generalize well-known results on the rationalized Gottlieb groups.Mathematics Subject Classification (2000): 55P62, 55Q05     

D.C. Versus Copositive Bounds for Standard QP

The standard quadratic program (QPS) is min_xεΔx^TQx, where is the simplex Δ = {x ⩽ 0 ∣ ∑_i=1ⁿ x_i = 1}. QPS can be used to formulate combinatorial problems such as the maximum stable set problem, and also arises in global optimization algorithms for general quadratic programming when the search space is partitioned using simplices. One class of ‘d.c.’ (for ‘difference between convex’) bounds for QPS is based on writing Q=S−T, where S and T are both positive semidefinite, and bounding x^T Sx (convex on Δ) and −x^Tx (concave on Δ) separately. We show that the maximum possible such bound can be obtained by solving a semidefinite programming (SDP) problem. The dual of this SDP problem corresponds to adding a simple constraint to the well-known Shor relaxation of QPS. We show that the max d.c. bound is dominated by another known bound based on a copositive relaxation of QPS, also obtainable via SDP at comparable computational expense. We also discuss extensions of the d.c. bound to more general quadratic programming problems. For the application of QPS to bounding the stability number of a graph, we use a novel formulation of the Lovasz ϑ number to compare ϑ, Schrijver’s ϑ′, and the max d.c. bound.     

Septal repair implants: evaluation of magnetic resonance imaging safety at 3 T

Specialized implants are used for transcatheter closure of septal defects, including atrial and ventricular septal defects, and patent foramen ovale. These metallic devices may pose a risk to patients undergoing magnetic resonance imaging (MRI) procedures especially if performed at 3 T. Therefore, this investigation evaluated MRI safety at 3 T for septal repair implants (CardioSEAL Septal Repair Implant and STARFlex Septal Repair Implant, NMT Medical, Boston, MA, USA) by characterizing magnetic field interactions, heating and artifacts. These implants exhibited minor magnetic field interactions; heating was not excessive (+0.5°C); and artifacts will only create a problem if the area of interest is in the same area as or near these devices. Thus, the findings indicated that it would be safe for a patient with these implants to undergo MRI at 3 T or lower. Importantly, because of the minor magnetic field interactions, MRI may be performed immediately after implantation.