Helium atom scattering from potassium tantalate/niobate(001) surfaces.

The results of He atom scattering experiments on KTa0.48Nb0.52O3(001) surfaces are presented and compared with similar experiments on mixed potassium tantalate/niobate perovskites with lower concentrations of Nb. The results are puzzling, unique and intriguing. Angular distributions of the He scattering intensities (the He surface diffraction pattern) are found to be very similar to those obtained from targets with lower Nb fractions. However, drift spectra (the intensity of the He specular reflection as a function of the He wave vector) are not. Whereas the drift spectra in the 〈10〉 azimuth do resemble those of the 0, 6 and 10% Nb fraction targets, in the 〈11〉 azimuth they are more similar to the strange drift spectra found from the 30% Nb-doped targets. Most intriguing are the surface temperature scans (the He specular intensity as a function of the target surface temperature); for they are quite distinct from those with lower Nb fractions. Finally, the inelastic He scattering experiments provide phonon dispersion results that are similar in most respects to those found for the lower Nb level samples. In particular, the most prominent feature is an Einstein-like mode at about 13.5 meV which spans the entire surface Brillouin zone in both 〈10〉 and 〈11〉 azimuths.

Organic Composomes as Supramolecular Aptamers.

Information contained in the sequences of biological polymers such as DNA and protein is crucial to determining their function. Lipids are not generally thought of as information-containing molecules. However, from a supramolecular perspective, the number of possible combinations of lipids in a mixture is comparable to the complexity of DNA or proteins. Here, we test the idea that an organic composome can exhibit molecular recognition. We use water/octanol as a model two-phase system and investigate the effect of organic solutes in different combinations in the organic phase on selective partitioning of two water-soluble dyes (Brilliant Blue FCF and Allura Red AC) from the aqueous phase into the organic phase. We found that variation in the concentration of the surfactant cetyltrimethylamonium bromide (CTAB) in the octanol phase alone was sufficient to cause a switch in selectivity, with low CTAB concentrations being selective for the red dye and high CTAB concentrations being selective for the blue dye. Other organic components were added to the organic phase to introduce molecular diversity into the composome and directed evolution was used to optimize the relative concentrations of the solutes. An improvement of selective partitioning in the heterogeneous system over the pure CTAB solution was observed. The results indicate that supramolecular composomes are sufficient for molecular recognition processes in a way analogous to nucleic acid aptamers.

Nonmonotonic DNA-length-dependent mobility in pluronic gels.

Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO_{100}PO_{70}EO_{100}) and pluronic P123 (EO_{20}PO_{70}EO_{20}). The 20-3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles. Brownian dynamics (BD) simulations with short-ranged intra-DNA hydrodynamic interactions were performed to numerically calculate the length-dependent mobility in pluronic lattices. The rising and falling trends, as well as the oscillations of mobility, were captured by the coarse-grained BD simulations. Molecular dynamics simulations in pluronic F127, with explicitly modeled micelle coronas, justified that the hydrodynamic interactions mediated by the complex fluid of hydrated poly(ethylene oxide) are a possible reason for the initial rise of mobility with DNA length.

Quantification of Protein-Induced Membrane Remodeling Kinetics In Vitro with Lipid Multilayer Gratings.

The dynamic self-organization of lipids in biological systems is a highly regulated process that enables the compartmentalization of living systems at micro- and nanoscopic scales. Consequently, quantitative methods for assaying the kinetics of supramolecular remodeling such as vesicle formation from planar lipid bilayers or multilayers are needed to understand cellular self-organization. Here, a new nanotechnology-based method for quantitative measurements of lipid-protein interactions is presented and its suitability for quantifying the membrane binding, inflation, and budding activity of the membrane-remodeling protein Sar1 is demonstrated. Lipid multilayer gratings are printed onto surfaces using nanointaglio and exposed to Sar1, resulting in the inflation of lipid multilayers into unilamellar structures, which can be observed in a label-free manner by monitoring the diffracted light. Local variations in lipid multilayer volume on the surface is used to vary substrate availability in a microarray format. A quantitative model is developed that allows quantification of binding affinity (K D ) and kinetics (kon and koff ). Importantly, this assay is uniquely capable of quantifying membrane remodeling. Upon Sar1-induced inflation of single bilayers from surface supported multilayers, the semicylindrical grating lines are observed to remodel into semispherical buds when a critical radius of curvature is reached.

The N-terminal region of wheat streak mosaic virus coat protein is a host- and strain-specific long-distance transport factor.

Understanding the genetics underlying host range differences among plant virus strains can provide valuable insights into viral gene functions and virus-host interactions. In this study, we examined viral determinants and mechanisms of differential infection of Zea mays inbred line SDp2 by Wheat streak mosaic virus (WSMV) isolates. WSMV isolates Sidney 81 (WSMV-S81) and Type (WSMV-T) share 98.7% polyprotein sequence identity but differentially infect SDp2: WSMV-S81 induces a systemic infection, but WSMV-T does not. Coinoculation and sequential inoculation of SDp2 with WSMV-T and/or WSMV-S81 did not affect systemic infection by WSMV-S81, suggesting that WSMV-T does not induce a restrictive defense response but that virus-encoded proteins may be involved in differential infection of SDp2. The viral determinant responsible for strain-specific host range was mapped to the N terminus of coat protein (CP) by systematic exchanges of WSMV-S81 sequences with those of WSMV-T and by reciprocal exchanges of CP or CP codons 1 to 74. Green fluorescent protein (GFP)-tagged WSMV-S81 with CP or CP residues 1 to 74 from WSMV-T produced similar numbers of infection foci and genomic RNAs and formed virions in inoculated leaves as those produced with WSMV-S81, indicating that failure to infect SDp2 systemically is not due to defects in replication, cell-to-cell movement, or virion assembly. However, these GFP-tagged hybrids showed profound defects in long-distance transport of virus through the phloem. Furthermore, we found that four of the five differing amino acids in the N terminus of CP between the WSMV-S81 and WSMV-T isolates were collectively involved in systemic infection of SDp2. Taken together, these results demonstrate that the N-terminal region of tritimoviral CP functions in host- and strain-specific long-distance movement.

Single molecule observation of DNA electrophoresis in pluronic f127.

Single molecule fluorescence microscopy is used to follow the motion of long DNA molecules undergoing electrophoresis in Pluronic gels. We find that for low fields most DNA molecules follow tortuous paths through the gels, at an angle up to 90 degrees from the field direction, while some molecules find paths along the field lines. In high fields, virtually all of the DNA molecules follow the field lines. In many cases, the molecules travel as compact coils with optically discernible radii smaller than in free solution. In other cases, the molecules extend and contract or travel in an extended configuration.

Surface structure of niobium-doped potassium tantalate KTa(1-x)Nb(x)O3 obtained from helium atom scattering studies.

Helium atom scattering experiments have been carried out on the (001) surface of KTaO(3) doped with 6, 10 and 15% Nb, produced by cleaving in situ single crystal samples. Several phenomena were observed through He atom diffraction measurements, including metastable behavior immediately after cleaving, reconstruction of a fraction of the surface to (2 × 1) domains after thermally cycling the surface temperatures, and the distribution of step heights of terraces at the surface as multiples of the unit cell dimension of ∼ 4 Å. In addition, a large hysteresis effect was found in the (100) azimuth in the variation of surface reflectivity with surface temperature; a much smaller hysteresis effect was found in the (110) azimuth. The hysteresis effects appear for all Nb doping concentrations. Finally, small oscillations in the specular and Bragg diffraction intensities near the surface temperature 80 K were also observed.

DNA electrophoresis in agarose gels: effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length.

Electrophoretic mobilities of DNA molecules ranging in length from 200 to 48 502 base pairs (bp) were measured in agarose gels with concentrations T = 0.5% to 1.3% at electric fields from E = 0.71 to 5.0 V/cm. This broad data set determines a range of conditions over which the new interpolation equation nu(L) = (beta+alpha(1+exp(-L/gamma))(-1) can be used to relate mobility to length with high accuracy. Mobility data were fit with chi(2) > 0.999 for all gel concentrations and fields ranging from 2.5 to 5 V/cm, and for lower fields at low gel concentrations. Analyses using so-called reptation plots (Rousseau, J., Drouin, G., Slater, G. W., Phys. Rev. Lett. 1997, 79, 1945-1948) indicate that this simple exponential relation is obeyed well when there is a smooth transition from the Ogston sieving regime to the reptation regime with increasing DNA length. Deviations from this equation occur when DNA migration is hindered, apparently by entropic-trapping, which is favored at low fields and high gel concentrations in the ranges examined.

Variation in growth and competitive ability between sexually and clonally produced hydroids.

In controlled laboratory experiments, colonies of Podocoryna carnea typically overgrow and kill colonies of Hydractinia symbiolongicarpus. Generally, these experiments have used colonies grown from tissue explants (clonal replicates) surgically removed from mature colonies taken from natural populations. In contrast, experiments involving interspecific bouts between small, sexually produced colonies reveal that both the characteristics and outcomes of competition differ from previous studies. During competition between small sexually produced colonies, H. symbiolongicarpus exhibits directional growth toward P. carnea and produces nematocyte-rich hyperplastic stolons more readily than P. carnea does. Nevertheless, P. carnea can still overcome H. symbiolongicarpus if it initially grows away from the contact zone and subsequently flanks H. symbiolongicarpus. Overall, sexually produced colonies of H. symbiolongicarpus destroyed their P. carnea counterparts in more than 35% of competitive bouts, whereas P. carnea dominated their H. symbiolongicarpus counterparts in all similar encounters between clonally produced colonies. In natural populations, competition between small sexually produced colonies of H. symbiolongicarpus may predominate, and these results support the hypothesis that this species is adapted to competition early in colony development. More generally, studies of competition between sexually produced colonies should complement similar studies of clonally produced colonies.