Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase

Oligonucleotides that recapitulate the acceptor stems of tRNAs are substrates for aminoacylation by many tRNA synthetases in vitro, even though these substrates are missing the anticodon trinucleotides of the genetic code. In the case of tRNAAla a single acceptor stem G⋅U base pair at position 3·70 is essential, based on experiments where the wobble pair has been replaced by alternatives such as I⋅U, G⋅C, and A⋅U, among others. These experiments led to the conclusion that the minor-groove free 2-amino group (of guanosine) of the G⋅U wobble pair is essential for charging. Moreover, alanine-inserting tRNAs (amber suppressors) that replace G⋅U with mismatches such as G⋅A and C⋅A are partially active in vivo and can support growth of an Escherichia coli tRNAAla knockout strain, leading to the hypothesis that a helix irregularity and nucleotide functionalities are important for recognition. Herein we investigate the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G⋅U pair. Although most of these substrates have undetectable activity, G⋅A and C⋅A variants retain some activity, which is, nevertheless, reduced by at least 100-fold. Thus, the in vivo assays are much less sensitive to large changes in aminoacylation kinetic efficiency of 3·70 variants than is the in vitro assay system. Although these functional data do not clarify all of the details, it is now clear that specific atomic groups are substantially more important in determining kinetic efficiency than is a helical distortion. By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency.

Geometry of circular vectors and pattern recognition of shape of a boundary

This paper deals with pattern recognition of the shape of the boundary of closed figures on the basis of a circular sequence of measurements taken on the boundary at equal intervals of a suitably chosen argument with an arbitrary starting point. A distance measure between two boundaries is defined in such a way that it has zero value when the associated sequences of measurements coincide by shifting the starting point of one of the sequences. Such a distance measure, which is invariant to the starting point of the sequence of measurements, is used in identification or discrimination by the shape of the boundary of a closed figure. The mean shape of a given set of closed figures is defined, and tests of significance of differences in mean shape between populations are proposed.

On the geometry of solutions of the quasi-geostrophic and Euler equations

We study solutions of the two-dimensional quasi-geostrophic thermal active scalar equation involving simple hyperbolic saddles. There is a naturally associated notion of simple hyperbolic saddle breakdown. It is proved that such breakdown cannot occur in finite time. At large time, these solutions may grow at most at a quadruple-exponential rate. Analogous results hold for the incompressible three-dimensional Euler equation.

Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending.

The effect of Fos and Jun binding on the structure of the AP-1 recognition site is controversial. Results from phasing analysis and phase-sensitive detection studies of DNA bending by Fos and Jun have led to opposite conclusions. The differences between these assays, the length of the spacer between two bends and the length of the sequences flanking the bends, are investigated here using intrinsic DNA bend standards. Both an increase in the spacer length as well as a decrease in the length of flanking sequences resulted in a reduction in the phase-dependent variation in electrophoretic mobilities. Probes with a wide separation between the bends and short flanking sequences, such as those used in the phase-sensitive detection studies, displayed no phase-dependent mobility variation. This shape-dependent variation in electrophoretic mobilities was reproduced by complexes formed by truncated Fos and Jun. Results from ligase-catalyzed cyclization experiments have been interpreted to indicate the absence of DNA bending in the Fos-Jun-AP-1 complex. However, truncated Fos and Jun can alter the relative rates of inter- and intramolecular ligation through mechanisms unrelated to DNA bending, confounding the interpretation of cyclization data. The analogous phase- and shape-dependence of the electrophoretic mobilities of the Fos-Jun-AP-1 complex and an intrinsic DNA bend confirm that Fos and Jun bend DNA, which may contribute to their functions in transcription regulation.

Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction.

The crystal structure of the decanucleotide d(CGCAATTGCG)2 has been solved by a combination of molecular replacement and heavy-atom procedures and has been refined to an R factor of 20.2% at 2.7 A. It is not a fully base-paired duplex but has a central core of eight Watson-Crick base pairs flanked by unpaired terminal guanosines and cytosines. These participate in hydrogen-bonding arrangements with adjacent decamer duplexes in the crystal lattice. The unpaired guanosines are bound in the G+C regions of duplex minor grooves. The cytosines have relatively high mobility, even though they are constrained to be in one region where they are involved in base-paired triplets with G.C base pairs. The 5'-AATT sequence in the duplex region has a narrow minor groove, providing further confirmation of the sequence-dependent nature of groove width.

Geometry of the SL(3,ℂ)-character variety of torus knots.

Let G be the fundamental group of the complement of the torus knot of type (m, n). It has a presentation G = . We find a geometric description of the character variety X(G) of characters of representations of G into SL(3,ℂ), GL(3,ℂ) and PGL(3,ℂ).

Finite-size scaling analysis of the distributions of pseudo-critical temperatures in spin glasses

Using the results of large scale numerical simulations we study the probability distribution of the pseudo critical temperature for the three dimensional Edwards Anderson Ising spin glass and for the fully connected Sherrington-Kirkpatrick model. We find that the behaviour of our data is nicely described by straightforward finitesize scaling relations.

Analysis of the spectral response of fractal antennas related with its geometry and current paths

Fractal antennas have been proposed to improve the bandwidth of resonant structures and optical antennas. Their multiband characteristics are of interest in radiofrequency and microwave technologies. In this contribution we link the geometry of the current paths built-in the fractal antenna with the spectral response. We have seen that the actual currents owing through the structure are not limited to the portion of the fractal that should be geometrically linked with the signal. This fact strongly depends on the design of the fractal and how the different scales are arranged within the antenna. Some ideas involving materials that could actively respond to the incoming radiation could be of help to spectrally select the response of the multiband design.

Pseudo-contractions in belief revision

Belief Revision addresses the problem of how to change epistemic states, usually represented in the literature by sets of logical sentences. Solid theoretical results were consolidated with the AGM paradigm, which deals with theories (logically closed sets of sentences). After that, the theory was extended to belief bases, that is, arbitrary sets of sentences. Besides all this theoretical framework, AI researchers face serious difficulties when trying to implement belief revision systems. One of the major complications is the closure required by AGM theory, which cannot be easily computed. Even belief bases, which do not require closure, seem to be improper for practical purposes, since their changes are usually very rigid (syntax dependent). Some operations, known as pseudo-contractions, are in the middle ground between belief set change and belief base change. In the present work we have proposed a new pseudo-contraction operation, studied its properties and characterized it. We have also found connections between this operator and some other pseudo-contractions.

The Adsorption of Polyatomic Molecules on Carbon Surfaces

Carbon nanotubes exhibit the structure and chemical properties that make them apt substrates for many adsorption applications. Of particular interest are carbon nanotube bundles, whose unique geometry is conducive to the formation of pseudo-one-dimensional phases of matter, and graphite, whose simple planar structure allows ordered phases to form in the absence of surface effects. Although both of these structures have been the focus of many research studies, knowledge gaps still remain. Much of the work with carbon nanotubes has used simple adsorbates1-43, and there is little kinetic data available. On the other hand, there are many studies of complex molecules adsorbing on graphite; however, there is almost no kinetic data reported for this substrate. We seek to close these knowledge gaps by performing a kinetic study of linear molecules of increasing length adsorbing on carbon nanotube bundles and on graphite. We elucidated the process of adsorption of complex admolecules on carbon nanotube bundles, while at the same time producing some of the first equilibrium results of the films formed by large adsorbates on these structures. We also extended the current knowledge of adsorption on graphite to include the kinetics of adsorption. The kinetic data that we have produced enables a more complete understanding of the process of adsorption of large admolecules on carbon nanotube bundles and graphite. We studied the adsorption of particles on carbon nanotube bundles and graphite using analytical and computational techniques. By employing these methods separately but in parallel, we were able to constantly compare and verify our results. We calculated and simulated the behavior of a given system throughout its evolution and then analyzed our results to determine which system parameters have the greatest effect on the kinetics of adsorption. Our analytical and computational results show good agreement with each other and with the experimental isotherm data provided by our collaborators. As a result of this project, we have gained a better understanding of the kinetics of adsorption. We have learned about the equilibration process of dimers on carbon nanotube bundles, identifying the “filling effect”, which increases the rate of total uptake, and explaining the cause of the transient “overshoot” in the coverage of the surface. We also measured the kinetic effect of particle-particle interactions between neighboring adsorbates on the lattice. For our simulations of monomers adsorbing on graphite, we succeeded in developing an analytical equation to predict the characteristic time as a function of chemical potential and of the adsorption and interaction energies of the system. We were able to further explore the processes of adsorption of dimers and trimers on graphite (again observing the filling effect and the overshoot). Finally, we were able to show that the kinetic behaviors of monomers, dimers, and trimers that have been reported in experimental results also arise organically from our model and simulations.

The influence of magnetic field geometry on magnetars X-ray spectra

Nowadays, the analysis of the X-ray spectra of magnetically powered neutron stars or magnetars is one of the most valuable tools to gain insight into the physical processes occurring in their interiors and magnetospheres. In particular, the magnetospheric plasma leaves a strong imprint on the observed X-ray spectrum by means of Compton up-scattering of the thermal radiation coming from the star surface. Motivated by the increased quality of the observational data, much theoretical work has been devoted to develop Monte Carlo (MC) codes that incorporate the effects of resonant Compton scattering (RCS) in the modeling of radiative transfer of photons through the magnetosphere. The two key ingredients in this simulations are the kinetic plasma properties and the magnetic field (MF) configuration. The MF geometry is expected to be complex, but up to now only mathematically simple solutions (self-similar solutions) have been employed. In this work, we discuss the effects of new, more realistic, MF geometries on synthetic spectra. We use new force-free solutions [14] in a previously developed MC code [9] to assess the influence of MF geometry on the emerging spectra. Our main result is that the shape of the final spectrum is mostly sensitive to uncertain parameters of the magnetospheric plasma, but the MF geometry plays an important role on the angle-dependence of the spectra.

Reverse Geometry Hybrid Contact Lens Fitting in a Case of Donor-Host Misalignment after Keratoplasty

Purpose: To report the successful outcome obtained after fitting a new hybrid contact lens in a cornea with an area of donor-host misalignment and significant levels of irregular astigmatism after penetrating keratoplasty (PKP). Materials and methods: A 41-year-old female with bilateral asymmetric keratoconus underwent PKP in her left eye due to the advanced status of the disease. One year after surgery, the patient referred a poor visual acuity and quality in this eye. The fitting of different types of rigid gas permeable contact lenses was performed, but with an unsuccessful outcome due to contact lens stability problems and uncomfortable wear. Scheimpflug imaging evaluation revealed that a donor-host misalignment was present at the nasal area. Contact lens fitting with a reverse geometry hybrid contact lens (Clearkone, SynergEyes Carlsbad) was then fitted. Visual, refractive, and ocular aberrometric outcomes were evaluated during a 1-year period after the fitting. Results: Uncorrected distance visual acuity improved from a prefitting value of 20/200 to a best corrected postfitting value of 20/20. Prefitting manifest refraction was +5.00 sphere and -5.50 cylinder at 75°, with a corrected distance visual acuity of 20/30. Higher order root mean square (RMS) for a 5 mm pupil changed from a prefitting value of 6.83 µm to a postfitting value of 1.57 µm (5 mm pupil). The contact lens wearing was referred as comfortable, with no anterior segment alterations. Conclusion: The SynergEyes Clearkone contact lens seems to be another potentially useful option for the visual rehabilitation after PKP, especially in cases of donor-host misalignment.

3D geometry of growth strata in a fault-propagation fold: insights into space–time evolution of the Crevillente Fault (Abanilla-Alicante sector), Betic Cordillera, Spain

This work presents a 3D geometric model of growth strata cropping out in a fault-propagation fold associated with the Crevillente Fault (Abanilla-Alicante sector) from the Bajo Segura Basin (eastern Betic Cordillera, southern Spain). The analysis of this 3D model enables us to unravel the along-strike and along-section variations of the growth strata, providing constraints to assess the fold development, and hence, the fault kinematic evolution in space and time. We postulate that the observed along-strike dip variations are related to lateral variation in fault displacement. Along-section variations of the progressive unconformity opening angles indicate greater fault slip in the upper Tortonian–Messinian time span; from the Messinian on, quantitative analysis of the unconformity indicate a constant or lower tectonic activity of the Crevillente Fault (Abanilla-Alicante sector); the minor abundance of striated pebbles in the Pliocene-Quaternary units could be interpreted as a decrease in the stress magnitude and consequently in the tectonic activity of the fault. At a regional scale, comparison of the growth successions cropping out in the northern and southern limits of the Bajo Segura Basin points to a southward migration of deformation in the basin. This means that the Bajo Segura Fault became active after the Crevillente Fault (Abanilla-Alicante sector), for which activity on the latter was probably decreasing according to our data. Consequently, we propose that the seismic hazard at the northern limit of the Bajo Segura Basin should be lower than at the southern limit.