Efficiency of the nuclease I-SceI in excising selectable marker genes from the plant genome

Gene stacking is a method used in biotechnology by which multiple genes can be placed at a single genomic site, thereby simplifying plant breeding. In this approach, DNA nucleases are used for excising selectable marker genes (SMG), which are the unneeded components of transgenic plants. The goal of this project is to evaluate the effectiveness of the nuclease I-SceI in excising DNA in plants. Specifically, this study tests heat-inducible I-SceI through the use of a heat-shock promoter (HS) in order to control SMG excision by heat application. The DNA plasmid containing a visual marker gene flanked by I-SceI target sites and the heat-inducible I-SceI gene has been created and confirmed. Arabidopsis thaliana plants have been transformed with the plasmid, which will be used for testing the efficiency of HS:I-SceI in excising DNA from plant genomes

Truncation of lattice fractional quantum Hall Hamiltonians derived from conformal field theory

Conformal field theory has recently been applied to derive few-body Hamiltonians whose ground states are lattice versions of fractional quantum Hall states. The exact lattice models involve interactions over long distances, which is difficult to realize in experiments. It seems, however, that such long-range interactions should not be necessary, as the correlations decay exponentially in the bulk. This poses the question, whether the Hamiltonians can be truncated to contain only local interactions without changing the physics of the ground state. Previous studies have in a couple of cases with particularly much symmetry obtained such local Hamiltonians by keeping only a few local terms and numerically optimizing the coefficients. Here, we investigate a different strategy to construct truncated Hamiltonians, which does not rely on optimization, and which can be applied independent of the choice of lattice. We test the approach on two models with bosonic Laughlin-like ground states with filling factor $1/2$ and $1/4$, respectively. We first investigate how the coupling strengths in the exact Hamiltonians depend on distance, and then we study the truncated models. For the case of $1/2$ filling, we find that the truncated model with truncation radius $\sqrt{2}$ lattice constants on the square lattice and $1$ lattice constant on the triangular lattice has an approximate twofold ground state degeneracy on the torus, and the overlap per site between these states and the states constructed from conformal field theory is higher than $0.99$ for the lattices considered. For the model at $1/4$ filling, our results give some hints that a truncation radius of $\sqrt{5}$ on the square lattice and $\sqrt{7}$ on the triangular lattice might be enough, but the finite size effects are too large to judge whether the topology is, indeed, present in the thermodynamic limit.Comment: 8 Pages, 10 Figure

Spin diffusion in perturbed isotropic Heisenberg spin chain

The isotropic Heisenberg chain represents a particular case of an integrable many-body system exhibiting superdiffusive spin transport at finite temperatures. Here, we show that this model has distinct properties also at finite magnetization $m\ne0$, even upon introducing the SU(2) invariant perturbations. Specifically, we observe nonmonotonic dependence of the diffusion constant ${\cal D}_0(\Delta)$ on the spin anisotropy $\Delta$, with a pronounced maximum at $\Delta =1$. The latter dependence remains true also in the zero magnetization sector, with superdiffusion at $\Delta=1$ that is remarkably stable against isotropic perturbation (at least in finite-size systems), consistent with recent experiments with cold atoms.Comment: 5+5 pages, 4+5 figure

A Reanalysis of theUltraviolet Extinction from Interstellar Dust in the Large Magellanic Cloud

We have reanalyzed the Large Magellanic Cloud's (LMC) ultraviolet (UV) extinction using data from the IUE final archive. Our new analysis takes advantage of the improved signal--to--noise of the IUE NEWSIPS reduction, the exclusion of stars with very low reddening, the careful selection of well matched comparison stars, and an analysis of the effects of Galactic foreground dust. Differences between the average extinction curves of the 30 Dor region and the rest of the LMC are reduced compared to previous studies. We find that there is a group of stars with very weak 2175 Ang. bumps that lie in or near the region occupied by the supergiant shell, LMC 2, on the southeast side of 30 Dor. The average extinction curves inside and outside LMC 2 show a very significant difference in 2175 Ang. bump strength, but their far--UV extinctions are similar. While it is unclear whether or not the extinction outside the LMC 2 region can be fit with the relation of Cardelli, Clayton and Mathis (CCM), sightlines near LMC 2 cannot be fit with CCM due to their weak 2175 Ang. bumps. While the extinction properties seen in the LMC lie within the range of properties seen in the Galaxy, the correlations of UV extinction properties with environment seen in the Galaxy do not appear to hold in the LMC.Comment: 29 pages, 10 figures, to be published in Ap

Dynamics of the fast solar tachocline: II. Migrating field

We present detailed numerical calculations of the fast solar tachocline based on the assumption that the dynamo field dominates over the dynamics of the tachocline. In the present paper of the series, we focus on three shortfalls of the earlier models. First, instead of the simple oscillating dipole poloidal field we study the more general magnetic field structures reminiscent of the butterfly diagram. The migrating field is prescribed as the observed axisymmetric radial magnetic field Stenflo (1988, 1994). Our results are in good agreement with our analitical estimate and our previous works in Forgacs-Dajka & Petrovay (2001,2002), but the polar "dip" in isorotational surfaces is strongly reduced in this case. On the other hand, a more realistic model should have a magnetic diffusivity decreasing significantly inside the radiative interior, so we also explore the effect of diffusivity and magnetic Prandtl number varying with depth. We found that the downwards decreasing magnetic diffusivity and Prandtl number have no significant effect on the solution, although the temporal variation of the tachocline thickness has decreased.Comment: 9 page

Empirical Relationship between Intra-Purine and Intra-Pyrimidine Differences in Conserved Gene Sequences

DNA sequences seen in the normal character-based representation appear to have a formidable mixing of the four nucleotides without any apparent order. Nucleotide frequencies and distributions in the sequences have been studied extensively, since the simple rule given by Chargaff almost a century ago that equates the total number of purines to the pyrimidines in a duplex DNA sequence. While it is difficult to trace any relationship between the bases from studies in the character representation of a DNA sequence, graphical representations may provide a clue. These novel representations of DNA sequences have been useful in providing an overview of base distribution and composition of the sequences and providing insights into many hidden structures. We report here our observation based on a graphical representation that the intra-purine and intra-pyrimidine differences in sequences of conserved genes generally follow a quadratic distribution relationship and show that this may have arisen from mutations in the sequences over evolutionary time scales. From this hitherto undescribed relationship for the gene sequences considered in this report we hypothesize that such relationships may be characteristic of these sequences and therefore could become a barrier to large scale sequence alterations that override such characteristics, perhaps through some monitoring process inbuilt in the DNA sequences. Such relationship also raises the possibility of intron sequences playing an important role in maintaining the characteristics and could be indicative of possible intron-late phenomena

Buoyancy-induced time delays in Babcock-Leighton flux-transport dynamo models

The Sun is a magnetic star whose cyclic activity is thought to be linked to internal dynamo mechanisms. A combination of numerical modelling with various levels of complexity is an efficient and accurate tool to investigate such intricate dynamical processes. We investigate the role of the magnetic buoyancy process in 2D Babcock-Leighton dynamo models, by modelling more accurately the surface source term for poloidal field. Methods. To do so, we reintroduce in mean-field models the results of full 3D MHD calculations of the non-linear evolution of a rising flux tube in a convective shell. More specifically, the Babcock-Leighton source term is modified to take into account the delay introduced by the rise time of the toroidal structures from the base of the convection zone to the solar surface. We find that the time delays introduced in the equations produce large temporal modulation of the cycle amplitude even when strong and thus rapidly rising flux tubes are considered. Aperiodic modulations of the solar cycle appear after a sequence of period doubling bifurcations typical of non-linear systems. The strong effects introduced even by small delays is found to be due to the dependence of the delays on the magnetic field strength at the base of the convection zone, the modulation being much less when time delays remain constant. We do not find any significant influence on the cycle period except when the delays are made artificially strong. A possible new origin of the solar cycle variability is here revealed. This modulated activity and the resulting butterfly diagram are then more compatible with observations than what the standard Babcock-Leighton model produces.Comment: 13 pages, 10 figures, accepted for publication in A&

Symmetries and novel universal properties of turbulent hydrodynamics in a symmetric binary fluid mixture

We elucidate the universal properties of the nonequilibrium steady states (NESS) in a driven symmetric binary fluid mixture, an example of active advection, in its miscible phase. We use the symmetries of the equations of motion to establish the appropriate form of the structure functions which characterise the statistical properties of the NESS of a driven symmetric binary fluid mixture. We elucidate the universal properties described by the scaling exponents and the amplitude ratios. Our results suggest that these exponents and amplitude ratios vary continuously with the degree of crosscorrelations between the velocity and the gradient of the concentration fields. Furthermore, we demonstrate, in agreement with Celani et al, Phys. Rev. Lett., 89, 234502 (2002, that the conventional structure functions as used in passive scalar turbulence studies exhibit only simple scaling in the problem of symmetric binary fluid mixture even in the weak concentration limit. We also discuss possible experimental verifications of our results.Comment: To appear in JSTAT (letters) (2005