Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria

The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNAAla; a G3A change in Ashbya abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched

Temperature dependence of Vortex Charges in High Temperature Superconductors

Using a model Hamiltonian with d-wave superconductivity and competing antiferromagnetic (AF) interactions, the temperature (T) dependence of the vortex charge in high T_c superconductors is investigated by numerically solving the Bogoliubov-de Gennes equations. The strength of the induced AF order inside the vortex core is T dependent. The vortex charge could be negative when the AF order with sufficient strength is present at low temperatures. At higher temperatures, the AF order may be completely suppressed and the vortex charge becomes positive. A first order like transition in the T dependent vortex charge is seen near the critical temperature T_{AF}. For underdoped sample, the spatial profiles of the induced spin-density wave and charge-density wave orders could have stripe like structures at T < T_s, and change to two-dimensional isotropic ones at T > T_s. As a result, a vortex charge discontinuity occurs at T_s.Comment: 5 pages, 5 figure

Upper critical field Hc2H_{c2} calculations for the high critical temperature superconductors considering inhomogeneities

We perform calculations to obtain the $H_{c2}$ curve of high temperature superconductors (HTSC). We consider explicitly the fact that the HTSC possess intrinsic inhomogeneities by taking into account a non uniform charge density $\rho(r)$. The transition to a coherent superconducting phase at a critical temperature $T_c$ corresponds to a percolation threshold among different superconducting regions, each one characterized by a given $T_c(\rho(r))$. Within this model we calculate the upper critical field $H_{c2}$ by means of an average linearized Ginzburg-Landau (GL) equation to take into account the distribution of local superconducting temperatures $T_c(\rho(r))$. This approach explains some of the anomalies associated with $H_{c2}$ and why several properties like the Meissner and Nernst effects are detected at temperatures much higher than $T_c$.Comment: Latex text, add reference

Superconducting Fluctuation and Pseudogap in Disordered Short Coherence Length Superconductor

We investigate the role of disorder on the superconducting (SC) fluctuation in short coherence length d-wave superconductors. The particular intetest is focused on the disorder-induced microscopic inhomogeneity of SC fluctuation and its effect on the pseudogap phenomena. We formulate the self-consistent 1-loop order theory for the SC fluctuation in inhomogeneous systems and analyze the disordered $t$-$t'$-$V$ model. The SC correlation function, electronic DOS and the critical temperature are estimated. The SC fluctuation is localized like a nanoscale granular structure when the coherence length is short, namely the transition temperature is high. This is contrasted to the long coherence length superconductors where the order parameter is almost uniform in the microscopic scale. In the former case, the SC fluctuation is enhanced by the disorder in contrast to the Abrikosov-Gorkov theory. These results are consistent with the STM, NMR and transport measurements in high-$T_{\rm c}$ cuprates and illuminate the essential role of the microscopic inhomogeneity. We calculate the spacial dependence of DOS around the single impurity and discuss the consistency with the NMR measurements

The Dependence of the Superconducting Transition Temperature of Organic Molecular Crystals on Intrinsically Non-Magnetic Disorder: a Signature of either Unconventional Superconductivity or Novel Local Magnetic Moment Formation

We give a theoretical analysis of published experimental studies of the effects of impurities and disorder on the superconducting transition temperature, T_c, of the organic molecular crystals kappa-ET_2X and beta-ET_2X (where ET is bis(ethylenedithio)tetrathiafulvalene and X is an anion eg I_3). The Abrikosov-Gorkov (AG) formula describes the suppression of T_c both by magnetic impurities in singlet superconductors, including s-wave superconductors and by non-magnetic impurities in a non-s-wave superconductor. We show that various sources of disorder lead to the suppression of T_c as described by the AG formula. This is confirmed by the excellent fit to the data, the fact that these materials are in the clean limit and the excellent agreement between the value of the interlayer hopping integral, t_perp, calculated from this fit and the value of t_perp found from angular-dependant magnetoresistance and quantum oscillation experiments. If the disorder is, as seems most likely, non-magnetic then the pairing state cannot be s-wave. We show that the cooling rate dependence of the magnetisation is inconsistent with paramagnetic impurities. Triplet pairing is ruled out by several experiments. If the disorder is non-magnetic then this implies that l>=2, in which case Occam's razor suggests that d-wave pairing is realised. Given the proximity of these materials to an antiferromagnetic Mott transition, it is possible that the disorder leads to the formation of local magnetic moments via some novel mechanism. Thus we conclude that either kappa-ET_2X and beta-ET_2X are d-wave superconductors or else they display a novel mechanism for the formation of localised moments. We suggest systematic experiments to differentiate between these scenarios.Comment: 18 pages, 5 figure

Inhomogeneous d-wave superconducting state of a doped Mott insulator

Recent scanning tunneling microscope (STM) measurements discovered remarkable electronic inhomogeneity, i.e. nano-scale spatial variations of the local density of states (LDOS) and the superconducting energy gap, in the high-Tc superconductor BSCCO. Based on the experimental findings we conjectured that the inhomogeneity arises from variations in local oxygen doping level and may be generic of doped Mott insulators which behave rather unconventionally in screening the dopant ionic potentials at atomic scales comparable to the short coherence length. Here, we provide theoretical support for this picture. We study a doped Mott insulator within a generalized t-J model, where doping is accompanied by ionic Coulomb potentials centered in the BiO plane. We calculate the LDOS spectrum, the integrated LDOS, and the local superconducting gap, make detailed comparisons to experiments, and find remarkable agreement with the experimental data. We emphasize the unconventional screening in a doped Mott insulator and show that nonlinear screening dominates at nano-meter scales which is the origin of the electronic inhomogeneity. It leads to strong inhomogeneous redistribution of the local hole density and promotes the notion of a local doping concentration. We find that the inhomogeneity structure manifests itself at all energy scales in the STM tunneling differential conductance, and elucidate the similarity and the differences between the data obtained in the constant tunneling current mode and the same data normalized to reflect constant tip-to-sample distance. We also discuss the underdoped case where nonlinear screening of the ionic potential turns the spatial electronic structure into a percolative mixture of patches with smaller pairing gaps embedded in a background with larger gaps to single particle excitations.Comment: 19 pages, final versio

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ∼40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ∼3 kb, inverted repeat and several potentially stable ∼40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved

Entropy of vortex cores on the border of the superconductor-to-insulator transition in an underdoped cuprate

We present a study of Nernst effect in underdoped $La_{2-x}Sr_xCuO_4$ in magnetic fields as high as 28T. At high fields, a sizeable Nernst signal was found to persist in presence of a field-induced non-metallic resistivity. By simultaneously measuring resistivity and the Nernst coefficient, we extract the entropy of vortex cores in the vicinity of this field-induced superconductor-insulator transition. Moreover, the temperature dependence of the thermo-electric Hall angle provides strong constraints on the possible origins of the finite Nernst signal above $T_c$, as recently discovered by Xu et al.Comment: 5 Pages inculding 4 figure