Positional Disorder (Random Gaussian Phase Shifts) in the Fully Frustrated Josephson Junction Array (2D XY Model)

We consider the effect of positional disorder on a Josephson junction array with an applied magnetic field of f=1/2 flux quantum per unit cell. This is equivalent to the problem of random Gaussian phase shifts in the fully frustrated 2D XY model. Using simple analytical arguments and numerical simulations, we present evidence that the ground state vortex lattice of the pure model becomes disordered, in the thermodynamic limit, by any amount of positional disorder.Comment: 4 pages, 4 eps figures embedde

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.

Genetic decoding is not 'frozen' as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5' or 3' of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3' from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.This work was supported by grants from Science Foundation Ireland [12/IP/1492 and 13/1A/1853 to J.F.A; 12/IA/1335 to P.V.B.], US. National Institutes of Health [RO3 MH098688 to J.F.A.], the Wellcome Trust [106207 to A.E.F and 094423 to P.V.B.] and the European Research Council (ERC) grant No. 646891 to A.E.F.]This is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/nar/gkw53

Structural basis of ribosomal frameshifting

Versatility in genetic decoding enriches gene expression. Programmed shifting of the reading frame during translation is a prominent feature productively utilized in probably all life forms. While the occurrences, function, and mechanistic components have been identified for many instances of frameshifting, structural understanding of their basis at the atomic level has been limited to the individual components in isolation. Here, I present atomic level information of the decoding apparatus relevant to both -1 and +1 frameshifting. The +1 frameshifting event investigated is that of a sensor and effector of an autoregulatory circuit present in the common ancestor between yeast and humans. In regulating intracellular polyamine levels, the mammalian antizyme 2 frameshifting studied interacts with ornithine decarboxylase and c-myc. The polyamine spermidine is shown here to be present proximal to but not interfering with the peptidyl transferase center, making stabilizing interactions with the terminal phosphate of the P-site tRNA. Spermidine occupancy at this location is inferred to preclude binding of the translation factor eIF5A by occlusion of its hypusine moiety. Visualization of the nascent chain reveals a network of interactions with key residues of the peptide exit tunnel that gate the transit of the growing polypeptide. The -1 frameshifting event investigated is that required by SARS-CoV-2, the causative virus of the COVID-19 pandemic. The downstream RNA element that stimulates frameshifting is seen to adopt a corkscrew-shaped 3-stemmed pseudoknot structure that lodges itself at the entrance of the ribosomal mRNA channel. Distinct functional interactions of the nascent chain with the ribosome exit tunnel are observed while the distal end of the nascent peptide begins to undergo co-translational folding into a zinc finger motif. The study highlights the frameshift-inhibitory properties of Merafloxacin, a small molecule that inhibits propagation of SARS-CoV-2

Crystal structure of 4-aminopyridinium 3-(4-aminopyridinium) succinate tetra hydrate: A new salt from 4-aminopyridine and maleic acid crystallization

International audienc

From recoding to peptides for MHC class I immune display: Enriching viral expression, virus vulnerability and virus evasion

Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined

Study of structural and magnetic properties of (Co-Cu)Fe2O4/PANI composites

The nanocomposites of the polyaniline and Co1-xCuxFe2O4 (PANI/CoCuFe) were prepared by in-situ oxidative polymerization of aniline. Prepared nanocomposites samples were characterized by using various experimental techniques like X-ray diffraction (XRD), Fourier transformed infrared spectroscopy (FT-IR), field emission scanning electron microscope (FE-SEM), vibrating sample magnetometer (VSM), Mossbauer spectroscopy and ultraviolet-visible spectrophotometty (UV-VIS). The elemental analysis as obtained from the energy dispersive X-ray spectroscopy (EDAX) measurement is in close agreement with the expected composition from the stoichiometry of the reactant solutions. XRD result confirms that all the samples have the single phase cubic spinet structure. Unit cell parameter 'a' is found to decrease with the increase in copper ion substitution. The crystallite size was investigated by using the Debye-Scherer formula and it was found in the range of similar to 28-37 nm. FE-SEM confirmed the homogeneous and well defined surface morphology of the synthesized samples. Fr-IR study showed the main absorption bands corresponding to the spinet structure those arose due to the tetrahedral and octahedral stretching vibrations. Cation distribution was estimated using XRD data. Hysteresis measurements revealed that the saturation magnetization decreased with increase in Cu2+ substitution. Magnetic environment of Fe-57 in Cu-doped cobalt ferrite was investigated by using Mossbauer spectroscopy. Mossbauer study evidenced the ferrimagnetic behavior of the synthesized samples

Structural development and magnetic phenomenon in Zn-Cr-Fe multi oxide nano-crystals

The Cr3+ ions doped multi-oxide ZnFe2-xCrxO4 ferrite nanoparticles have been synthesized by chemical co-precipitation method. Site occupancies of Zn2+, Cr3+ and Fe3+ ions were analyzed using X-ray diffraction data and Buerger's method. The effect of the constituent phase variation on the magnetic hysteresis behavior was examined by saturation magnetization which decreases with the increase in Cr3+ content in place of Fe3+ ions at octahedral B-site. Typical blocking temperature (TB) around 90 K was observed by zero field cooling and field cooling magnetization study. Room temperature Mossbauer spectra show two paramagnetic doublets (tetrahedral and octahedral sites). The isomer shifts of both doublets decrease whereas quadrupole splitting and relative area of tetrahedral A-site increases with increasing Cr3+ substitution. The dielectric constant (measured on compositions x=0, 0.4, 0.8 and 1.0) increases when the temperature increases as in the semiconductor. This behavior is attributed to the hopping of electrons between Fe2+ and Fe3+ ions with a thermal activation

Influence of Ni2+ substitution on the structural, dielectric and magnetic properties of Cu-Cd ferrite nanoparticles

Nanoparticles with compositions of Cu0.4 0.5xCd0.2Ni0.4+xFe2 O-0.5x(4) (0.0 <= x <= 0.5) were successfully synthesized by a citrate-nitrate sol-gel auto combustion route. The combusted powder was calcinated at four hours in a furnace and then slowly cooled to room temperature. The analysis methods of FTIR, XRD, FESEM, VSM and dielectric measurements were used to characterize prepared magnetic particles. The effect of Ni2+ substitution on structural, magnetic and dielectric properties of Cu-Cd ferrite nanoparticles was studied. The comprehensive studies on compositional and frequency dependent dielectric properties were carried out by means of AC conductivity (sigma(ac)), imaginary dielectric constant (epsilon ''), loss tangent (tan delta), impedance and dielectric modulus (real and imaginary) measurements in frequency range of 50 Hz-5 MHz at room temperature. The structural properties investigated by using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. X-ray diffraction pattern and FTIR results revealed that synthesized samples are in single phase. It is observed that the dielectric constant (epsilon '') and dielectric loss (tan delta) value decreases with increase in Ni2+ concentration (x). At low frequency the Maxwell type interfacial polarization was observed. Magnetization measurement shows that the Curie temperature of the samples increases with Ni2+ concentration, which is explained by a change in the A-O-B super exchange interaction

Exploring the structural, Mossbauer and dielectric properties of Co2 incorporated Mg0.5Zn0.5-xCoxFe2O4 nanocrystalline ferrite

The nanocrystalline Mg0.5Zn0.5-xCoxFe2O4 (x=0, 0.1, 0.2, 0.3, 0.4 and 0.5) ferrites have been synthesized by sol-gel auto ignition method. Rietveld refinement of X-ray diffraction (XRD) patterns of all concentrations show mixed cubic spinel structure. The lattice constant values infer decreasing trend from 8.420 to 8.392 A with the substitution of Co2+. The crystallite size calculated from Scherer formula lies in the range between 28 and 37 um which confirms the nanocrystalline nature of synthesized samples. In order to study the morphology and phase structure of the synthesized samples, samples were examined by transmission electron microscopy (TEM). Scanning electron microscopy (SEM) confirmed the homogeneous and well defined surface morphology of the synthesized samples. The elemental analysis as obtained from energy dispersive X-ray (EDAX) is in close agreement with the expected composition from the stoichiometry of reactant solutions used. The valence states of the CO2+ ions have been confirmed with the help of X-ray photoelectron spectroscopy. Magnetization results obtained from the vibrating sample magnetometer (VSM) confirm that the substitution of Co2+ for Zn2+ caused an increase in the saturation magnetization and coercivity. The dependence of Mtissbauer parameters, viz., line width, isomer shift, quadrupole splitting and hyperfine magnetic field on Co2+ substitution have been analyzed. Cation distribution estimated from XRD and Mtissbauer spectroscopy are in good agreement with each other. The frequency dependent dielectric properties were studied by measuring dielectric constant (epsilon') and ac conductivity (sigma(ac) at 300 K in the frequency range of 50 Hz-5 MHz. The highest value for epsilon' and sigma(ac) is observed for x=0.5

Investigation of structural, dielectric, magnetic and antibacterial activity of Cu-Cd-Ni-FeO4 nanoparticles

Nanoparticles of Cu-Cd-Ni-FeO4 were synthesized by the auto-combustion process using a modified citric acid method. Antibacterial activity, structural, dielectric and magnetic properties were investigated. An assay showed the broad spectrum antibacterial activity of Cu-Cd-Ni-FeO4 against Gram positive and Gram negative pathogenic bacterial strains. The existence of single phase cubic spinel structure of ferrites was confirmed by X-ray diffraction measurement. Fourier transform infrared spectroscopy shows the two main absorption bands at lower frequency region. Surface morphology and compositional features were studied by scanning electron microscopy and energy dispersive X-ray spectroscopy analysis, respectively. Results indicated that the nanosize particles greatly influenced the antibacterial activity, as well as structural, dielectric and magnetic properties of the samples. Magnetic measurements of the samples were carried out by means of vibrating sample magnetometry and Mossbauer spectroscopy. Magnetic properties are strongly affected by Ni2+ substitution