Conversion of the Bifunctional 8-oxoguanine/β-δ AP DNA Repair Activities of Drosophila Ribosomal Protein S3 into the Human S3 Monofunctional β- elimination Catalyst Through a Single Amino Acid Change

The Drosophila S3 ribosomal protein has important roles in both protein translation and DNA repair. In regards to the latter activity, it has been shown that S3 contains vigorous N-glycosylase activity for the removal of 8-oxoguanine residues in DNA that leaves baseless sites in their places. Drosophila S3 also possesses an apurinic/apyrimidinic (AP) lyase activity in which the enzyme catalyzes a β-elimination reaction that cleaves phosphodiester bonds 3′ and adjacent to an AP lesion in DNA. In certain situations, this is followed by a δ-elimination reaction that ultimately leads to the formation of a single nucleotide gap in DNA bordered by 5′- and 3′-phosphate groups. The human S3 protein, although 80% identical to its Drosophila homolog and shorter by only two amino acids, has only marginal N-glycosylase activity. Its lyase activity only cleaves AP DNA by a β-elimination reaction, thus further distinguishing itself from the Drosophila S3 protein in lacking a δ-elimination activity. Using a hidden Markov model analysis based on the crystal structures of several DNA repair proteins, the enzymatic differences between Drosophila and human S3 were suggested by the absence of a conserved glutamine residue in human S3 that usually resides at the cleft of the deduced active site pocket of DNA glycosylases. Here we show that the replacement of the Drosophila glutamine by an alanine residue leads to the complete loss of glycosylase activity. Unexpectedly, the δ-elimination reaction at AP sites was also abrogated by a change in the Drosophila glutamine residue. Thus, a single amino acid change converted the Drosophila activity into one that is similar to that possessed by the human S3 protein. In support of this were experiments executed in vivo that showed that human S3 and the Drosophila site-directed glutamine-changed S3 performed poorly when compared with Drosophilawild-type S3 and its ability to protect a bacterial mutant from the harmful effects of DNA-damaging agents

Quantum correlations and synchronization measures

The phenomenon of spontaneous synchronization is universal and only recently advances have been made in the quantum domain. Being synchronization a kind of temporal correlation among systems, it is interesting to understand its connection with other measures of quantum correlations. We review here what is known in the field, putting emphasis on measures and indicators of synchronization which have been proposed in the literature, and comparing their validity for different dynamical systems, highlighting when they give similar insights and when they seem to fail.Comment: book chapter, 18 pages, 7 figures, Fanchini F., Soares Pinto D., Adesso G. (eds) Lectures on General Quantum Correlations and their Applications. Quantum Science and Technology. Springer (2017

Particle production in time-dependent gravitational fields: the expanding mass shell

We compute the production of particles from the gravitational field of an expanding mass shell. Contrary to the situation of Hawking radiation and the production of cosmological perturbations during cosmological inflation, the example of an expanding mass shell has no horizon and no singularity. We apply the method of `ray-tracing', first introduced by Hawking, and calculate the energy spectrum of the produced particles. The result depends on three parameters: the expansion velocity of the mass shell, its radius, and its mass. Contrary to the situation of a collapsing mass shell, the energy spectrum is non-thermal. Invoking time reversal we reproduce Hawking's thermal spectrum in a certain limit.Comment: 19 pages, 8 figure

Renormalization Group Flows for Brane Couplings

Field theories in the presence of branes encounter localized divergences that renormalize brane couplings. The sources of these brane-localized divergences are understood as arising either from broken translation invariance, or from short distance singularities as the brane thickness vanishes. While the former are generated only by quantum corrections, the latter can appear even at the classical level. Using as an example six-dimensional scalar field theory in the background of a 3-brane, we show how to interpret such classical divergences by the usual regularization and renormalization procedure of quantum field theory. In our example, the zero thickness divergences are logarithmic, and lead classically to non-trivial renormalization group flows for the brane couplings. We construct the tree level renormalization group equations for these couplings as well as the one-loop corrections to these flows from bulk-to-brane renormalization effects.Comment: 16 pages, LaTeX. References and an appendix adde

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the tex

An alternative approach to the construction of Schur-Weyl transform

We propose an alternative approach for the construction of the unitary matrix which performs generalized unitary rotations of the system consisting of independent identical subsystems (for example spin system). This matrix, when applied to the system, results in a change of degrees of freedom, uncovering the information hidden in non-local degrees of freedom. This information can be used, inter alia, to study the structure of entangled states, their classification and may be useful for construction of quantum algorithms.Comment: 6 page

Unveiling the nature of INTEGRAL objects through optical spectroscopy. VIII. Identification of 44 newly detected hard X-ray sources

(abridged) Hard X-ray surveys performed by the INTEGRAL satellite have discovered a conspicuous fraction (up to 30%) of unidentified objects among the detected sources. Here we continue our identification program by selecting probable optical candidates using positional cross-correlation with soft X-ray, radio, and/or optical archives, and performing optical spectroscopy on them. As a result, we identified or more accurately characterized 44 counterparts of INTEGRAL sources: 32 active galactic nuclei, with redshift 0.019 < z < 0.6058, 6 cataclysmic variables (CVs), 5 high-mass X-ray binaries (2 of which in the Small Magellanic Cloud), and 1 low-mass X-ray binary. This was achieved by using 7 telescopes of various sizes and archival data from two online spectroscopic surveys. The main physical parameters of these hard X-ray sources were also determined using the available multiwavelength information. AGNs are the most abundant population among hard X-ray objects, and our results confirm this tendency when optical spectroscopy is used as an identification tool. The deeper sensitivity of recent INTEGRAL surveys enables one to begin detecting hard X-ray emission above 20 keV from sources such as LINER-type AGNs and non-magnetic CVs.Comment: 22 pages, 14 figures, 6 tables, accepted for publication on A&A, main journa

Unveiling the nature of INTEGRAL objects through optical spectroscopy. IX. 22 more identifications, and a glance into the far hard X-ray Universe

(Abridged) Since its launch in October 2002, the INTEGRAL satellite has revolutionized our knowledge of the hard X-ray sky thanks to its unprecedented imaging capabilities and source detection positional accuracy above 20 keV. Nevertheless, many of the newly-detected sources in the INTEGRAL sky surveys are of unknown nature. The combined use of available information at longer wavelengths (mainly soft X-rays and radio) and of optical spectroscopy on the putative counterparts of these new hard X-ray objects allows us to pinpoint their exact nature. Continuing our long-standing program that has been running since 2004, and using 6 different telescopes of various sizes, we report the classification through optical spectroscopy of 22 more unidentified or poorly studied high-energy sources detected with the IBIS instrument onboard INTEGRAL. We found that 16 of them are active galactic nuclei (AGNs), while the remaining 6 objects are within our Galaxy. Among the identified extragalactic sources, 14 are Type 1 AGNs; of these, 6 lie at redshift larger than 0.5 and one has z = 3.12, which makes it the second farthest object detected in the INTEGRAL surveys up to now. The remaining AGNs are of type 2, and one of them is a pair of interacting Seyfert 2 galaxies. The Galactic objects are identified as two cataclysmic variables, one high-mass X-ray binary, one symbiotic binary and two chromospherically active stars. We thus still find that AGNs are the most abundant population among hard X-ray objects identified through optical spectroscopy. Moreover, we note that the higher sensitivity of the more recent INTEGRAL surveys is now enabling the detection of high-redshift AGNs, thus allowing the exploration of the most distant hard X-ray emitting sources and possibly of the most extreme blazars.Comment: 18 pages, 9 figures, 8 tables, accepted for publication on Astronomy & Astrophysics, main journa

Atomic Resonance and Scattering

Contains research objectives and summary of research on eight research projects.National Science Foundation (Grant PHY75-15421-A01)U. S. Air Force - Office of Scientific Research (Grant AFOSR 76-2972)Joint Services Electronics Program (Contract DAAB07-76-C-1400)U. S. Air Force - Office of Scientific Research (Contract F44620-72-C-0057