Double standard polynucleotides: two typical alternative conformations for nucleic acids

Two typical alternative conformations for double strandee polynucleotides with Watson-Crick base pairing scheme are presented. these types avoid tangling of the chains. Representative models of these types with two different views, to show the similarity and dissimilarity between these models and the Watson-Crick model, are given

Description of ring puckering of furanose: an analytical approach

An analytical approach for the description of the ring puckerings from the endocyclic ring torsion angles of a five-membered saturated ring is given. This description is independent of any reference conformation. For the description, a revised notation for the endocyclic ring torsion angles has been suggested. The application of this method to the furanose ring is described in detail

High-spin structure and Band Termination in 103^{103}Cd

Excited states of the neutron deficient $^{103}$Cd nucleus have been investigated via the $^{72}$Ge($^{35}$Cl, p3n) reaction at beam energy of 135 MeV by use of in-beam spectroscopic methods. Gamma rays depopulating the excited states were detected using the Gammasphere spectrometer with high-fold $\gamma$-ray coincidences. A quadrupole $\gamma$-ray coincidence analysis ($\gamma^{4}$) has been used to extend the known level scheme. The positive parity levels have been established up to $J = 35/2\hbar$ and $E_{x} = 7.071$ MeV. In addition to the observation of highly-fragmented level scheme belonging to the positive-parity sequences at E$_{x}\sim$ 5 MeV, the termination of a negative-parity sequence connected by $E2$ transitions has been established at $J = 47/2 \hbar$ and $E_{x} = 11.877$ MeV. The experimental results corresponding to both the positive- and negative-parity sequences have been theoretically interpreted in the framework of the core particle coupling model. Evidence is presented for a shape change from collective prolate to non-collective oblate above the $J^{\pi} = 39/2^{-}$ (8011 keV) level and for a smooth termination of the negative-parity band.Comment: 19 pages, 8 figures. Submitted to Phys. Rev.

High-spin structure and Band Termination in 103^{103}Cd

Excited states of the neutron deficient $^{103}$Cd nucleus have been investigated via the $^{72}$Ge($^{35}$Cl, p3n) reaction at beam energy of 135 MeV by use of in-beam spectroscopic methods. Gamma rays depopulating the excited states were detected using the Gammasphere spectrometer with high-fold $\gamma$-ray coincidences. A quadrupole $\gamma$-ray coincidence analysis ($\gamma^{4}$) has been used to extend the known level scheme. The positive parity levels have been established up to $J = 35/2\hbar$ and $E_{x} = 7.071$ MeV. In addition to the observation of highly-fragmented level scheme belonging to the positive-parity sequences at E$_{x}\sim$ 5 MeV, the termination of a negative-parity sequence connected by $E2$ transitions has been established at $J = 47/2 \hbar$ and $E_{x} = 11.877$ MeV. The experimental results corresponding to both the positive- and negative-parity sequences have been theoretically interpreted in the framework of the core particle coupling model. Evidence is presented for a shape change from collective prolate to non-collective oblate above the $J^{\pi} = 39/2^{-}$ (8011 keV) level and for a smooth termination of the negative-parity band.Comment: 19 pages, 8 figures. Submitted to Phys. Rev.

A Composite Chiral Pair of Rotational Bands in the odd-A Nucleus 135Nd

High-spin states in 135Nd were populated with the 110Pd(30Si,5n)135Nd reaction at a 30Si bombarding energy of 133 MeV. Two Delta(I)=1 bands with close excitation energies and the same parity were observed. These bands are directly linked by Delta(I)=1 and Delta(I)=2 transitions. The chiral nature of these two bands is confirmed by comparison with three-dimensional tilted axis cranking calculations. This is the first observation of a three-quasiparticle chiral structure and established the primarily geometric nature of this phenomenon.Comment: 10 pages, 5 figures (1 in color), 1 table, submitted to Physics Review Letters, written in REVTEX4 forma

Lifetime measurements of Triaxial Strongly Deformed bands in 163^{163}Tm

With the Doppler Shift Attenuation Method, quadrupole transition moments, $Q_t$, were determined for the two recently proposed Triaxial Strongly Deformed (TSD) bands in $^{163}$Tm. The measured $Q_t$ moments indicate that the deformation of these bands is larger than that of the yrast, signature partners. However, the measured values are smaller than those predicted by theory. This observation appears to be valid for TSD bands in several nuclei of the regionComment: 8 pages, 5 figures. Submitted to Physical Review

Impact of germline and somatic missense variations on drug binding sites.

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein\u27s gene. To identify the nsSNVs that may affect drug binding, protein-drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein-drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein-drug binding sites. Using this method we identified 12 993 amino acid-drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid-drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid-drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid-drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein-drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein-drug binding predicted drug target proteins and prevalence of both somatic and germline nsSNVs that disrupt these binding sites can provide valuable knowledge for personalized medicine treatment. A web portal is available where nsSNVs from individual patient can be checked by scanning against DrugVar to determine whether any of the SNVs affect the binding of any drug in the database.The Pharmacogenomics Journal advance online publication, 26 January 2016; doi:10.1038/tpj.2015.97

An Intrinsically Disordered Region of the Acetyltransferase p300 with Similarity to Prion-Like Domains Plays a Role in Aggregation

Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface for various misfolded proteins, promoting their aggregation. p300 enhances aggregation of TAU and of p53 and is a component of cellular aggregates in both tissue culture cells and in alpha-synuclein positive Lewy bodies of patients affected by Parkinson disease. Down-regulation of p300 impairs aggresome formation and enhances cytotoxicity induced by misfolded protein stress. These data unravel a novel activity of p300, offer new insights into the function of disordered domains and implicate p300 in pathological aggregation that occurs in neurodegeneration and cancer

Cast CF8C-Plus Stainless Steel for Turbocharger Applications

The purpose of this Cooperative Research and Development Agreement (CRADA) project is to provide the critical test data needed to qualify CF8C-Plus cast stainless steel for commercial production and use for turbocharger housings with upgraded performance and durability relative to standard commercial cast irons or stainless steels. The turbocharger technologies include, but are not limited to, heavy-duty highway diesel engines, and passenger vehicle diesel and gasoline engines. This CRADA provides additional critical high-temperature mechanical properties testing and data analysis needed to quality the new CF8C-Plus steels for turbocharger housing applications

Level Structure of 103Ag at high spins

High spin states in $^{103}$Ag were investigated with the Gammasphere array, using the $^{72}$Ge($^{35}$Cl,$2p2n$)$^{103}$Ag reaction at an incident beam energy of 135 MeV. A $\Delta J$=1 sequence with predominantly magnetic transitions and two nearly-degenerate $\Delta J=1$ doublet bands have been observed. The dipole band shows a decreasing trend in the $B(M1)$ strength as function of spin, a well established feature of magnetic bands. The nearly-degenerate band structures satisfy the three experimental signatures of chirality in the nuclei; however microscopic calculations are indicative of a magnetic phenomeno