d_{x^2-y^2} Symmetry and the Pairing Mechanism

An important question is if the gap in the high temperature cuprates has d_{x^2-y^2} symmetry, what does that tell us about the underlying interaction responsible for pairing. Here we explore this by determining how three different types of electron-phonon interactions affect the d_{x^2-y^2} pairing found within an RPA treatment of the 2D Hubbard model. These results imply that interactions which become more positive as the momentum transfer increases favor d_{x^2-y^2} pairing in a nearly half-filled band.Comment: 9 pages and 2 eps figs, uses revtex with epsf, in press, PR

Nonlinear Meissner Effect in CuO Superconductors

Recent theories of the NMR in the CuO superconductors are based on a spin-singlet $d_{x^2-y^2}$ order parameter. Since this state has nodal lines on the Fermi surface, nonlinear effects associated with low-energy quasiparticles become important, particularly at low temperatures. We show that the field-dependence of the supercurrent, below the nucleation field for vortices, can be used to locate the positions of the nodal lines of an unconventional gap in momentum space, and hence test the proposed $d_{x^2-y^2}$ state.Comment: 5 pages (RevTex), 1 figure (postscript file incl.

Quasiparticle Dispersion of the 2D Hubbard Model: From an Insulator to a Metal

On the basis of Quantum-Monte-Carlo results the evolution of the spectral weight $A(\vec k, \omega)$ of the two-dimensional Hubbard model is studied from insulating to metallic behavior. As observed in recent photoemission experiments for cuprates, the electronic excitations display essentially doping-independent features: a quasiparticle-like dispersive narrow band of width of the order of the exchange interaction $J$ and a broad valence- and conduction-band background. The continuous evolution is traced back to one and the same many-body origin: the doping-dependent antiferromagnetic spin-spin correlation.Comment: 11 pages, REVtex, 4 figures (in uuencoded postscript format

HOT or not: examining the basis of high-occupancy target regions

High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solemnly defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed 'hyper-ChIPable' regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies

OH+ in astrophysical media: state-to-state formation rates, Einstein coefficients and inelastic collision rates with He

The rate constants required to model the OH$^+$ observations in different regions of the interstellar medium have been determined using state of the art quantum methods. First, state-to-state rate constants for the H$_2(v=0,J=0,1)$+ O$^+$($^4S$) $\rightarrow$ H + OH$^+(X ^3\Sigma^-, v', N)$ reaction have been obtained using a quantum wave packet method. The calculations have been compared with time-independent results to asses the accuracy of reaction probabilities at collision energies of about 1 meV. The good agreement between the simulations and the existing experimental cross sections in the $0.01-$1 eV energy range shows the quality of the results. The calculated state-to-state rate constants have been fitted to an analytical form. Second, the Einstein coefficients of OH$^+$ have been obtained for all astronomically significant ro-vibrational bands involving the $X^3\Sigma^-$ and/or $A^3\Pi$ electronic states. For this purpose the potential energy curves and electric dipole transition moments for seven electronic states of OH$^+$ are calculated with {\it ab initio} methods at the highest level and including spin-orbit terms, and the rovibrational levels have been calculated including the empirical spin-rotation and spin-spin terms. Third, the state-to-state rate constants for inelastic collisions between He and OH$^+(X ^3\Sigma^-)$ have been calculated using a time-independent close coupling method on a new potential energy surface. All these rates have been implemented in detailed chemical and radiative transfer models. Applications of these models to various astronomical sources show that inelastic collisions dominate the excitation of the rotational levels of OH$^+$. In the models considered the excitation resulting from the chemical formation of OH$^+$ increases the line fluxes by about 10 % or less depending on the density of the gas

Clinical and molecular findings in 37 Turkish patients with isolated methylmalonic acidemia

BACKGROUND/AIM: Isolated methylmalonic acidemia is caused by complete or partial deficiency of the enzyme methylmalonyl-CoA mutase (mut0 or mut? enzymatic subtype), a defect of its cofactor adenosyl-cobalamin (cblA, cblB, or cblD-MMA) or deficiency of the enzyme methylmalonyl-CoA epimerase. While onset of the disease ranges from the neonatal period to adulthood, most cases present with lethargy, vomiting and ketoacidosis in the early infancy. Major secondary complications are; growth failure, developmental delay, interstitial nephritis with progressive renal failure, basal ganglia injury and cardiomyopathy. We aimed to demonstrate clinical and molecular findings based on long-term follow up in our patient cohort. MATERIALS AND METHODS: The study includes 37 Turkish patients with isolated MMA who were followed up for long term complications 1 to 14 years. All patients were followed up regularly with clinical, biochemical and dietary monitoring to determine long term complications. Next Generation Sequencing technique was used for mutation screening in five disease-causing genes including; MUT, MMAA, MMAB, MMADHC, MCEE genes. Mutation screening identified 30 different types of mutations. RESULTS: While 28 of these mutations were previously reported, one novel MMAA mutation p.H382Pfs*24 (c.1145delA) and one novel MUT mutation IVS3+1G>T(c.752+1G>T) has been reported. The most common clinical complications were growth retardation, renal involvement, mental motor retardation and developmental delay. Furthermore, one of our patients developed cardiomyopathy, another one died because of hepatic failure and one presented with lactic acidosis after linezolid exposure. CONCLUSIONS: We have detected two novel mutations, including one splice-site mutation in the MUT gene and one frame shift mutation in the MMAA gene in 37 Turkish patients. We confirm the genotype-phenotype correlation in the study population according to the long term complications

Understanding the Potential In Vitro Modes of Action of Bis(beta-diketonato) Oxovanadium(IV) Complexes

To understand the potential in vitro modes of action of bis(β-diketonato) oxovanadium(IV) complexes, nine compounds of varying functionality have been screened using a range of biological techniques. The antiproliferative activity against a range of cancerous and normal cell lines has been determined, and show these complexes are particularly sensitive against the lung carcinoma cell line, A549. Annexin V (apoptosis) and Caspase-3/7 assays were studied to confirm these complexes induce programmed cell death. While gel electrophoresis was used to determine DNA cleavage activity and production of reactive oxygen species (ROS), the Comet assay was used to determine induced genomic DNA damage. Additionally, Förster resonance energy transfer (FRET)-based DNA melting and fluorescent intercalation displacement assays have been used to determine the interaction of the complexes with double strand (DS) DNA and to establish preferential DNA base-pair binding (AT versus GC)

Slow release and delivery of antisense oligonucleotide drug by self-assembled peptide amphiphile nanofibers

Cataloged from PDF version of article.Antisense oligonucleotides provide a promising therapeutic approach for several disorders including cancer. Chemical stability, controlled release, and intracellular delivery are crucial factors determining their efficacy. Gels composed of nanofibrous peptide network have been previously suggested as carriers for controlled delivery of drugs to improve stability and to provide controlled release, but have not been used for oligonucleotide delivery. In this work, a self-assembled peptide nanofibrous system is formed by mixing a cationic peptide amphiphile (PA) with Bcl-2 antisense oligodeoxynucleotide (ODN), G3139, through electrostatic interactions. The self-assembly of PA-ODN gel was characterized by circular dichroism, rheology, atomic force microscopy (AFM) and scanning electron microscopy (SEM). AFM and SEM images revealed establishment of the nanofibrous PA-ODN network. Due to the electrostatic interactions between PA and ODN, ODN release can be controlled by changing PA and ODN concentrations in the PA-ODN gel. Cellular delivery of the ODN by PA-ODN nanofiber complex was observed by using fluorescently labeled ODN molecule. Cells incubated with PA-ODN complex had enhanced cellular uptake compared to cells incubated with naked ODN. Furthermore, Bcl-2 mRNA amounts were lower in MCF-7 human breast cancer cells in the presence of PA-ODN complex compared to naked ODN and mismatch ODN evidenced by quantitative RT-PCR studies. These results suggest that PA molecules can control ODN release, enhance cellular uptake and present a novel efficient approach for gene therapy studies and oligonucleotide based drug deliver