Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Background: Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. Results: Common fragile sites were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Moreover we showed how the internal organization of the graph in communities and even in very simple subgraphs can be a starting point for the identification of new factors of instability at common fragile sites. Conclusion: We developed a computational method addressing the fundamental issue of studying the functional content of common fragile sites. Our analysis integrated two different approaches. First, data on common fragile site expression were analyzed in a complex networks framework. Second, outcomes of the network statistical description served as sources for the functional annotation of genes at common fragile sites by means of the Gene Ontology vocabulary. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression

Implementation of screened hybrid functionals based on the Yukawa potential within the LAPW basis set

The implementation of screened hybrid functionals into the WIEN2k code, which is based on the LAPW basis set, is reported. The Hartree-Fock exchange energy and potential are screened by means of the Yukawa potential as proposed by Bylander and Kleinman [Phys. Rev. B 41, 7868 (1990)] for the calculation of the electronic structure of solids with the screened-exchange local density approximation. Details of the formalism, which is based on the method of Massidda, Posternak, and Baldereschi [Phys. Rev. B 48, 5058 (1993)] for the unscreened Hartree-Fock exchange are given. The results for the transition-energy and structural properties of several test cases are presented. Results of calculations of the Cu electric-field gradient in Cu2O are also presented, and it is shown that the hybrid functionals are much more accurate than the standard local-density or generalized gradient approximations

Chiral Plaquette Polaron Theory of Cuprate Superconductivity

Ab-initio density functional calculations on explicitly doped La(2-x)Sr(x)CuO4 find doping creates localized holes in out-of-plane orbitals. A model for superconductivity is developed based on the assumption that doping leads to the formation of holes on a four-site Cu plaquette composed of the out-of-plane A1 orbitals apical O pz, planar Cu dz2, and planar O psigma. This is in contrast to the assumption of hole doping into planar Cu dx2-y2 and O psigma orbitals as in the t-J model. Interaction of holes with the d9 spin background leads to chiral polarons with either a clockwise or anti-clockwise charge current. When the polaron plaquettes percolate through the crystal at x~0.05 for LaSrCuO, a Cu dx2-y2 and planar O psigma band is formed. Spin exchange Coulomb repulsion with chiral polarons leads to D-wave superconductivity. The equivalent of the Debye energy in phonon superconductivity is the maximum energy separation between a chiral polaron and its time-reversed partner. An additive skew-scattering contribution to the Hall effect is induced by chiral polarons and leads to a temperature dependent Hall effect that fits the measured values for LaSrCuO. The integrated imaginary susceptibility satisfies omega/T scaling due to chirality and spin-flip scattering of polarons along with a uniform distribution of polaron energy splittings. The derived functional form is compatible with experiments. The static spin structure factor is computed and is incommensurate with a separation distance from (pi,pi) given by ~(2pi)x. Coulomb scattering of the x2-y2 band with polarons leads to linear resistivity. Coupling of the x2-y2 band to the undoped Cu d9 spins leads to the ARPES pseudogap and its doping and temperature dependence.Comment: 32 pages, 17 figure

The importance of anisotropic Coulomb interaction in LaMnO3

In low-temperature anti-ferromagnetic LaMnO3, strong and localized electronic interactions among Mn 3d electrons prevent a satisfactory description from standard local density and generalized gradient approximations in density functional theory calculations. Here we show that the strong on-site electronic interactions are described well only by using direct and exchange corrections to the intra-orbital Coulomb potential. Only DFT+U calculations with explicit exchange corrections produce a balanced picture of electronic, magnetic and structural observables in agreement with experiment. To understand the reason, a rewriting of the functional form of the +U corrections is presented that leads to a more physical and transparent understanding of the effect of these correction terms. The approach highlights the importance of Hund’s coupling (intra-orbital exchange) in providing anisotropy across the occupation and energy eigenvalues of the Mn d states. This intra-orbital exchange is the key to fully activating the Jahn-Teller distortion, reproducing the experimental band gap and stabilizing the correct magnetic ground state in LaMnO3. The best parameter values for LaMnO3 within the DFT(PBEsol)+U framework are determined to be U = 8 eV and J = 1.9 eV

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. CFS were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression.Comment: 18 pages, accepted for publication in BMC Bioinformatic

Graphitic Carbon Nitride Materials for Energy Applications

Polymeric layered carbon nitrides were investigated for use as catalyst support materials for proton exchange membrane fuel cells (PEMFCs) and water electrolyzers (PEMWEs). Three different carbon nitride materials were prepared: a heptazine-based graphitic carbon nitride material (gCNM), poly (triazine) imide carbon nitride intercalated with LiCl component (PTI-Li+Cl-) and boron-doped graphitic carbon nitride (B-gCNM). Following accelerated corrosion testing, all graphitic carbon nitride materials were found to be more electrochemically stable compared to conventional carbon black (Vulcan XC-72R) with B-gCNM support showing the best stability. For the supported Pt, Pt/PTI-Li+Cl- exhibited the best durability with only 19% electrochemical surface area (ECSA) loss versus 36% for Pt/Vulcan. Superior methanol oxidation activity was observed for all gCNM supported Pt catalysts on the basis of the catalyst ECSA. Preliminary results on IrO2 supported on gCNM using a PEMWE cell revealed an enhancement in the charge-transfer resistance as the current density increases when compared to unsupported IrO2. This may be attributed to a higher active surface area of the catalyst nanoparticles on the gCNM support

Production of Magnetic Arsenic–Phosphorus Alloy Nanoribbons with Small Band Gaps and High Hole Conductivities

Quasi-1D nanoribbons provide a unique route to diversifying the properties of their parent 2D nanomaterial, introducing lateral quantum confinement and an abundance of edge sites. Here, a new family of nanomaterials is opened with the creation of arsenic–phosphorus alloy nanoribbons (AsPNRs). By ionically etching the layered crystal black arsenic–phosphorus using lithium electride followed by dissolution in amidic solvents, solutions of AsPNRs are formed. The ribbons are typically few-layered, several micrometers long with widths tens of nanometers across, and both highly flexible and crystalline. The AsPNRs are highly electrically conducting above 130 K due to their small band gap (ca. 0.035 eV), paramagnetic in nature, and have high hole mobilities, as measured with the first generation of AsP devices, directly highlighting their properties and utility in electronic devices such as near-infrared detectors, quantum computing, and charge carrier layers in solar cells

Spectroscopic and computational insights on catalytic synergy in bimetallic aluminophosphate catalysts

A combined electronic structure computational and X-ray absorption spectroscopy study was used to investigate the nature of the active sites responsible for catalytic synergy in Co-Ti bimetallic nanoporous frameworks. Probing the nature of the molecular species at the atomic level has led to the identification of a unique Co-O-Ti bond, which serves as the loci for the superior performance of the bimetallic catalyst, when compared with its analogous monometallic counterpart. The structural and spectroscopic features associated with this active site have been characterized and contrasted, with a view to affording structure property relationships, in the wider context of designing sustainable catalytic oxidations with porous solids

Vitamin C Enhances Vitamin E Status and Reduces Oxidative Stress Indicators in Sea Bass Larvae Fed High DHA Microdiets

Docosahexaenoic acid (DHA) is an essential fatty acid necessary for many biochemical, cellular and physiological functions in fish. However, high dietary levels of DHA increase free radical injury in sea bass (Dicentrarchus labrax) larvae muscle, even when vitamin E (α-tocopherol, α-TOH) is increased. Therefore, the inclusion of other nutrients with complementary antioxidant functions, such as vitamin C (ascorbic acid, vitC), could further contribute to prevent these lesions. The objective of the present study was to determine the effect of vitC inclusion (3,600 mg/kg) in high DHA (5 % DW) and α-TOH (3,000 mg/kg) microdiets (diets 5/3,000 and 5/3,000 + vitC) in comparison to a control diet (1 % DHA DW and 1,500 mg/kg of α-TOH; diet 1/1,500) on sea bass larvae growth, survival, whole body biochemical composition and thiobarbituric acid reactive substances (TBARS) content, muscle morphology, skeletal deformities and antioxidant enzymes, insulin-like growth factors (IGFs) and myosin expression (MyHC). Larvae fed diet 1/1,500 showed the best performance in terms of total length, incidence of muscular lesions and ossification degree. IGFs gene expression was elevated in 5/3,000 diet larvae, suggesting an increased muscle mitogenesis that was confirmed by the increase in the mRNA copies of MyHC. vitC effectively controlled oxidative damages in muscle, increased α-TOH larval contents and reduced TBARS content and the occurrence of skull deformities. The results of the present study showed the antioxidant synergism between vitamins E and C when high contents of DHA are included in sea bass larvae diets

Genome wide survey of MicroRNA-transcription factor feed-forward regulatory circuits in human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail