Large Charge Four-Dimensional Non-Extremal N=2 Black Holes with R^2-Terms

We consider N=2 supergravity in four dimensions with small R^2 curvature corrections. We construct large charge non-extremal black hole solutions in all space, with either a supersymmetric or a non-supersymmetric extremal limit, and analyze their thermodynamic properties. This generalizes some of the extremal solutions presented in [arXiv:0902.0831]. The indexed entropy of the non-extremal extension of the supersymmetric black hole, has the form of the extremal entropy, with the charges replaced by a function of the charges, the moduli at infinity and the non-extremality parameter. This is the same behavior as in the case without R^2-terms.Comment: 13 pages. v2: stripped down to letter format, based on the background given in [arXiv:0902.0831]. v3: up to date with CQG versio

Black Holes in Ho\v{r}ava Gravity with Higher Derivative Magnetic Terms

We consider Horava gravity coupled to Maxwell and higher derivative magnetic terms. We construct static spherically symmetric black hole solutions in the low-energy approximation. We calculate the horizon locations and temperatures in the near-extremal limit, for asymptotically flat and (anti-)de Sitter spaces. We also construct a detailed balanced version of the theory, for which we find projectable and non-projectable, non-perturbative solutions.Comment: 17 pages. v2: Up to date with published version; some minor remarks and more reference

Molecular Anthropology Meets Genetic Medicine to Treat Blindness in the North African Jewish Population: Human Gene Therapy Initiated in Israel

Abstract The history of the North African Jewish community is ancient and complicated with a number of immigration waves and persecutions dramatically affecting its population size. A decade-long process in Israel of clinicalmolecular screening of North African Jews with incurable autosomal recessive blindness led to the identification of a homozygous splicing mutation (c.95-2A > T; IVS2-2A > T) in RPE65, the gene encoding the isomerase that catalyzes a key step in the retinoid-visual cycle, in patients from 10 unrelated families. A total of 33 patients (four now deceased) had the severe childhood blindness known as Leber congenital amaurosis (LCA), making it the most common cause of retinal degeneration in this population. Haplotype analysis in seven of the patients revealed a shared homozygous region, indicating a population-specific founder mutation. The age of the RPE65 founder mutation was estimated to have emerged 100-230 (mean, 153) generations ago, suggesting it originated before the establishment of the Jewish community in North Africa. Individuals with this RPE65 mutation were characterized with retinal studies to determine if they were candidates for gene replacement, the recent and only therapy to date for this otherwise incurable blindness. The step from molecular anthropological studies to application of genetic medicine was then taken, and a representative of this patient subgroup was treated with subretinal rAAV2-RPE65 gene therapy. An increase in vision was present in the treated area as early as 15 days after the intervention. This process of genetically analyzing affected isolated populations as a screen for genebased therapy suggests a new paradigm for disease diagnosis and treatment

Monte Carlo Techniques for Drug Design: The Success Case of PELE

This chapter summarizes the most representative software packages that readily allow running Monte Carlo (MC) simulations in relevant scenarios for drug design. It explores in detail the Protein Energy Landscape Exploration (PELE) program, providing first the main characteristics of the technique, followed by an analysis of the different application studies in mapping protein‐ligand interactions. The ligand, formed by a rigid core and a set of rotatable side chains, is perturbed by translating and rotating it. PELE creates a list of perturbation poses, and then chooses the one with the lowest system energy. PELE was originally designed to map ligand migration pathways: its first applications aimed at finding exit pathways starting from ligand‐bound crystallographic structures. Additional applied studies have centered on modeling enzymatic mechanisms and engineering; the same techniques applied in mapping protein‐drug interactions can be used in the study of substrate recognition by enzymes.Along the development of PELE in the last years, we gratefully acknowledge financial support from the European Union (in particular from the ERC program) and from the Catalan and Spanish Governments. In addition we want to thank all present and past members from the EAPM lab. at BSC for their dedication and work.Peer ReviewedPostprint (author's final draft

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Protein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate—the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Rotamerically Induced Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to its computational efficiency, RIP can be applied to every residue in a protein, producing a global map of deformability. This map is remarkably sparse, with the dominant sites of deformation generally found on the protein surface. The global map can be used to identify loops and helices that are less tightly bound to the protein and thus are likely sites of dynamic modulation that may have important functional consequences. Additionally, they identify individual residues that have the potential to drive large-scale coherent conformational change. Applying RIP to two well-studied proteins, Dihdydrofolate Reductase and Triosephosphate Isomerase, which possess functionally-relevant mobile loops that fluctuate on the microsecond/millisecond timescale, the RIP deformation map identifies and recapitulates the flexibility of these elements. In contrast, the RIP deformation map of α-lytic protease, a kinetically stable protein, results in a map with no significant deformations. In the N-terminal domain of HSP90, the RIP deformation map clearly identifies the ligand-binding lid as a highly flexible region capable of large conformational changes. In the Estrogen Receptor ligand-binding domain, the RIP deformation map is quite sparse except for one large conformational change involving Helix-12, which is the structural element that allosterically links ligand binding to receptor activation. RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states

Loss of the Metalloprotease ADAM9 Leads to Cone-Rod Dystrophy in Humans and Retinal Degeneration in Mice

Cone-rod dystrophy (CRD) is an inherited progressive retinal dystrophy affecting the function of cone and rod photoreceptors. By autozygosity mapping, we identified null mutations in the ADAM metallopeptidase domain 9 (ADAM9) gene in four consanguineous families with recessively inherited early-onset CRD. We also found reduced photoreceptor responses in Adam9 knockout mice, previously reported to be asymptomatic. In 12-month-old knockout mice, photoreceptors appear normal, but the apical processes of the retinal pigment epithelium (RPE) cells are disorganized and contact between photoreceptor outer segments (POSs) and the RPE apical surface is compromised. In 20-month-old mice, there is clear evidence of progressive retinal degeneration with disorganized POS and thinning of the outer nuclear layer (ONL) in addition to the anomaly at the POS-RPE junction. RPE basal deposits and macrophages were also apparent in older mice. These findings therefore not only identify ADAM9 as a CRD gene but also identify a form of pathology wherein retinal disease first manifests at the POS-RPE junction

Mutagenesis and Functional Studies with Succinate Dehydrogenase Inhibitors in the Wheat Pathogen Mycosphaerella graminicola

A range of novel carboxamide fungicides, inhibitors of the succinate dehydrogenase enzyme (SDH, EC 1.3.5.1) is currently being introduced to the crop protection market. The aim of this study was to explore the impact of structurally distinct carboxamides on target site resistance development and to assess possible impact on fitness

Cash transfers for sustainable rural livelihoods? Examining the long-term productive effects of the Child Support Grant in South Africa

Cash transfers have received increased scholarly and policy attention, as a means of reducing poverty in the global South. While cash transfers are primarily intended to prevent impoverishment and deprivation, several studies suggest they can have 'productive' impacts, contributing to building sustainable livelihoods. However, pilot projects of unconditional cash transfers have often been too brief or too recent to determine how small, but regular, transfers can improve rural livelihoods over time. This paper explores potential long-term productive effects of cash transfers on rural household's livelihoods. This is done through revisiting, after 14 years, all (273) households in two South African villages included in an extensive livelihood and asset survey in 2002. That survey predated the phasing in of the Child Support Grant (CSG), targeted at impoverished children. When re-surveyed in 2016, some households had cumulatively received significant, while others little or no CSG income. Multivariate regression analysis shows how households that received more CGS income were more likely to invest in productive assets (e.g. small ploughs), and engage in poultry, staple crop and vegetable production