The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain

Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region.Fil: Collin, Alejandro Alberto. Universidad Nacional de Córdoba. Facultad de Medicina. Cátedra de Bioquímica y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Ciencias de la Salud. Universidad Nacional de Córdoba. Instituto de Investigaciones en Ciencias de la Salud; ArgentinaFil: González Jiménez, Araceli. Universidad de Salamanca; EspañaFil: González Jiménez, María Del Carmen. Universidad de Salamanca; EspañaFil: Alfonso, Manuel J. Universidad de Salamanca; EspañaFil: Calvo, Olga. Universidad de Salamanca; Españ

Microstructure Effects for Casimir Forces in Chiral Metamaterials

We examine a recent prediction for the chirality-dependence of the Casimir force in chiral metamaterials by numerical computation of the forces between the exact microstructures, rather than homogeneous approximations. We compute the exact force for a chiral bent-cross pattern, as well as forces for an idealized "omega"-particle medium in the dilute approximation and identify the effects of structural inhomogeneity (i.e. proximity forces and anisotropy). We find that these microstructure effects dominate the force for separations where chirality was predicted to have a strong influence. To get observations of chirality free from microstructure effects, one must go to large separations where the effect of chirality is at most $\sim10^{-4}$ of the total force.Comment: 5 pages, 4 figure

Mass uptake during oxidation of metallic alloys: literature data collection, analysis, and FAIR sharing

The area-normalized change of mass ($\Delta$m/A) with time during the oxidation of metallic alloys is commonly used to assess oxidation resistance. Analyses of such data can also aid in evaluating underlying oxidation mechanisms. We performed an exhaustive literature search and digitized normalized mass change vs. time data for 407 alloys. To maximize the impact of these and future mass uptake data, we developed and published an open, online, computational workflow that fits the data to various models of oxidation kinetics, uses Bayesian statistics for model selection, and makes the raw data and model parameters available via a queryable database. The tool, Refractory Oxidation Database (https://nanohub.org/tools/refoxdb/), uses nanoHUB's Sim2Ls to make the workflow and data (including metadata) findable, accessible, interoperable, and reusable (FAIR). We find that the models selected by the original authors do not match the most likely one according to the Bayesian information criterion (BIC) in 71% of the cases. Further, in 56% of the cases, the published model was not even in the top 3 models according to the BIC. These numbers were obtained assuming an experimental noise of 2.5% of the mass gain range, a smaller noise leads to more discrepancies. The RefOxDB tool is open access and researchers can add their own raw data (those to be included in future publications, as well as negative results) for analysis and to share their work with the community. Such consistent and systematic analysis of open, community generated data can significantly accelerate the development of machine-learning models for oxidation behavior and assist in the understanding and improvement of oxidation resistance

Dissipation-driven generation of two-qubit entanglement mediated by plasmonic waveguides

We study the generation of entanglement between two distant qubits mediated by the surface plasmons of a metallic waveguide. We show that a V-shaped channel milled in a flat metallic surface is much more efficient for this purpose than a metallic cylinder. The role of the misalignments of the dipole moments of the qubits, an aspect of great importance for experimental implementations, is also studied. A careful analysis of the quantum-dynamics of the system by means of a master equation shows that two-qubit entanglement generation is essentially due to the dissipative part of the effective qubit-qubit coupling provided by the surface plasmons. The influence of a coherent external pumping, needed to achieve a steady state entanglement, is discussed. Finally, we pay attention to the question of how to get information experimentally on the degree of entanglement achieved in the system.Comment: 13 pages, 12 figure

Ionization electron signal processing in single phase LArTPCs. Part I. Algorithm Description and quantitative evaluation with MicroBooNE simulation

We describe the concept and procedure of drifted-charge extraction developed in the MicroBooNE experiment, a single-phase liquid argon time projection chamber (LArTPC). This technique converts the raw digitized TPC waveform to the number of ionization electrons passing through a wire plane at a given time. A robust recovery of the number of ionization electrons from both induction and collection anode wire planes will augment the 3D reconstruction, and is particularly important for tomographic reconstruction algorithms. A number of building blocks of the overall procedure are described. The performance of the signal processing is quantitatively evaluated by comparing extracted charge with the true charge through a detailed TPC detector simulation taking into account position-dependent induced current inside a single wire region and across multiple wires. Some areas for further improvement of the performance of the charge extraction procedure are also discussed. Keywords: MicroBooNE, Signal Processing, Deconvolution, ROIUnited States. Department of Energy. High Energy Physics DivisionNational Science Foundation (U.S.)Swiss National Science FoundationScience and Technology Facilities Council (Great Britain)Royal Society (Great Britain

Antisense oligonucleotide-based splicing correction in individuals with leber congenital amaurosis due to compound heterozygosity for the c.2991+1655A>G mutation in CEP290

Leber congenital amaurosis (LCA) is a rare inherited retinal disorder affecting approximately 1:50,000 people worldwide. So far, mutations in 25 genes have been associated with LCA, with CEP290 (encoding the Centrosomal protein of 290 kDa) being the most frequently mutated gene. The most recurrent LCA-causing CEP290 mutation, c.2991+1655A>G, causes the insertion of a pseudoexon into a variable proportion of CEP290 transcripts. We previously demonstrated that antisense oligonucleotides (AONs) have a high therapeutic potential for patients homozygously harbouring this mutation, although to date, it is unclear whether rescuing one single allele is enough to restore CEP290 function. Here, we assessed the AON efficacy at RNA, protein and cellular levels in samples that are compound heterozygous for this mutation, together with a protein-truncating mutation in CEP290. We demonstrate that AONs can efficiently restore splicing and increase protein levels. However, due to a high variability in ciliation among the patient-derived cell lines, the efficacy of the AONs was more difficult to assess at the cellular level. This observation points towards the importance of the severity of the second allele and possibly other genetic variants present in each individual. Overall, AONs seem to be a promising tool to treat CEP290-associated LCA, not only in homozygous but also in compound heterozygous carriers of the c.2991+1655A>G variant

Nonmonotonic effects of parallel sidewalls on Casimir forces between cylinders

We analyze the Casimir force between two parallel infinite metal cylinders, with nearby metal plates (sidewalls), using complementary methods for mutual confirmation. The attractive force between cylinders is shown to have a nonmonotonic dependence on the separation to the plates. This intrinsically multi-body phenomenon, which occurs with either one or two sidewalls (generalizing an earlier result for squares between two sidewalls), does not follow from any simple two-body force description. We can, however, explain the nonmonotonicity by considering the screening (enhancement) of the interactions by the fluctuating charges (currents) on the two cylinders, and their images on the nearby plate(s). Furthermore, we show that this effect also implies a nonmonotonic dependence of the cylinder-plate force on the cylinder-cylinder separation.Comment: 5 pages, 4 figure

Directive excitation of guided electromagnetic waves through polarization control

Experimental evidence is reported on the control of the directionality of guided electromagnetic microwaves by the polarization of the exciting wave. Experiments are conducted using a two-dimensional waveguide made of two parallel aluminum plates. The upper plate, which has a linear array of holes, is externally illuminated by a polarized wave whose incident wavevector is contained within the mirror-symmetry plane defined by the linear array. Surprisingly, the measurements show that the propagation inside the waveguide is highly asymmetrical, and it is controlled by the polarization of the incoming wave. This extraordinary phenomenon is explained in terms of a simple model involving a set of dipoles that are excited at the hole positions. Our finding provides a powerful method to sort different polarizations of a free-space beam to different propagation directions of guided electromagnetic waves.The authors gratefully acknowledge B. Bernardo and A. Vila at Electromagnetic Radiation Group Universitat Politecnica de Valencia for the generous donation of the circular polarization antenna for the experiments. J.S.-D. thanks D. Torrent for useful discussions. Financial support from the Spanish Ministry of Economy and Competitiveness (Grants No. TEC2010-19751, No. TEC2011-28664-C02, and No. Consolider CSD2008-00066) is also acknowledged.Carbonell Olivares, J.; Rodríguez Fortuño, FJ.; Díaz Rubio, A.; Martínez Abietar, AJ.; Cervera Moreno, FS.; Sánchez-Dehesa Moreno-Cid, J. (2014). Directive excitation of guided electromagnetic waves through polarization control. Physical Review B. 89:155121-1-155121-7. https://doi.org/10.1103/PhysRevB.89.155121S155121-1155121-789Lin, J., Mueller, J. P. B., Wang, Q., Yuan, G., Antoniou, N., Yuan, X.-C., & Capasso, F. (2013). Polarization-Controlled Tunable Directional Coupling of Surface Plasmon Polaritons. Science, 340(6130), 331-334. doi:10.1126/science.1233746Huang, L., Chen, X., Bai, B., Tan, Q., Jin, G., Zentgraf, T., & Zhang, S. (2013). Helicity dependent directional surface plasmon polariton excitation using a metasurface with interfacial phase discontinuity. Light: Science & Applications, 2(3), e70-e70. doi:10.1038/lsa.2013.26Tsema, B. B., Tsema, Y. B., Shcherbakov, M. R., Lin, Y.-H., Liu, D.-R., Klimov, V. V., … Tsai, D. P. (2012). Handedness-sensitive emission of surface plasmon polaritons by elliptical nanohole ensembles. Optics Express, 20(10), 10538. doi:10.1364/oe.20.010538Drezet, A., Genet, C., Laluet, J.-Y., & Ebbesen, T. W. (2008). Optical chirality without optical activity: How surface plasmons give a twist to light. Optics Express, 16(17), 12559. doi:10.1364/oe.16.012559Schwanecke, A. S., Fedotov, V. A., Khardikov, V. V., Prosvirnin, S. L., Chen, Y., & Zheludev, N. I. (2008). Nanostructured Metal Film with Asymmetric Optical Transmission. Nano Letters, 8(9), 2940-2943. doi:10.1021/nl801794dMenzel, C., Helgert, C., Rockstuhl, C., Kley, E.-B., Tünnermann, A., Pertsch, T., & Lederer, F. (2010). Asymmetric Transmission of Linearly Polarized Light at Optical Metamaterials. Physical Review Letters, 104(25). doi:10.1103/physrevlett.104.253902Kang, M., Chen, J., Cui, H.-X., Li, Y., & Wang, H.-T. (2011). Asymmetric transmission for linearly polarized electromagnetic radiation. Optics Express, 19(9), 8347. doi:10.1364/oe.19.008347Mutlu, M., Akosman, A. E., Serebryannikov, A. E., & Ozbay, E. (2012). Diodelike Asymmetric Transmission of Linearly Polarized Waves Using Magnetoelectric Coupling and Electromagnetic Wave Tunneling. Physical Review Letters, 108(21). doi:10.1103/physrevlett.108.213905Lee, S. H., Choi, M., Kim, T.-T., Lee, S., Liu, M., Yin, X., … Min, B. (2012). Switching terahertz waves with gate-controlled active graphene metamaterials. Nature Materials, 11(11), 936-941. doi:10.1038/nmat3433Beruete, M., Navarro-Cía, M., & Sorolla, M. (2010). Strong lateral displacement in polarization anisotropic extraordinary transmission metamaterial. New Journal of Physics, 12(6), 063037. doi:10.1088/1367-2630/12/6/063037Rodriguez-Fortuno, F. J., Marino, G., Ginzburg, P., O’Connor, D., Martinez, A., Wurtz, G. A., & Zayats, A. V. (2013). Near-Field Interference for the Unidirectional Excitation of Electromagnetic Guided Modes. Science, 340(6130), 328-330. doi:10.1126/science.1233739Lee, S.-Y., Lee, I.-M., Park, J., Oh, S., Lee, W., Kim, K.-Y., & Lee, B. (2012). Role of Magnetic Induction Currents in Nanoslit Excitation of Surface Plasmon Polaritons. Physical Review Letters, 108(21). doi:10.1103/physrevlett.108.213907Pfeiffer, C., & Grbic, A. (2013). Metamaterial Huygens’ Surfaces: Tailoring Wave Fronts with Reflectionless Sheets. Physical Review Letters, 110(19). doi:10.1103/physrevlett.110.197401Carbonell, J., Díaz-Rubio, A., Torrent, D., Cervera, F., Kirleis, M. A., Piqué, A., & Sánchez-Dehesa, J. (2012). Radial Photonic Crystal for detection of frequency and position of radiation sources. Scientific Reports, 2(1). doi:10.1038/srep0055