NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules

Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/

An aperture masking mode for the MICADO instrument

MICADO is a near-IR camera for the Europea ELT, featuring an extended field (75" diameter) for imaging, and also spectrographic and high contrast imaging capabilities. It has been chosen by ESO as one of the two first-light instruments. Although it is ultimately aimed at being fed by the MCAO module called MAORY, MICADO will come with an internal SCAO system that will be complementary to it and will deliver a high performance on axis correction, suitable for coronagraphic and pupil masking applications. The basis of the pupil masking approach is to ensure the stability of the optical transfer function, even in the case of residual errors after AO correction (due to non common path errors and quasi-static aberrations). Preliminary designs of pupil masks are presented. Trade-offs and technical choices, especially regarding redundancy and pupil tracking, are explained.Comment: SPIE 2014 Proceeding -- Montrea

Detection of the Sgr A* activity at 3.8 and 4.8 microns with NACO

L'-band (lambda=3.8 microns) and M'-band (lambda=4.8 microns) observations of the Galactic Center region, performed in 2003 at VLT (ESO) with the adaptive optics imager NACO, have lead to the detection of an infrared counterpart of the radio source Sgr A* at both wavelengths. The measured fluxes confirm that the Sgr A* infrared spectrum is dominated by the synchrotron emission of nonthermal electrons. The infrared counterpart exhibits no significant short term variability but demonstrates flux variations on daily and yearly scales. The observed emission arises away from the position of the dynamical center of the S2 orbit and would then not originate from the closest regions of the black hole.Comment: 5 pages, 3 figures, accepted in Astronomy & Astrophysic

Src phosphorylation converts Mdm2 from a ubiquitinating to a neddylating E3 ligase

Murine double minute-2 protein (Mdm2) is a multifaceted phosphorylated protein that plays a role in regulating numerous proteins including the tumor suppressor protein p53. Mdm2 binds to and is involved in conjugating either ubiquitin or Nedd8 (Neural precursor cell expressed, developmentally down-regulated 8) to p53. Although regulation of the E3 ubiquitin activity of Mdm2 has been investigated, regulation of the neddylating activity of Mdm2 remains to be defined. Here we show that activated c-Src kinase phosphorylates Y281 and Y302 of Mdm2, resulting in an increase in Mdm2 stability and its association with Ubc12, the E2 enzyme of the neddylating complex. Mdm2-dependent Nedd8 conjugation of p53 results in transcriptionally inactive p53, a process that is reversed with a small molecule inhibitor to either Src or Ubc12. Thus, our studies reveal how Mdm2 may neutralize and elevate p53 in actively proliferating cells and also provides a rationale for using therapies that target the Nedd8 pathway in wild-type p53 tumors

The FALCON concept: multi-object spectroscopy combined with MCAO in near-IR

A large fraction of the present-day stellar mass was formed between z=0.5 and z~3 and our understanding of the formation mechanisms at work at these epochs requires both high spatial and high spectral resolution: one shall simultaneously} obtain images of objects with typical sizes as small as 1-2kpc(~0''.1), while achieving 20-50 km/s (R >= 5000) spectral resolution. The obvious instrumental solution to adopt in order to tackle the science goal is therefore a combination of multi-object 3D spectrograph with multi-conjugate adaptive optics in large fields. A partial, but still competitive correction shall be prefered, over a much wider field of view. This can be done by estimating the turbulent volume from sets of natural guide stars, by optimizing the correction to several and discrete small areas of few arcsec2 selected in a large field (Nasmyth field of 25 arcmin) and by correcting up to the 6th, and eventually, up to the 60th Zernike modes. Simulations on real extragalactic fields, show that for most sources (>80%), the recovered resolution could reach 0".15-0".25 in the J and H bands. Detection of point-like objects is improved by factors from 3 to >10, when compared with an instrument without adaptive correction. The proposed instrument concept, FALCON, is equiped with deployable mini-integral field units (IFUs), achieving spectral resolutions between R=5000 and 20000. Its multiplex capability, combined with high spatial and spectral resolution characteristics, is a natural ground based complement to the next generation of space telescopes.Comment: ESO Workshop Proceedings: Scientific Drivers for ESO Future VLT/VLTI Instrumentation, 10 pages and 5 figure

Adaptive Optics for Astronomy

Adaptive Optics is a prime example of how progress in observational astronomy can be driven by technological developments. At many observatories it is now considered to be part of a standard instrumentation suite, enabling ground-based telescopes to reach the diffraction limit and thus providing spatial resolution superior to that achievable from space with current or planned satellites. In this review we consider adaptive optics from the astrophysical perspective. We show that adaptive optics has led to important advances in our understanding of a multitude of astrophysical processes, and describe how the requirements from science applications are now driving the development of the next generation of novel adaptive optics techniques.Comment: to appear in ARA&A vol 50, 201

VLT/NACO adaptive optics imaging of the TY CrA system - A fourth stellar component candidate detected

We report the detection of a possible subsolar mass companion to the triple young system TY CrA using the NACO instrument at the VLT UT4 during its commissioning. Assuming for TY CrA a distance similar to that of the close binary system HD 176386, the photometric spectral type of this fourth stellar component candidate is consistent with an ~M4 star. We discuss the dynamical stability of this possible quadruple system as well as the possible location of dusty particles inside or outside the system.Comment: 4 pages, 2 figures postscrip

A fast ILP-based Heuristic for the robust design of Body Wireless Sensor Networks

We consider the problem of optimally designing a body wireless sensor network, while taking into account the uncertainty of data generation of biosensors. Since the related min-max robustness Integer Linear Programming (ILP) problem can be difficult to solve even for state-of-the-art commercial optimization solvers, we propose an original heuristic for its solution. The heuristic combines deterministic and probabilistic variable fixing strategies, guided by the information coming from strengthened linear relaxations of the ILP robust model, and includes a very large neighborhood search for reparation and improvement of generated solutions, formulated as an ILP problem solved exactly. Computational tests on realistic instances show that our heuristic finds solutions of much higher quality than a state-of-the-art solver and than an effective benchmark heuristic.Comment: This is the authors' final version of the paper published in G. Squillero and K. Sim (Eds.): EvoApplications 2017, Part I, LNCS 10199, pp. 1-17, 2017. DOI: 10.1007/978-3-319-55849-3\_16. The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-55849-3_1

EAGLE multi-object AO concept study for the E-ELT

EAGLE is the multi-object, spatially-resolved, near-IR spectrograph instrument concept for the E-ELT, relying on a distributed Adaptive Optics, so-called Multi Object Adaptive Optics. This paper presents the results of a phase A study. Using 84x84 actuator deformable mirrors, the performed analysis demonstrates that 6 laser guide stars and up to 5 natural guide stars of magnitude R<17, picked-up in a 7.3' diameter patrol field of view, allow us to obtain an overall performance in terms of Ensquared Energy of 35% in a 75x75 mas^2 spaxel at H band, whatever the target direction in the centred 5' science field for median seeing conditions. The computed sky coverage at galactic latitudes |b|~60 is close to 90%.Comment: 6 pages, to appear in the proceedings of the AO4ELT conference, held in Paris, 22-26 June 200