Labeling the human respiratory syncytial virus genomic RNA with exogenous probes for fluorescence and electron microscopy

A method for labeling the genomic RNA of the human respiratory syncytial virus, as well as for isolating and examining the labeled filamentous virions was achieved. This method utilized the multiply labeled tetravalent probe design, first described in Santangelo et al. 2009. It was shown that by introducing MTRIPs into RSV infected cells immediately before isolating virus, the genomic RNA within individual filamentous virions could be labeled and imaged. This process did not seem to decrease viral titer or affect viral morphology, and allowed for the imaging of the virus using fixed and live cell conventional fluorescence microscopy and super-resolution microscopic techniques such as dSTORM and STED. The imaging of other structural components of the virus, such as the M protein, and as was discovered, the M2-1 protein was also shown. Additionally, the virus was examined for host proteins of the RLR family, which are involved in the cellular innate immune response. It was found that the protein MDA5 was localized in the isolated filaments. Finally, gold nanoclusters were covalently bound to the RNA probe to create a probe that would generate contrast in cryo-TEM and cryo-ET. By hybridizing the probe to an mRNA encoding GFP, complexing it with a cationic lipid transfection agent, and delivering it to cells before plunge-freezing, it was demonstrated that the mRNA-lipoplex granules could be detected. In conclusion, the method allows for both dynamic and ultrastructural information about the viral genome to be gathered.Ph.D

Cutting sequences on Bouw-Moeller surfaces : an S-adic characterization.

Résumé. On considère un codage symbolique des géodésiques sur une famille de surfaces de Veech (surfaces de translation riches en symétries affines) récemment découverte par Bouw et Möller. Ces surfaces, comme l’a remarqué Hooper, peuvent être réalisées en coupant et collant une collection de polygones semi-réguliers. Dans cet article, on caractérise l’ensemble des suites symboliques (“suites de coupage”) qui correspondent au codage de trajectoires linéaires, à l’aide de la suite des côtés des polygones croisés. On donne une caractérisation complète de l’adhérence de l’ensemble des suites de coupage, dans l’esprit de la caractérisation classique des suites sturmiennes et de la récente caractérisation par Smillie-Ulcigrai des suites de coupage des trajectoires linéaires dans les polygones réguliers. La caractérisation est donnée en termes d’un système fini de substitutions (connu aussi sous le nom de présentation S-adique), réglé par une transformation unidimensionnelle qui ressemble à l’algorithme de fraction continue. Comme dans le cas sturmien et dans celui des polygones réguliers, la caractérisation est basée sur la renormalisation et sur la définition d’un opérateur combinatoire de dérivation approprié. Une des nouveautés est que la dérivation se fait en deux étapes, sans utiliser directement les éléments du groupe de Veech, mais en utilisant un difféomorphisme affine qui envoie une surface de Bouw-Möller vers sa surface “duale”, qui est dans le même disque de Teichmüller. Un outil technique utilisé est la présentation des surfaces de Bouw-Möller par les diagrammes de Hooper. ABSTRACT. We consider a symbolic coding for geodesics on the family of Veech surfaces (translation surfaces rich with affine symmetries) recently discovered by Bouw and Möller. These surfaces, as noticed by Hooper, can be realized by cutting and pasting a collection of semi-regular polygons. We characterize the set of symbolic sequences (cutting sequences) that arise by coding linear trajectories by the sequence of polygon sides crossed. We provide a full characterization for the closure of the set of cutting sequences, in the spirit of the classical characterization of Sturmian sequences and the recent characterization of Smillie-Ulcigrai of cutting sequences of linear trajectories on regular polygons. The characterization is in terms of a system of finitely many substitutions (also known as an S-adic presentation), governed by a one-dimensional continued fraction-like map. As in the Sturmian and regular polygon case, the characterization is based on renormalization and the definition of a suitable combinatorial derivation operator. One of the novelties is that derivation is done in two steps, without directly using Veech group elements, but by exploiting an affine diffeomorphism that maps a Bouw- Möller surface to the dual Bouw-Möller surface in the same Teichmüller disk. As a technical tool, we crucially exploit the presentation of Bouw-Möller surfaces via Hooper diagrams

SIMULATING SEISMIC WAVE PROPAGATION IN TWO-DIMENSIONAL MEDIA USING DISCONTINUOUS SPECTRAL ELEMENT METHODS

We introduce a discontinuous spectral element method for simulating seismic wave in 2- dimensional elastic media. The methods combine the flexibility of a discontinuous finite element method with the accuracy of a spectral method. The elastodynamic equations are discretized using high-degree of Lagrange interpolants and integration over an element is accomplished based upon the Gauss-Lobatto-Legendre integration rule. This combination of discretization and integration results in a diagonal mass matrix and the use of discontinuous finite element method makes the calculation can be done locally in each element. Thus, the algorithm is simplified drastically. We validated the results of one-dimensional problem by comparing them with finite-difference time-domain method and exact solution. The comparisons show excellent agreement