Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species

A Reeb graph-based representation for non-sequential construction of topologically complex shapes

The shape data of many complex objects, such as anatomical structures, are available in the form of contour slices. To visualize these complex shapes, most existing methods focus on resolving the contours connectivities and generating surface models. These methods do not offer any way of abstracting characteristic features from these complex shapes. To address this problem, Morse theory has previously been proposed as a topological abstraction tool, and a Morse theory-based surface coding system has been developed to code complex shapes as a sequence of basic operators. The topological structure of the coded surface is, however, implicitly stored in the operators. Topological information is thus not readily available without evaluating the operators. This paper proposes a more versatile representation by incorporating a contour containment relation into the earlier representation. With the explicit topological information. non-sequential construction and modifications can be performed without violating topological integrity. Editing operators similar to the Euler operators are also proposed. (C) 1998 Elsevier Science Ltd. All rights reserved

Adam’s Hand: An Underactuated Robotic End-Effector

This paper describes recent efforts by the authors in the development of a robotic hand, referred to as the Adam’s hand. The end-effector is underactuated through a multiple bevel-gear differential system that is used to operate all five fingers, resulting in 15 degrees of freedom actuated by just 1 degree of actuation. Special focus is devoted to the transmission ratios and gear dimensions of the system to maintain the kinematic behaviour and the dimensions of the prototype as close as possible to that of human hand

Cloth Animation with Self-Collision Detection

This paper addresses the problem of detecting collisions of very flexible objects, such as clothes with almost rigid bodies, such as human bodies. In our method, collision avoidance consists of creating a very thin force field around the obstacle surface to avoid collisions. This force field acts like a shield rejecting the points. This volume is divided into small contiguous non-overlapped cells which completely surround the surface. As soon as a point enters into a cell, a repulsive force is applied. The direction and the magnitude of this force are dependent on the velocities, the normals and the distance between the point and the surface. Particular cases are discussed with the ways of solving them